Starting phenix.real_space_refine on Fri Mar 6 13:41:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qo4_53256/03_2026/9qo4_53256.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qo4_53256/03_2026/9qo4_53256.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9qo4_53256/03_2026/9qo4_53256.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qo4_53256/03_2026/9qo4_53256.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9qo4_53256/03_2026/9qo4_53256.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qo4_53256/03_2026/9qo4_53256.map" } resolution = 2.95 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= 0.002 sd= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 6 5.49 5 S 175 5.16 5 C 19487 2.51 5 N 5222 2.21 5 O 5787 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 93 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30681 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 3308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3308 Classifications: {'peptide': 414} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 404} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 3267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3267 Classifications: {'peptide': 398} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 386} Chain breaks: 3 Chain: "C" Number of atoms: 3191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3191 Classifications: {'peptide': 400} Link IDs: {'PTRANS': 13, 'TRANS': 386} Chain breaks: 1 Chain: "D" Number of atoms: 3050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 3050 Classifications: {'peptide': 379} Link IDs: {'PTRANS': 9, 'TRANS': 369} Chain breaks: 1 Chain: "E" Number of atoms: 2381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2381 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 10, 'TRANS': 289} Chain breaks: 1 Chain: "F" Number of atoms: 2244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2244 Classifications: {'peptide': 282} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 271} Chain breaks: 1 Chain: "G" Number of atoms: 1705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1705 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 4, 'TRANS': 211} Chain: "H" Number of atoms: 1374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1374 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 161} Chain breaks: 1 Chain: "I" Number of atoms: 5049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 619, 5049 Classifications: {'peptide': 619} Link IDs: {'PTRANS': 10, 'TRANS': 608} Chain breaks: 5 Chain: "J" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 701 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "L" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1021 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "M" Number of atoms: 2565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2565 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 13, 'TRANS': 310} Chain: "N" Number of atoms: 614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 614 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 6, 'TRANS': 64} Chain: "P" Number of atoms: 170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 170 Classifications: {'peptide': 20} Modifications used: {'COO': 1} Link IDs: {'TRANS': 19} Chain: "B" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 25766 SG CYS J 42 69.559 61.910 86.172 1.00 83.98 S ATOM 25785 SG CYS J 45 68.925 58.190 87.002 1.00 81.70 S ATOM 26080 SG CYS J 83 67.044 60.296 88.675 1.00121.73 S ATOM 26009 SG CYS J 75 71.095 74.085 91.748 1.00 82.86 S ATOM 26176 SG CYS J 94 72.292 70.369 92.526 1.00100.17 S ATOM 25852 SG CYS J 53 64.122 58.140 86.617 1.00111.43 S ATOM 25875 SG CYS J 56 60.967 55.056 87.484 1.00 66.47 S ATOM 25959 SG CYS J 68 60.448 58.439 86.400 1.00 76.27 S Time building chain proxies: 6.42, per 1000 atoms: 0.21 Number of scatterers: 30681 At special positions: 0 Unit cell: (135, 206.28, 186.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 175 16.00 P 6 15.00 O 5787 8.00 N 5222 7.00 C 19487 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS G 178 " - pdb=" SG CYS G 181 " distance=2.14 Simple disulfide: pdb=" SG CYS M 240 " - pdb=" SG CYS M 266 " distance=2.04 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: 2.18 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN E 401 " pdb="ZN ZN E 401 " - pdb=" NE2 HIS E 140 " pdb="ZN ZN E 401 " - pdb=" NE2 HIS E 138 " pdb=" ZN J 200 " pdb="ZN ZN J 200 " - pdb=" ND1 HIS J 80 " pdb="ZN ZN J 200 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 200 " - pdb=" SG CYS J 83 " pdb="ZN ZN J 200 " - pdb=" SG CYS J 42 " pdb=" ZN J 201 " pdb="ZN ZN J 201 " - pdb=" SG CYS J 75 " pdb="ZN ZN J 201 " - pdb=" SG CYS J 94 " pdb=" ZN J 202 " pdb="ZN ZN J 202 " - pdb=" SG CYS J 68 " pdb="ZN ZN J 202 " - pdb=" SG CYS J 56 " pdb="ZN ZN J 202 " - pdb=" ND1 HIS J 82 " pdb="ZN ZN J 202 " - pdb=" SG CYS J 53 " Number of angles added : 6 7490 Ramachandran restraints generated. 3745 Oldfield, 0 Emsley, 3745 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7310 Finding SS restraints... Secondary structure from input PDB file: 189 helices and 14 sheets defined 65.7% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid 43 through 48 Processing helix chain 'A' and resid 53 through 66 removed outlier: 3.643A pdb=" N ILE A 57 " --> pdb=" O GLY A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 82 Processing helix chain 'A' and resid 87 through 105 removed outlier: 3.660A pdb=" N GLU A 92 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N GLU A 93 " --> pdb=" O ASP A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 148 removed outlier: 3.567A pdb=" N GLU A 132 " --> pdb=" O THR A 128 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASP A 148 " --> pdb=" O LYS A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 156 removed outlier: 3.649A pdb=" N TYR A 152 " --> pdb=" O ASP A 148 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS A 153 " --> pdb=" O LEU A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 176 Processing helix chain 'A' and resid 177 through 187 Processing helix chain 'A' and resid 194 through 213 removed outlier: 3.684A pdb=" N VAL A 198 " --> pdb=" O SER A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 228 Processing helix chain 'A' and resid 240 through 260 removed outlier: 4.026A pdb=" N LEU A 246 " --> pdb=" O THR A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 271 removed outlier: 3.566A pdb=" N ALA A 266 " --> pdb=" O LYS A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 298 removed outlier: 3.975A pdb=" N VAL A 289 " --> pdb=" O SER A 285 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA A 290 " --> pdb=" O PRO A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 310 Processing helix chain 'A' and resid 316 through 322 removed outlier: 3.919A pdb=" N LEU A 322 " --> pdb=" O LEU A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 335 removed outlier: 4.036A pdb=" N ARG A 327 " --> pdb=" O GLU A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 353 removed outlier: 4.147A pdb=" N ASN A 351 " --> pdb=" O GLU A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 379 removed outlier: 4.059A pdb=" N GLN A 368 " --> pdb=" O THR A 364 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N PHE A 378 " --> pdb=" O LEU A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 393 Processing helix chain 'A' and resid 396 through 411 Processing helix chain 'A' and resid 430 through 462 removed outlier: 3.502A pdb=" N THR A 434 " --> pdb=" O ASP A 430 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN A 462 " --> pdb=" O ALA A 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 41 removed outlier: 3.920A pdb=" N SER B 39 " --> pdb=" O GLN B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 60 Processing helix chain 'B' and resid 67 through 81 removed outlier: 4.194A pdb=" N LYS B 81 " --> pdb=" O LYS B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 98 Processing helix chain 'B' and resid 104 through 122 Processing helix chain 'B' and resid 124 through 140 removed outlier: 4.180A pdb=" N GLN B 129 " --> pdb=" O MET B 125 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N GLU B 130 " --> pdb=" O ASP B 126 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS B 140 " --> pdb=" O LEU B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 162 Processing helix chain 'B' and resid 167 through 180 removed outlier: 3.510A pdb=" N ILE B 171 " --> pdb=" O LYS B 167 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLN B 180 " --> pdb=" O HIS B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 208 removed outlier: 3.797A pdb=" N ALA B 207 " --> pdb=" O GLN B 203 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLN B 208 " --> pdb=" O MET B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 220 removed outlier: 3.914A pdb=" N TYR B 218 " --> pdb=" O LEU B 214 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLU B 219 " --> pdb=" O LYS B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 247 removed outlier: 3.618A pdb=" N MET B 234 " --> pdb=" O HIS B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 269 removed outlier: 4.004A pdb=" N THR B 256 " --> pdb=" O GLU B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 288 removed outlier: 3.871A pdb=" N CYS B 276 " --> pdb=" O ARG B 272 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU B 277 " --> pdb=" O ARG B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 303 Processing helix chain 'B' and resid 305 through 320 removed outlier: 3.999A pdb=" N ALA B 310 " --> pdb=" O PRO B 306 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N MET B 311 " --> pdb=" O GLU B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 333 Processing helix chain 'B' and resid 342 through 345 Processing helix chain 'B' and resid 346 through 363 removed outlier: 3.501A pdb=" N LEU B 350 " --> pdb=" O HIS B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 379 Processing helix chain 'B' and resid 381 through 395 Processing helix chain 'B' and resid 419 through 441 removed outlier: 3.553A pdb=" N LYS B 426 " --> pdb=" O THR B 422 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N TRP B 427 " --> pdb=" O ALA B 423 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N THR B 428 " --> pdb=" O LEU B 424 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ASN B 429 " --> pdb=" O ASP B 425 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLN B 436 " --> pdb=" O ASN B 432 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS B 441 " --> pdb=" O ALA B 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 16 removed outlier: 3.543A pdb=" N SER C 16 " --> pdb=" O VAL C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 31 removed outlier: 3.783A pdb=" N CYS C 25 " --> pdb=" O MET C 21 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU C 26 " --> pdb=" O THR C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 66 Processing helix chain 'C' and resid 73 through 87 removed outlier: 3.643A pdb=" N LEU C 77 " --> pdb=" O ASP C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 94 removed outlier: 3.783A pdb=" N ILE C 93 " --> pdb=" O ASN C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 115 removed outlier: 3.656A pdb=" N GLY C 102 " --> pdb=" O ASP C 98 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N CYS C 104 " --> pdb=" O PHE C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 131 Processing helix chain 'C' and resid 141 through 152 Processing helix chain 'C' and resid 158 through 162 Processing helix chain 'C' and resid 171 through 175 Processing helix chain 'C' and resid 177 through 195 removed outlier: 3.828A pdb=" N PHE C 181 " --> pdb=" O ASP C 177 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLY C 189 " --> pdb=" O TYR C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 210 Processing helix chain 'C' and resid 217 through 236 Processing helix chain 'C' and resid 246 through 252 removed outlier: 4.239A pdb=" N GLY C 250 " --> pdb=" O SER C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 257 removed outlier: 3.510A pdb=" N LEU C 256 " --> pdb=" O PHE C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 269 removed outlier: 3.649A pdb=" N THR C 269 " --> pdb=" O GLN C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 282 Processing helix chain 'C' and resid 282 through 289 Processing helix chain 'C' and resid 294 through 310 removed outlier: 3.909A pdb=" N SER C 300 " --> pdb=" O LYS C 296 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR C 303 " --> pdb=" O LEU C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 326 Processing helix chain 'C' and resid 330 through 344 removed outlier: 3.989A pdb=" N ALA C 334 " --> pdb=" O GLY C 330 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU C 335 " --> pdb=" O PRO C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 400 removed outlier: 4.143A pdb=" N LEU C 373 " --> pdb=" O ASN C 369 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N HIS C 374 " --> pdb=" O PRO C 370 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ASN C 375 " --> pdb=" O ALA C 371 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU C 379 " --> pdb=" O ASN C 375 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL C 399 " --> pdb=" O GLN C 395 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASN C 400 " --> pdb=" O GLU C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 408 Processing helix chain 'D' and resid 23 through 36 Processing helix chain 'D' and resid 38 through 50 removed outlier: 4.413A pdb=" N LYS D 46 " --> pdb=" O LEU D 42 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA D 47 " --> pdb=" O GLU D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 53 No H-bonds generated for 'chain 'D' and resid 51 through 53' Processing helix chain 'D' and resid 61 through 73 removed outlier: 3.796A pdb=" N LEU D 65 " --> pdb=" O ILE D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 89 Processing helix chain 'D' and resid 100 through 117 removed outlier: 3.667A pdb=" N ALA D 104 " --> pdb=" O GLU D 100 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N SER D 105 " --> pdb=" O GLU D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 127 removed outlier: 3.689A pdb=" N LEU D 127 " --> pdb=" O ALA D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 130 No H-bonds generated for 'chain 'D' and resid 128 through 130' Processing helix chain 'D' and resid 140 through 157 removed outlier: 3.665A pdb=" N LYS D 144 " --> pdb=" O ASN D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 159 No H-bonds generated for 'chain 'D' and resid 158 through 159' Processing helix chain 'D' and resid 160 through 163 Processing helix chain 'D' and resid 164 through 176 removed outlier: 3.816A pdb=" N ASN D 176 " --> pdb=" O SER D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 198 removed outlier: 3.697A pdb=" N GLN D 184 " --> pdb=" O ASN D 180 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N HIS D 186 " --> pdb=" O GLN D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 212 removed outlier: 3.657A pdb=" N GLN D 206 " --> pdb=" O ILE D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 236 Processing helix chain 'D' and resid 240 through 252 removed outlier: 3.511A pdb=" N ASP D 252 " --> pdb=" O THR D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 258 removed outlier: 3.543A pdb=" N GLN D 256 " --> pdb=" O GLU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 269 Processing helix chain 'D' and resid 274 through 283 removed outlier: 3.598A pdb=" N LEU D 278 " --> pdb=" O ARG D 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 285 No H-bonds generated for 'chain 'D' and resid 284 through 285' Processing helix chain 'D' and resid 286 through 290 Processing helix chain 'D' and resid 298 through 313 Processing helix chain 'D' and resid 321 through 329 Processing helix chain 'D' and resid 331 through 346 Processing helix chain 'D' and resid 365 through 390 removed outlier: 3.527A pdb=" N THR D 369 " --> pdb=" O GLU D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 392 through 405 Processing helix chain 'E' and resid 26 through 30 Processing helix chain 'E' and resid 32 through 42 Processing helix chain 'E' and resid 44 through 49 removed outlier: 3.987A pdb=" N ASP E 48 " --> pdb=" O PRO E 44 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N HIS E 49 " --> pdb=" O TRP E 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 44 through 49' Processing helix chain 'E' and resid 59 through 72 removed outlier: 3.790A pdb=" N GLY E 72 " --> pdb=" O HIS E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 125 removed outlier: 3.898A pdb=" N ALA E 112 " --> pdb=" O ASN E 108 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS E 125 " --> pdb=" O ILE E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 160 removed outlier: 3.754A pdb=" N GLN E 160 " --> pdb=" O MET E 156 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 179 Processing helix chain 'E' and resid 210 through 217 removed outlier: 3.612A pdb=" N VAL E 216 " --> pdb=" O GLU E 212 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N HIS E 217 " --> pdb=" O ASP E 213 " (cutoff:3.500A) Processing helix chain 'E' and resid 231 through 240 Processing helix chain 'E' and resid 241 through 244 Processing helix chain 'E' and resid 245 through 251 removed outlier: 3.709A pdb=" N THR E 249 " --> pdb=" O TYR E 245 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 281 removed outlier: 3.644A pdb=" N ALA E 278 " --> pdb=" O GLU E 274 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLN E 279 " --> pdb=" O GLN E 275 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU E 280 " --> pdb=" O SER E 276 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLY E 281 " --> pdb=" O GLU E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 329 removed outlier: 3.604A pdb=" N LYS E 302 " --> pdb=" O ASP E 298 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU E 313 " --> pdb=" O LYS E 309 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ALA E 314 " --> pdb=" O THR E 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 44 through 62 removed outlier: 4.107A pdb=" N ILE F 48 " --> pdb=" O HIS F 44 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 114 removed outlier: 3.571A pdb=" N GLU F 110 " --> pdb=" O TYR F 106 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLN F 114 " --> pdb=" O GLU F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 143 removed outlier: 3.881A pdb=" N ILE F 136 " --> pdb=" O ASP F 132 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N HIS F 137 " --> pdb=" O PRO F 133 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N VAL F 138 " --> pdb=" O SER F 134 " (cutoff:3.500A) Processing helix chain 'F' and resid 193 through 205 Processing helix chain 'F' and resid 215 through 248 removed outlier: 3.708A pdb=" N GLU F 219 " --> pdb=" O SER F 215 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ALA F 223 " --> pdb=" O GLU F 219 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLN F 224 " --> pdb=" O HIS F 220 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA F 227 " --> pdb=" O ALA F 223 " (cutoff:3.500A) Processing helix chain 'F' and resid 253 through 266 removed outlier: 3.561A pdb=" N LEU F 257 " --> pdb=" O ASN F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 272 through 313 removed outlier: 3.948A pdb=" N VAL F 311 " --> pdb=" O ASN F 307 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU F 312 " --> pdb=" O LYS F 308 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR F 313 " --> pdb=" O PHE F 309 " (cutoff:3.500A) Processing helix chain 'G' and resid 11 through 19 removed outlier: 3.818A pdb=" N PHE G 15 " --> pdb=" O LEU G 11 " (cutoff:3.500A) Processing helix chain 'G' and resid 25 through 35 Processing helix chain 'G' and resid 43 through 48 Processing helix chain 'G' and resid 49 through 54 Processing helix chain 'G' and resid 60 through 73 removed outlier: 3.734A pdb=" N LEU G 64 " --> pdb=" O ASN G 60 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 81 Processing helix chain 'G' and resid 82 through 85 removed outlier: 3.821A pdb=" N LEU G 85 " --> pdb=" O LYS G 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 82 through 85' Processing helix chain 'G' and resid 89 through 108 removed outlier: 4.276A pdb=" N ARG G 107 " --> pdb=" O SER G 103 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N MET G 108 " --> pdb=" O LEU G 104 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 121 Processing helix chain 'G' and resid 124 through 138 removed outlier: 3.788A pdb=" N LEU G 128 " --> pdb=" O ASN G 124 " (cutoff:3.500A) Processing helix chain 'G' and resid 166 through 225 removed outlier: 3.624A pdb=" N ILE G 170 " --> pdb=" O ASP G 166 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLN G 206 " --> pdb=" O HIS G 202 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLN G 207 " --> pdb=" O ASN G 203 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLN G 208 " --> pdb=" O ARG G 204 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL G 209 " --> pdb=" O THR G 205 " (cutoff:3.500A) Processing helix chain 'H' and resid 12 through 26 Processing helix chain 'H' and resid 33 through 47 Processing helix chain 'H' and resid 49 through 60 removed outlier: 3.613A pdb=" N ALA H 53 " --> pdb=" O ASP H 49 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 66 Processing helix chain 'H' and resid 69 through 83 removed outlier: 3.621A pdb=" N VAL H 77 " --> pdb=" O GLY H 73 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN H 83 " --> pdb=" O GLN H 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 94 removed outlier: 3.538A pdb=" N TYR H 90 " --> pdb=" O PHE H 86 " (cutoff:3.500A) Processing helix chain 'H' and resid 102 through 124 Processing helix chain 'H' and resid 130 through 138 Processing helix chain 'H' and resid 140 through 151 removed outlier: 3.624A pdb=" N ALA H 144 " --> pdb=" O PRO H 140 " (cutoff:3.500A) Processing helix chain 'H' and resid 196 through 208 Processing helix chain 'I' and resid 17 through 31 removed outlier: 4.127A pdb=" N ASP I 22 " --> pdb=" O ASP I 18 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N ASP I 23 " --> pdb=" O GLN I 19 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN I 30 " --> pdb=" O ALA I 26 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL I 31 " --> pdb=" O GLY I 27 " (cutoff:3.500A) Processing helix chain 'I' and resid 38 through 54 removed outlier: 3.659A pdb=" N TYR I 42 " --> pdb=" O ALA I 38 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N MET I 43 " --> pdb=" O LYS I 39 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU I 44 " --> pdb=" O SER I 40 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR I 46 " --> pdb=" O TYR I 42 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N HIS I 48 " --> pdb=" O GLU I 44 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL I 49 " --> pdb=" O LEU I 45 " (cutoff:3.500A) Processing helix chain 'I' and resid 85 through 108 removed outlier: 3.943A pdb=" N ASP I 106 " --> pdb=" O ASN I 102 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU I 108 " --> pdb=" O LEU I 104 " (cutoff:3.500A) Processing helix chain 'I' and resid 111 through 137 removed outlier: 3.945A pdb=" N LEU I 116 " --> pdb=" O ASP I 112 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LYS I 117 " --> pdb=" O GLU I 113 " (cutoff:3.500A) Processing helix chain 'I' and resid 137 through 151 removed outlier: 3.500A pdb=" N ASN I 141 " --> pdb=" O CYS I 137 " (cutoff:3.500A) Processing helix chain 'I' and resid 158 through 172 removed outlier: 4.034A pdb=" N ASP I 169 " --> pdb=" O VAL I 165 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N CYS I 170 " --> pdb=" O THR I 166 " (cutoff:3.500A) Processing helix chain 'I' and resid 173 through 188 removed outlier: 3.803A pdb=" N LYS I 177 " --> pdb=" O ARG I 173 " (cutoff:3.500A) Processing helix chain 'I' and resid 189 through 192 Processing helix chain 'I' and resid 198 through 211 removed outlier: 4.570A pdb=" N VAL I 204 " --> pdb=" O LEU I 200 " (cutoff:3.500A) Processing helix chain 'I' and resid 226 through 254 removed outlier: 3.595A pdb=" N PHE I 232 " --> pdb=" O TYR I 228 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N SER I 234 " --> pdb=" O GLU I 230 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N GLN I 235 " --> pdb=" O SER I 231 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N THR I 245 " --> pdb=" O GLU I 241 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N THR I 249 " --> pdb=" O THR I 245 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N GLU I 250 " --> pdb=" O ARG I 246 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLN I 253 " --> pdb=" O THR I 249 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N GLN I 254 " --> pdb=" O GLU I 250 " (cutoff:3.500A) Processing helix chain 'I' and resid 259 through 279 removed outlier: 3.977A pdb=" N GLN I 272 " --> pdb=" O LEU I 268 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ARG I 273 " --> pdb=" O LEU I 269 " (cutoff:3.500A) Processing helix chain 'I' and resid 283 through 297 removed outlier: 4.025A pdb=" N LYS I 290 " --> pdb=" O GLU I 286 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE I 296 " --> pdb=" O GLU I 292 " (cutoff:3.500A) Processing helix chain 'I' and resid 299 through 313 removed outlier: 3.763A pdb=" N PHE I 303 " --> pdb=" O HIS I 299 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLN I 308 " --> pdb=" O HIS I 304 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ASN I 309 " --> pdb=" O THR I 305 " (cutoff:3.500A) Processing helix chain 'I' and resid 318 through 327 removed outlier: 4.005A pdb=" N MET I 322 " --> pdb=" O ASP I 318 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N TYR I 323 " --> pdb=" O LEU I 319 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN I 324 " --> pdb=" O GLY I 320 " (cutoff:3.500A) Processing helix chain 'I' and resid 335 through 354 removed outlier: 4.414A pdb=" N LEU I 339 " --> pdb=" O GLU I 335 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU I 340 " --> pdb=" O LEU I 336 " (cutoff:3.500A) Processing helix chain 'I' and resid 357 through 361 removed outlier: 3.742A pdb=" N LEU I 360 " --> pdb=" O GLU I 357 " (cutoff:3.500A) Processing helix chain 'I' and resid 362 through 384 removed outlier: 3.696A pdb=" N VAL I 373 " --> pdb=" O THR I 369 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N HIS I 374 " --> pdb=" O VAL I 370 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ALA I 379 " --> pdb=" O LYS I 375 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LEU I 380 " --> pdb=" O LYS I 376 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N VAL I 381 " --> pdb=" O TYR I 377 " (cutoff:3.500A) Processing helix chain 'I' and resid 388 through 404 removed outlier: 3.612A pdb=" N ASN I 404 " --> pdb=" O GLY I 400 " (cutoff:3.500A) Processing helix chain 'I' and resid 406 through 410 Processing helix chain 'I' and resid 417 through 430 removed outlier: 3.564A pdb=" N LEU I 421 " --> pdb=" O LYS I 417 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU I 422 " --> pdb=" O SER I 418 " (cutoff:3.500A) Processing helix chain 'I' and resid 438 through 454 removed outlier: 3.558A pdb=" N LYS I 454 " --> pdb=" O MET I 450 " (cutoff:3.500A) Processing helix chain 'I' and resid 458 through 477 removed outlier: 4.327A pdb=" N PHE I 462 " --> pdb=" O ASP I 458 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N HIS I 476 " --> pdb=" O LYS I 472 " (cutoff:3.500A) Processing helix chain 'I' and resid 481 through 496 removed outlier: 3.733A pdb=" N GLU I 485 " --> pdb=" O SER I 481 " (cutoff:3.500A) Processing helix chain 'I' and resid 497 through 500 Processing helix chain 'I' and resid 501 through 526 removed outlier: 3.635A pdb=" N ILE I 511 " --> pdb=" O MET I 507 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS I 515 " --> pdb=" O ILE I 511 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ASP I 516 " --> pdb=" O GLY I 512 " (cutoff:3.500A) Processing helix chain 'I' and resid 556 through 559 Processing helix chain 'I' and resid 560 through 574 Processing helix chain 'I' and resid 604 through 613 removed outlier: 4.368A pdb=" N GLN I 613 " --> pdb=" O ALA I 609 " (cutoff:3.500A) Processing helix chain 'I' and resid 614 through 616 No H-bonds generated for 'chain 'I' and resid 614 through 616' Processing helix chain 'I' and resid 621 through 630 Processing helix chain 'I' and resid 632 through 644 Processing helix chain 'J' and resid 53 through 59 removed outlier: 3.828A pdb=" N GLN J 57 " --> pdb=" O CYS J 53 " (cutoff:3.500A) Processing helix chain 'J' and resid 62 through 66 Processing helix chain 'J' and resid 81 through 88 Processing helix chain 'L' and resid 17 through 23 removed outlier: 3.870A pdb=" N ALA L 21 " --> pdb=" O ASP L 17 " (cutoff:3.500A) Processing helix chain 'L' and resid 25 through 33 removed outlier: 4.003A pdb=" N ASP L 33 " --> pdb=" O THR L 29 " (cutoff:3.500A) Processing helix chain 'L' and resid 51 through 65 removed outlier: 4.146A pdb=" N LYS L 57 " --> pdb=" O ALA L 53 " (cutoff:3.500A) Processing helix chain 'L' and resid 89 through 93 Processing helix chain 'L' and resid 99 through 111 Processing helix chain 'L' and resid 113 through 126 Processing helix chain 'L' and resid 134 through 139 Processing helix chain 'L' and resid 149 through 157 Processing helix chain 'M' and resid 101 through 110 Processing helix chain 'M' and resid 113 through 121 Processing helix chain 'M' and resid 124 through 132 removed outlier: 3.645A pdb=" N SER M 132 " --> pdb=" O TYR M 128 " (cutoff:3.500A) Processing helix chain 'M' and resid 148 through 158 removed outlier: 3.515A pdb=" N THR M 152 " --> pdb=" O HIS M 148 " (cutoff:3.500A) Processing helix chain 'M' and resid 194 through 203 Processing helix chain 'M' and resid 219 through 227 Processing helix chain 'M' and resid 244 through 255 removed outlier: 3.897A pdb=" N LEU M 248 " --> pdb=" O SER M 244 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER M 253 " --> pdb=" O GLN M 249 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N SER M 254 " --> pdb=" O THR M 250 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N CYS M 255 " --> pdb=" O LEU M 251 " (cutoff:3.500A) Processing helix chain 'M' and resid 270 through 281 Processing helix chain 'M' and resid 298 through 307 removed outlier: 3.638A pdb=" N LEU M 302 " --> pdb=" O GLN M 298 " (cutoff:3.500A) Processing helix chain 'M' and resid 324 through 328 Processing helix chain 'M' and resid 330 through 334 removed outlier: 3.706A pdb=" N GLN M 333 " --> pdb=" O GLU M 330 " (cutoff:3.500A) Processing helix chain 'M' and resid 352 through 359 removed outlier: 3.638A pdb=" N GLY M 357 " --> pdb=" O LEU M 354 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE M 359 " --> pdb=" O LEU M 356 " (cutoff:3.500A) Processing helix chain 'M' and resid 374 through 383 removed outlier: 4.141A pdb=" N LEU M 378 " --> pdb=" O GLY M 374 " (cutoff:3.500A) Processing helix chain 'N' and resid 25 through 30 removed outlier: 3.528A pdb=" N LYS N 30 " --> pdb=" O LYS N 26 " (cutoff:3.500A) Processing helix chain 'N' and resid 39 through 47 removed outlier: 3.564A pdb=" N GLY N 47 " --> pdb=" O TRP N 43 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 110 through 112 removed outlier: 6.581A pdb=" N GLN G 142 " --> pdb=" O ASP G 155 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N THR B 367 " --> pdb=" O LEU B 411 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N VAL A 382 " --> pdb=" O ALA A 426 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N LEU C 315 " --> pdb=" O ALA A 415 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N VAL A 417 " --> pdb=" O LEU C 315 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N LEU C 317 " --> pdb=" O VAL A 417 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N LEU C 315 " --> pdb=" O PHE C 360 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N THR H 126 " --> pdb=" O ALA C 349 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ILE C 351 " --> pdb=" O THR H 126 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N ILE H 128 " --> pdb=" O ILE C 351 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLN H 154 " --> pdb=" O LEU H 163 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 137 through 138 Processing sheet with id=AA3, first strand: chain 'E' and resid 54 through 58 removed outlier: 6.817A pdb=" N TYR E 54 " --> pdb=" O MET E 90 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N ILE E 92 " --> pdb=" O TYR E 54 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N LYS E 56 " --> pdb=" O ILE E 92 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N ASP E 94 " --> pdb=" O LYS E 56 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N SER E 58 " --> pdb=" O ASP E 94 " (cutoff:3.500A) removed outlier: 11.538A pdb=" N PHE E 96 " --> pdb=" O SER E 58 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N MET E 90 " --> pdb=" O ASP E 86 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N ASP E 86 " --> pdb=" O MET E 90 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N ILE E 92 " --> pdb=" O LYS E 84 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N LYS E 84 " --> pdb=" O ILE E 92 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ASP E 94 " --> pdb=" O LEU E 82 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY E 135 " --> pdb=" O MET E 81 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N TRP E 136 " --> pdb=" O VAL E 168 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N ILE E 170 " --> pdb=" O TRP E 136 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N HIS E 138 " --> pdb=" O ILE E 170 " (cutoff:3.500A) removed outlier: 9.529A pdb=" N LEU E 183 " --> pdb=" O VAL E 226 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N VAL E 226 " --> pdb=" O LEU E 183 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N ALA E 185 " --> pdb=" O LEU E 224 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE E 229 " --> pdb=" O ILE E 57 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 178 through 186 removed outlier: 4.455A pdb=" N VAL F 167 " --> pdb=" O LEU F 186 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N PHE F 121 " --> pdb=" O GLY F 74 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N GLY F 74 " --> pdb=" O PHE F 121 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLY F 123 " --> pdb=" O LEU F 72 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N LYS F 75 " --> pdb=" O VAL F 83 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N VAL F 83 " --> pdb=" O LYS F 75 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N SER F 40 " --> pdb=" O ILE F 81 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N VAL F 83 " --> pdb=" O SER F 40 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ALA F 42 " --> pdb=" O VAL F 83 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N ASN F 85 " --> pdb=" O ALA F 42 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 92 through 93 Processing sheet with id=AA6, first strand: chain 'I' and resid 534 through 540 Processing sheet with id=AA7, first strand: chain 'I' and resid 534 through 540 removed outlier: 4.768A pdb=" N VAL J 30 " --> pdb=" O LEU I 585 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LEU I 585 " --> pdb=" O VAL J 30 " (cutoff:3.500A) removed outlier: 11.856A pdb=" N LEU J 32 " --> pdb=" O TYR I 583 " (cutoff:3.500A) removed outlier: 10.501A pdb=" N TYR I 583 " --> pdb=" O LEU J 32 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 600 through 601 Processing sheet with id=AA9, first strand: chain 'J' and resid 70 through 71 Processing sheet with id=AB1, first strand: chain 'M' and resid 185 through 187 removed outlier: 3.512A pdb=" N ARG M 164 " --> pdb=" O LEU M 140 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N THR M 139 " --> pdb=" O LEU M 416 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'M' and resid 210 through 212 removed outlier: 3.691A pdb=" N SER M 264 " --> pdb=" O LEU M 237 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'M' and resid 339 through 341 Processing sheet with id=AB4, first strand: chain 'N' and resid 7 through 8 removed outlier: 3.632A pdb=" N TYR N 12 " --> pdb=" O TYR N 19 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'N' and resid 7 through 8 1713 hydrogen bonds defined for protein. 5004 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: 5.76 Time building geometry restraints manager: 2.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10034 1.34 - 1.46: 6885 1.46 - 1.58: 14044 1.58 - 1.71: 6 1.71 - 1.83: 271 Bond restraints: 31240 Sorted by residual: bond pdb=" C LEU G 174 " pdb=" O LEU G 174 " ideal model delta sigma weight residual 1.236 1.290 -0.054 1.26e-02 6.30e+03 1.81e+01 bond pdb=" C LYS G 172 " pdb=" O LYS G 172 " ideal model delta sigma weight residual 1.236 1.283 -0.046 1.15e-02 7.56e+03 1.62e+01 bond pdb=" N VAL F 311 " pdb=" CA VAL F 311 " ideal model delta sigma weight residual 1.459 1.507 -0.048 1.25e-02 6.40e+03 1.45e+01 bond pdb=" O14 IHP B 501 " pdb=" P4 IHP B 501 " ideal model delta sigma weight residual 1.671 1.596 0.075 2.00e-02 2.50e+03 1.41e+01 bond pdb=" O12 IHP B 501 " pdb=" P2 IHP B 501 " ideal model delta sigma weight residual 1.675 1.601 0.074 2.00e-02 2.50e+03 1.36e+01 ... (remaining 31235 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.50: 41535 2.50 - 4.99: 583 4.99 - 7.49: 75 7.49 - 9.98: 7 9.98 - 12.48: 4 Bond angle restraints: 42204 Sorted by residual: angle pdb=" N ASP G 179 " pdb=" CA ASP G 179 " pdb=" C ASP G 179 " ideal model delta sigma weight residual 111.28 103.12 8.16 1.09e+00 8.42e-01 5.60e+01 angle pdb=" N ILE I 201 " pdb=" CA ILE I 201 " pdb=" C ILE I 201 " ideal model delta sigma weight residual 111.90 106.32 5.58 8.10e-01 1.52e+00 4.74e+01 angle pdb=" CA ALA F 204 " pdb=" C ALA F 204 " pdb=" O ALA F 204 " ideal model delta sigma weight residual 120.42 114.67 5.75 1.06e+00 8.90e-01 2.94e+01 angle pdb=" C CYS G 178 " pdb=" CA CYS G 178 " pdb=" CB CYS G 178 " ideal model delta sigma weight residual 109.55 120.39 -10.84 2.03e+00 2.43e-01 2.85e+01 angle pdb=" N LEU G 174 " pdb=" CA LEU G 174 " pdb=" C LEU G 174 " ideal model delta sigma weight residual 111.82 106.26 5.56 1.16e+00 7.43e-01 2.30e+01 ... (remaining 42199 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.14: 17401 25.14 - 50.29: 1418 50.29 - 75.43: 201 75.43 - 100.58: 23 100.58 - 125.72: 12 Dihedral angle restraints: 19055 sinusoidal: 7816 harmonic: 11239 Sorted by residual: dihedral pdb=" C CYS G 178 " pdb=" N CYS G 178 " pdb=" CA CYS G 178 " pdb=" CB CYS G 178 " ideal model delta harmonic sigma weight residual -122.60 -142.59 19.99 0 2.50e+00 1.60e-01 6.39e+01 dihedral pdb=" N CYS G 178 " pdb=" C CYS G 178 " pdb=" CA CYS G 178 " pdb=" CB CYS G 178 " ideal model delta harmonic sigma weight residual 122.80 139.33 -16.53 0 2.50e+00 1.60e-01 4.37e+01 dihedral pdb=" CA GLY E 87 " pdb=" C GLY E 87 " pdb=" N GLU E 88 " pdb=" CA GLU E 88 " ideal model delta harmonic sigma weight residual 180.00 155.50 24.50 0 5.00e+00 4.00e-02 2.40e+01 ... (remaining 19052 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.019: 4757 1.019 - 2.039: 0 2.039 - 3.058: 0 3.058 - 4.078: 0 4.078 - 5.097: 4 Chirality restraints: 4761 Sorted by residual: chirality pdb=" C2 IHP B 501 " pdb=" C1 IHP B 501 " pdb=" C3 IHP B 501 " pdb=" O12 IHP B 501 " both_signs ideal model delta sigma weight residual False -2.52 2.58 -5.10 2.00e-01 2.50e+01 6.49e+02 chirality pdb=" C5 IHP B 501 " pdb=" C4 IHP B 501 " pdb=" C6 IHP B 501 " pdb=" O15 IHP B 501 " both_signs ideal model delta sigma weight residual False -2.42 2.51 -4.93 2.00e-01 2.50e+01 6.08e+02 chirality pdb=" C3 IHP B 501 " pdb=" C2 IHP B 501 " pdb=" C4 IHP B 501 " pdb=" O13 IHP B 501 " both_signs ideal model delta sigma weight residual False -2.34 2.53 -4.87 2.00e-01 2.50e+01 5.92e+02 ... (remaining 4758 not shown) Planarity restraints: 5382 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN F 310 " 0.027 2.00e-02 2.50e+03 5.27e-02 2.77e+01 pdb=" C ASN F 310 " -0.091 2.00e-02 2.50e+03 pdb=" O ASN F 310 " 0.033 2.00e-02 2.50e+03 pdb=" N VAL F 311 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG F 205 " 0.026 2.00e-02 2.50e+03 5.19e-02 2.70e+01 pdb=" C ARG F 205 " -0.090 2.00e-02 2.50e+03 pdb=" O ARG F 205 " 0.033 2.00e-02 2.50e+03 pdb=" N MET F 206 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG G 204 " -0.258 9.50e-02 1.11e+02 1.16e-01 9.25e+00 pdb=" NE ARG G 204 " 0.022 2.00e-02 2.50e+03 pdb=" CZ ARG G 204 " -0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG G 204 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG G 204 " -0.004 2.00e-02 2.50e+03 ... (remaining 5379 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.27: 17 2.27 - 2.92: 13065 2.92 - 3.58: 43457 3.58 - 4.24: 63689 4.24 - 4.90: 111150 Nonbonded interactions: 231378 Sorted by model distance: nonbonded pdb="ZN ZN E 401 " pdb=" O HOH E 501 " model vdw 1.608 2.230 nonbonded pdb=" OD2 ASP E 151 " pdb="ZN ZN E 401 " model vdw 1.929 2.230 nonbonded pdb=" O31 IHP B 501 " pdb=" O36 IHP B 501 " model vdw 2.071 3.040 nonbonded pdb=" O ILE P 56 " pdb=" OXT GLN P 57 " model vdw 2.094 3.040 nonbonded pdb=" N GLN I 602 " pdb=" OE1 GLN I 602 " model vdw 2.130 3.120 ... (remaining 231373 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.380 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 30.420 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.334 31254 Z= 0.228 Angle : 0.726 21.081 42214 Z= 0.386 Chirality : 0.148 5.097 4761 Planarity : 0.005 0.121 5382 Dihedral : 17.835 125.719 11739 Min Nonbonded Distance : 1.608 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 2.22 % Allowed : 24.96 % Favored : 72.82 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.14), residues: 3745 helix: 1.11 (0.11), residues: 2296 sheet: -0.59 (0.35), residues: 213 loop : -1.88 (0.17), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG G 204 TYR 0.039 0.002 TYR I 50 PHE 0.018 0.001 PHE L 14 TRP 0.018 0.001 TRP N 43 HIS 0.013 0.001 HIS B 176 Details of bonding type rmsd covalent geometry : bond 0.00433 (31240) covalent geometry : angle 0.70554 (42204) SS BOND : bond 0.07797 ( 2) SS BOND : angle 5.99974 ( 4) hydrogen bonds : bond 0.15118 ( 1704) hydrogen bonds : angle 5.31537 ( 5004) metal coordination : bond 0.11803 ( 12) metal coordination : angle 13.70734 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7490 Ramachandran restraints generated. 3745 Oldfield, 0 Emsley, 3745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7490 Ramachandran restraints generated. 3745 Oldfield, 0 Emsley, 3745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 936 residues out of total 3383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 861 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 257 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7959 (mm-30) REVERT: A 280 PHE cc_start: 0.7061 (p90) cc_final: 0.6762 (p90) REVERT: A 383 SER cc_start: 0.8999 (t) cc_final: 0.8672 (p) REVERT: B 74 GLN cc_start: 0.7954 (tp-100) cc_final: 0.7449 (mt0) REVERT: B 75 MET cc_start: 0.8238 (mtp) cc_final: 0.7785 (mtp) REVERT: B 79 ASN cc_start: 0.8241 (t0) cc_final: 0.7850 (t0) REVERT: B 89 MET cc_start: 0.7015 (tpp) cc_final: 0.5881 (tpp) REVERT: B 93 LYS cc_start: 0.8620 (mtmt) cc_final: 0.7753 (mtmt) REVERT: B 118 TYR cc_start: 0.7932 (t80) cc_final: 0.7499 (t80) REVERT: B 129 GLN cc_start: 0.8448 (tp40) cc_final: 0.7987 (tm-30) REVERT: B 131 PHE cc_start: 0.8045 (OUTLIER) cc_final: 0.7837 (t80) REVERT: B 204 MET cc_start: 0.8172 (tmm) cc_final: 0.7701 (tmm) REVERT: B 278 LYS cc_start: 0.8470 (mtmm) cc_final: 0.8045 (mtpp) REVERT: B 340 ASP cc_start: 0.8293 (p0) cc_final: 0.7934 (p0) REVERT: B 364 LYS cc_start: 0.8517 (ttpp) cc_final: 0.8266 (ttpp) REVERT: B 379 ASN cc_start: 0.8316 (t0) cc_final: 0.7981 (t0) REVERT: C 67 SER cc_start: 0.7997 (t) cc_final: 0.7404 (m) REVERT: C 75 GLU cc_start: 0.6796 (tp30) cc_final: 0.6522 (tm-30) REVERT: C 118 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8402 (tt) REVERT: C 172 GLU cc_start: 0.8283 (mt-10) cc_final: 0.8059 (mt-10) REVERT: D 28 GLN cc_start: 0.8163 (mm110) cc_final: 0.7902 (mm110) REVERT: D 67 THR cc_start: 0.8446 (t) cc_final: 0.8219 (p) REVERT: D 110 LEU cc_start: 0.8399 (tp) cc_final: 0.8170 (tt) REVERT: D 146 GLU cc_start: 0.7737 (mm-30) cc_final: 0.7429 (tm-30) REVERT: D 158 ASP cc_start: 0.8068 (t70) cc_final: 0.7753 (t70) REVERT: D 159 ASP cc_start: 0.7951 (t0) cc_final: 0.7667 (t0) REVERT: D 188 LYS cc_start: 0.8324 (mttt) cc_final: 0.8078 (mttt) REVERT: D 266 LYS cc_start: 0.8771 (mttp) cc_final: 0.8534 (mmtp) REVERT: D 347 ARG cc_start: 0.8586 (mtp85) cc_final: 0.8316 (mtp180) REVERT: D 401 GLU cc_start: 0.7625 (tm-30) cc_final: 0.7281 (tm-30) REVERT: D 404 MET cc_start: 0.7469 (tmm) cc_final: 0.7149 (tmm) REVERT: E 265 GLN cc_start: 0.7963 (mm110) cc_final: 0.7677 (mm110) REVERT: E 286 MET cc_start: 0.6120 (mtm) cc_final: 0.5805 (mtm) REVERT: E 319 MET cc_start: 0.8791 (mtm) cc_final: 0.8485 (mtm) REVERT: E 325 ASP cc_start: 0.8551 (t70) cc_final: 0.8219 (t0) REVERT: F 132 ASP cc_start: 0.7746 (m-30) cc_final: 0.7300 (m-30) REVERT: F 135 ASP cc_start: 0.8204 (m-30) cc_final: 0.7987 (m-30) REVERT: F 193 GLU cc_start: 0.7135 (mp0) cc_final: 0.6846 (mp0) REVERT: F 219 GLU cc_start: 0.7180 (tp30) cc_final: 0.6772 (tp30) REVERT: G 118 LYS cc_start: 0.8392 (ttpp) cc_final: 0.8129 (ttpp) REVERT: G 162 ILE cc_start: 0.8785 (OUTLIER) cc_final: 0.8417 (pp) REVERT: G 197 GLN cc_start: 0.8121 (tm-30) cc_final: 0.7786 (tm-30) REVERT: H 37 TYR cc_start: 0.8108 (OUTLIER) cc_final: 0.6817 (m-10) REVERT: I 20 ILE cc_start: 0.8479 (mm) cc_final: 0.8085 (tt) REVERT: I 39 LYS cc_start: 0.8924 (tttp) cc_final: 0.8669 (tttp) REVERT: I 133 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7848 (tt) REVERT: I 136 ILE cc_start: 0.9076 (mt) cc_final: 0.8856 (tp) REVERT: I 154 LYS cc_start: 0.8291 (mttt) cc_final: 0.7933 (tppp) REVERT: I 187 ILE cc_start: 0.8435 (mm) cc_final: 0.8204 (tp) REVERT: I 211 LEU cc_start: 0.9145 (mp) cc_final: 0.8945 (mm) REVERT: I 240 THR cc_start: 0.8106 (m) cc_final: 0.7768 (p) REVERT: I 272 GLN cc_start: 0.8181 (tm-30) cc_final: 0.7032 (tm-30) REVERT: I 276 GLN cc_start: 0.8131 (mm110) cc_final: 0.7568 (mm110) REVERT: I 306 GLU cc_start: 0.7511 (tp30) cc_final: 0.6874 (tm-30) REVERT: I 330 GLN cc_start: 0.7654 (pm20) cc_final: 0.7276 (pp30) REVERT: I 338 LYS cc_start: 0.8360 (mmmm) cc_final: 0.8150 (mmmm) REVERT: I 353 GLU cc_start: 0.8039 (tm-30) cc_final: 0.7612 (tm-30) REVERT: I 372 ASP cc_start: 0.7899 (m-30) cc_final: 0.7581 (m-30) REVERT: I 432 LYS cc_start: 0.8507 (ptmm) cc_final: 0.8280 (pttp) REVERT: I 463 GLN cc_start: 0.8112 (tm-30) cc_final: 0.7751 (tm-30) REVERT: I 464 LYS cc_start: 0.7946 (mmtm) cc_final: 0.7657 (mmtm) REVERT: I 522 LYS cc_start: 0.8539 (tttt) cc_final: 0.8104 (tmmt) REVERT: I 587 LYS cc_start: 0.8158 (pttm) cc_final: 0.7875 (pttt) REVERT: I 607 GLN cc_start: 0.8203 (mt0) cc_final: 0.7978 (mp10) REVERT: L 94 LYS cc_start: 0.8894 (mttm) cc_final: 0.8606 (ttmm) REVERT: L 121 LYS cc_start: 0.8011 (tmmt) cc_final: 0.7729 (tmmt) REVERT: M 106 LEU cc_start: 0.8113 (mp) cc_final: 0.7863 (mm) REVERT: M 116 GLU cc_start: 0.7435 (mt-10) cc_final: 0.7201 (mt-10) REVERT: M 125 LYS cc_start: 0.8750 (mmtp) cc_final: 0.8309 (mmtp) REVERT: M 130 LEU cc_start: 0.8447 (tp) cc_final: 0.8095 (tt) REVERT: M 168 SER cc_start: 0.8916 (t) cc_final: 0.8603 (p) REVERT: M 186 MET cc_start: 0.8185 (ttp) cc_final: 0.7910 (ttt) REVERT: M 294 ARG cc_start: 0.8251 (OUTLIER) cc_final: 0.6785 (ptm160) REVERT: M 310 PRO cc_start: 0.8722 (Cg_endo) cc_final: 0.8352 (Cg_exo) outliers start: 75 outliers final: 59 residues processed: 903 average time/residue: 0.7251 time to fit residues: 756.5781 Evaluate side-chains 898 residues out of total 3383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 833 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain B residue 131 PHE Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 287 MET Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 361 LYS Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 43 ASP Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 289 ASP Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 355 ASP Chi-restraints excluded: chain C residue 357 MET Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 117 GLU Chi-restraints excluded: chain D residue 286 MET Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 356 ASP Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 333 ILE Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 206 MET Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 81 ASN Chi-restraints excluded: chain G residue 103 SER Chi-restraints excluded: chain G residue 162 ILE Chi-restraints excluded: chain G residue 210 GLU Chi-restraints excluded: chain G residue 214 THR Chi-restraints excluded: chain G residue 216 ILE Chi-restraints excluded: chain H residue 37 TYR Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain I residue 133 LEU Chi-restraints excluded: chain I residue 170 CYS Chi-restraints excluded: chain I residue 177 LYS Chi-restraints excluded: chain I residue 273 ARG Chi-restraints excluded: chain I residue 349 LEU Chi-restraints excluded: chain I residue 371 LEU Chi-restraints excluded: chain I residue 402 PHE Chi-restraints excluded: chain I residue 451 VAL Chi-restraints excluded: chain I residue 536 SER Chi-restraints excluded: chain I residue 567 THR Chi-restraints excluded: chain I residue 605 THR Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 97 ASP Chi-restraints excluded: chain M residue 191 SER Chi-restraints excluded: chain M residue 226 LEU Chi-restraints excluded: chain M residue 290 LEU Chi-restraints excluded: chain M residue 294 ARG Chi-restraints excluded: chain M residue 361 THR Chi-restraints excluded: chain M residue 394 THR Chi-restraints excluded: chain M residue 400 THR Chi-restraints excluded: chain N residue 13 ASP Chi-restraints excluded: chain N residue 51 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 197 optimal weight: 0.5980 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 0.4980 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 GLN B 297 GLN C 400 ASN E 158 ASN E 243 ASN E 258 ASN E 329 ASN F 137 HIS F 141 GLN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 293 GLN I 346 ASN J 92 GLN M 325 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.141048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.120107 restraints weight = 48712.761| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 2.33 r_work: 0.3470 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.0965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.108 31254 Z= 0.142 Angle : 0.594 14.440 42214 Z= 0.304 Chirality : 0.041 0.508 4761 Planarity : 0.004 0.055 5382 Dihedral : 6.762 59.675 4266 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 3.90 % Allowed : 22.39 % Favored : 73.71 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % 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: 0.35 (0.14), residues: 3745 helix: 1.30 (0.11), residues: 2340 sheet: -0.14 (0.37), residues: 193 loop : -1.86 (0.17), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 204 TYR 0.019 0.001 TYR I 260 PHE 0.014 0.001 PHE A 280 TRP 0.021 0.001 TRP N 43 HIS 0.010 0.001 HIS B 176 Details of bonding type rmsd covalent geometry : bond 0.00307 (31240) covalent geometry : angle 0.58750 (42204) SS BOND : bond 0.02207 ( 2) SS BOND : angle 4.46369 ( 4) hydrogen bonds : bond 0.05467 ( 1704) hydrogen bonds : angle 4.23111 ( 5004) metal coordination : bond 0.01320 ( 12) metal coordination : angle 6.62848 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7490 Ramachandran restraints generated. 3745 Oldfield, 0 Emsley, 3745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7490 Ramachandran restraints generated. 3745 Oldfield, 0 Emsley, 3745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1000 residues out of total 3383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 868 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 LYS cc_start: 0.8761 (tppp) cc_final: 0.8505 (tmtm) REVERT: A 141 LYS cc_start: 0.9018 (mmmm) cc_final: 0.8660 (mmmm) REVERT: A 151 ASN cc_start: 0.8306 (t0) cc_final: 0.8103 (t0) REVERT: A 280 PHE cc_start: 0.7190 (p90) cc_final: 0.6837 (p90) REVERT: A 383 SER cc_start: 0.8983 (t) cc_final: 0.8602 (p) REVERT: B 67 TRP cc_start: 0.7857 (m-90) cc_final: 0.7623 (m-90) REVERT: B 74 GLN cc_start: 0.7898 (tp-100) cc_final: 0.7339 (mt0) REVERT: B 75 MET cc_start: 0.8329 (mtp) cc_final: 0.7822 (mtp) REVERT: B 79 ASN cc_start: 0.8269 (t0) cc_final: 0.7845 (t0) REVERT: B 89 MET cc_start: 0.7120 (tpp) cc_final: 0.6004 (tpp) REVERT: B 93 LYS cc_start: 0.8645 (mtmt) cc_final: 0.7821 (mtmt) REVERT: B 118 TYR cc_start: 0.7992 (t80) cc_final: 0.7619 (t80) REVERT: B 131 PHE cc_start: 0.8149 (OUTLIER) cc_final: 0.7892 (t80) REVERT: B 204 MET cc_start: 0.8219 (tmm) cc_final: 0.7809 (tmm) REVERT: B 278 LYS cc_start: 0.8613 (mtmm) cc_final: 0.8270 (mtpp) REVERT: B 327 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.7786 (mp0) REVERT: B 379 ASN cc_start: 0.8338 (t0) cc_final: 0.7979 (t160) REVERT: C 75 GLU cc_start: 0.6717 (tp30) cc_final: 0.6416 (tm-30) REVERT: C 118 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8191 (tt) REVERT: C 222 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7528 (mp0) REVERT: C 266 VAL cc_start: 0.7786 (t) cc_final: 0.7482 (p) REVERT: C 388 GLU cc_start: 0.8049 (mm-30) cc_final: 0.7675 (mm-30) REVERT: D 28 GLN cc_start: 0.8232 (mm110) cc_final: 0.7916 (mm110) REVERT: D 67 THR cc_start: 0.8459 (t) cc_final: 0.8225 (p) REVERT: D 110 LEU cc_start: 0.8352 (tp) cc_final: 0.8106 (tt) REVERT: D 114 TYR cc_start: 0.8324 (OUTLIER) cc_final: 0.8085 (m-10) REVERT: D 146 GLU cc_start: 0.7908 (mm-30) cc_final: 0.7552 (tm-30) REVERT: D 158 ASP cc_start: 0.8152 (t70) cc_final: 0.7895 (t70) REVERT: D 159 ASP cc_start: 0.8188 (t0) cc_final: 0.7937 (t0) REVERT: D 188 LYS cc_start: 0.8269 (mttt) cc_final: 0.8016 (mttt) REVERT: D 301 ASP cc_start: 0.8008 (m-30) cc_final: 0.7772 (m-30) REVERT: D 401 GLU cc_start: 0.7653 (tm-30) cc_final: 0.7205 (tm-30) REVERT: D 404 MET cc_start: 0.7541 (tmm) cc_final: 0.7094 (tmm) REVERT: E 171 ASP cc_start: 0.7918 (t0) cc_final: 0.7529 (t0) REVERT: E 265 GLN cc_start: 0.8137 (mm110) cc_final: 0.7880 (mm110) REVERT: E 286 MET cc_start: 0.6333 (mtm) cc_final: 0.6120 (mtm) REVERT: E 319 MET cc_start: 0.8811 (mtm) cc_final: 0.8530 (mtm) REVERT: E 325 ASP cc_start: 0.8712 (t70) cc_final: 0.8426 (t0) REVERT: F 30 VAL cc_start: 0.8714 (m) cc_final: 0.8459 (t) REVERT: F 132 ASP cc_start: 0.7854 (m-30) cc_final: 0.7354 (m-30) REVERT: F 135 ASP cc_start: 0.8181 (m-30) cc_final: 0.7936 (m-30) REVERT: F 206 MET cc_start: 0.8246 (OUTLIER) cc_final: 0.7714 (mmt) REVERT: F 219 GLU cc_start: 0.7167 (tp30) cc_final: 0.6742 (tp30) REVERT: F 246 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7645 (tt0) REVERT: G 118 LYS cc_start: 0.8438 (ttpp) cc_final: 0.8179 (ttpp) REVERT: G 197 GLN cc_start: 0.8248 (tm-30) cc_final: 0.7958 (tm-30) REVERT: H 50 MET cc_start: 0.8223 (tpp) cc_final: 0.8011 (mmm) REVERT: H 106 MET cc_start: 0.7123 (mmt) cc_final: 0.6879 (mmt) REVERT: I 133 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.8017 (tt) REVERT: I 154 LYS cc_start: 0.8346 (mttt) cc_final: 0.7989 (tppp) REVERT: I 177 LYS cc_start: 0.8115 (tppp) cc_final: 0.7675 (mmmm) REVERT: I 185 LYS cc_start: 0.8079 (mmpt) cc_final: 0.7726 (mmpt) REVERT: I 187 ILE cc_start: 0.8444 (mm) cc_final: 0.8193 (tp) REVERT: I 230 GLU cc_start: 0.7600 (pm20) cc_final: 0.7336 (pm20) REVERT: I 240 THR cc_start: 0.7929 (OUTLIER) cc_final: 0.7611 (p) REVERT: I 241 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.7235 (mp0) REVERT: I 272 GLN cc_start: 0.8023 (tm-30) cc_final: 0.6310 (tm-30) REVERT: I 276 GLN cc_start: 0.8004 (mm110) cc_final: 0.7206 (mm110) REVERT: I 306 GLU cc_start: 0.7536 (tp30) cc_final: 0.6924 (tm-30) REVERT: I 330 GLN cc_start: 0.7661 (pm20) cc_final: 0.7364 (pp30) REVERT: I 353 GLU cc_start: 0.8224 (tm-30) cc_final: 0.7823 (tm-30) REVERT: I 372 ASP cc_start: 0.7971 (m-30) cc_final: 0.7689 (m-30) REVERT: I 402 PHE cc_start: 0.8602 (OUTLIER) cc_final: 0.8311 (t80) REVERT: I 460 ASP cc_start: 0.7981 (p0) cc_final: 0.7683 (p0) REVERT: I 461 VAL cc_start: 0.8423 (m) cc_final: 0.8194 (p) REVERT: I 463 GLN cc_start: 0.8236 (tm-30) cc_final: 0.7906 (tm-30) REVERT: I 464 LYS cc_start: 0.7936 (mmtm) cc_final: 0.7612 (mmtm) REVERT: I 522 LYS cc_start: 0.8529 (tttt) cc_final: 0.8155 (tmmt) REVERT: I 587 LYS cc_start: 0.8427 (pttm) cc_final: 0.8120 (pttt) REVERT: I 607 GLN cc_start: 0.8263 (mt0) cc_final: 0.7950 (mp10) REVERT: J 90 THR cc_start: 0.8843 (m) cc_final: 0.8518 (t) REVERT: L 29 THR cc_start: 0.7983 (m) cc_final: 0.7640 (p) REVERT: L 94 LYS cc_start: 0.8835 (mttm) cc_final: 0.8504 (ttmm) REVERT: L 121 LYS cc_start: 0.8093 (tmmt) cc_final: 0.7835 (tmmt) REVERT: M 106 LEU cc_start: 0.8122 (mp) cc_final: 0.7854 (mm) REVERT: M 116 GLU cc_start: 0.7450 (mt-10) cc_final: 0.7240 (mt-10) REVERT: M 125 LYS cc_start: 0.8738 (mmtp) cc_final: 0.8334 (mmtp) REVERT: M 130 LEU cc_start: 0.8455 (tp) cc_final: 0.8094 (tt) REVERT: M 168 SER cc_start: 0.8894 (t) cc_final: 0.8628 (p) REVERT: M 193 ILE cc_start: 0.8617 (OUTLIER) cc_final: 0.8211 (mt) REVERT: M 259 ASP cc_start: 0.7901 (t70) cc_final: 0.7578 (t0) REVERT: M 294 ARG cc_start: 0.8231 (OUTLIER) cc_final: 0.6882 (ptm160) REVERT: M 310 PRO cc_start: 0.8746 (Cg_endo) cc_final: 0.8333 (Cg_exo) REVERT: M 387 GLN cc_start: 0.7297 (tt0) cc_final: 0.7074 (mt0) REVERT: N 20 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.7852 (ttm170) REVERT: N 71 ARG cc_start: 0.8414 (ttt-90) cc_final: 0.7941 (ttt180) outliers start: 132 outliers final: 57 residues processed: 929 average time/residue: 0.7075 time to fit residues: 762.5013 Evaluate side-chains 895 residues out of total 3383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 824 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 TYR Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 131 PHE Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 263 LYS Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 327 GLU Chi-restraints excluded: chain B residue 361 LYS Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain C residue 222 GLU Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 114 TYR Chi-restraints excluded: chain D residue 117 GLU Chi-restraints excluded: chain D residue 155 TYR Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 112 PHE Chi-restraints excluded: chain F residue 150 LEU Chi-restraints excluded: chain F residue 206 MET Chi-restraints excluded: chain F residue 246 GLU Chi-restraints excluded: chain G residue 65 GLN Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 162 ILE Chi-restraints excluded: chain G residue 216 ILE Chi-restraints excluded: chain H residue 150 GLU Chi-restraints excluded: chain H residue 157 SER Chi-restraints excluded: chain I residue 37 MET Chi-restraints excluded: chain I residue 133 LEU Chi-restraints excluded: chain I residue 141 ASN Chi-restraints excluded: chain I residue 192 ASN Chi-restraints excluded: chain I residue 224 THR Chi-restraints excluded: chain I residue 240 THR Chi-restraints excluded: chain I residue 241 GLU Chi-restraints excluded: chain I residue 257 VAL Chi-restraints excluded: chain I residue 349 LEU Chi-restraints excluded: chain I residue 395 LEU Chi-restraints excluded: chain I residue 402 PHE Chi-restraints excluded: chain I residue 451 VAL Chi-restraints excluded: chain I residue 501 THR Chi-restraints excluded: chain I residue 555 LEU Chi-restraints excluded: chain I residue 572 SER Chi-restraints excluded: chain I residue 633 MET Chi-restraints excluded: chain J residue 49 ILE Chi-restraints excluded: chain J residue 104 GLN Chi-restraints excluded: chain L residue 131 THR Chi-restraints excluded: chain M residue 117 LEU Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain M residue 193 ILE Chi-restraints excluded: chain M residue 226 LEU Chi-restraints excluded: chain M residue 283 GLU Chi-restraints excluded: chain M residue 294 ARG Chi-restraints excluded: chain M residue 322 MET Chi-restraints excluded: chain M residue 361 THR Chi-restraints excluded: chain N residue 13 ASP Chi-restraints excluded: chain N residue 20 ARG Chi-restraints excluded: chain N residue 59 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 66 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 245 optimal weight: 0.7980 chunk 137 optimal weight: 0.6980 chunk 236 optimal weight: 3.9990 chunk 370 optimal weight: 0.5980 chunk 181 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 chunk 241 optimal weight: 0.5980 chunk 240 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 363 ASN E 132 ASN E 158 ASN E 258 ASN E 329 ASN F 141 GLN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 304 HIS I 387 ASN L 64 HIS M 325 ASN N 45 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.141147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.120210 restraints weight = 48943.012| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 2.32 r_work: 0.3475 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3316 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.1271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 31254 Z= 0.130 Angle : 0.573 12.079 42214 Z= 0.292 Chirality : 0.040 0.324 4761 Planarity : 0.004 0.054 5382 Dihedral : 5.990 59.663 4184 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 4.08 % Allowed : 23.43 % Favored : 72.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % 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: 0.41 (0.14), residues: 3745 helix: 1.33 (0.11), residues: 2343 sheet: 0.01 (0.38), residues: 188 loop : -1.84 (0.17), residues: 1214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 160 TYR 0.019 0.001 TYR I 50 PHE 0.014 0.001 PHE A 280 TRP 0.020 0.001 TRP J 33 HIS 0.009 0.001 HIS B 176 Details of bonding type rmsd covalent geometry : bond 0.00288 (31240) covalent geometry : angle 0.56887 (42204) SS BOND : bond 0.01911 ( 2) SS BOND : angle 2.54907 ( 4) hydrogen bonds : bond 0.04902 ( 1704) hydrogen bonds : angle 4.05687 ( 5004) metal coordination : bond 0.00994 ( 12) metal coordination : angle 5.50447 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7490 Ramachandran restraints generated. 3745 Oldfield, 0 Emsley, 3745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7490 Ramachandran restraints generated. 3745 Oldfield, 0 Emsley, 3745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 987 residues out of total 3383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 849 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 LYS cc_start: 0.8742 (tppp) cc_final: 0.8472 (tmtm) REVERT: A 141 LYS cc_start: 0.9002 (mmmm) cc_final: 0.8551 (mmmm) REVERT: A 280 PHE cc_start: 0.7198 (p90) cc_final: 0.6822 (p90) REVERT: A 355 ASP cc_start: 0.8412 (t0) cc_final: 0.8165 (t70) REVERT: A 383 SER cc_start: 0.8969 (t) cc_final: 0.8563 (p) REVERT: A 461 ARG cc_start: 0.8501 (OUTLIER) cc_final: 0.8192 (ptp90) REVERT: B 55 GLN cc_start: 0.7691 (OUTLIER) cc_final: 0.7203 (pp30) REVERT: B 74 GLN cc_start: 0.7917 (tp-100) cc_final: 0.7287 (mt0) REVERT: B 75 MET cc_start: 0.8306 (mtp) cc_final: 0.7787 (mtp) REVERT: B 79 ASN cc_start: 0.8231 (t0) cc_final: 0.7808 (t0) REVERT: B 89 MET cc_start: 0.7179 (tpp) cc_final: 0.6580 (tpp) REVERT: B 93 LYS cc_start: 0.8659 (mtmt) cc_final: 0.8142 (mmmm) REVERT: B 118 TYR cc_start: 0.7967 (t80) cc_final: 0.7607 (t80) REVERT: B 131 PHE cc_start: 0.8138 (OUTLIER) cc_final: 0.7874 (t80) REVERT: B 204 MET cc_start: 0.8166 (tmm) cc_final: 0.7734 (tmm) REVERT: B 228 ILE cc_start: 0.8538 (mt) cc_final: 0.8173 (mp) REVERT: B 298 GLU cc_start: 0.8113 (mp0) cc_final: 0.7579 (mp0) REVERT: B 327 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.7805 (mp0) REVERT: B 379 ASN cc_start: 0.8321 (t0) cc_final: 0.7959 (t160) REVERT: C 75 GLU cc_start: 0.6661 (tp30) cc_final: 0.6310 (tm-30) REVERT: C 118 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8181 (tt) REVERT: C 222 GLU cc_start: 0.7723 (mp0) cc_final: 0.7413 (mp0) REVERT: C 266 VAL cc_start: 0.7733 (t) cc_final: 0.7410 (p) REVERT: C 388 GLU cc_start: 0.8083 (mm-30) cc_final: 0.7717 (mm-30) REVERT: D 67 THR cc_start: 0.8438 (t) cc_final: 0.8223 (p) REVERT: D 110 LEU cc_start: 0.8371 (tp) cc_final: 0.8117 (tt) REVERT: D 114 TYR cc_start: 0.8295 (OUTLIER) cc_final: 0.8054 (m-10) REVERT: D 121 ARG cc_start: 0.8143 (tpp80) cc_final: 0.7723 (tpp80) REVERT: D 158 ASP cc_start: 0.8133 (t70) cc_final: 0.6882 (t70) REVERT: D 159 ASP cc_start: 0.8157 (t0) cc_final: 0.7913 (t0) REVERT: D 188 LYS cc_start: 0.8179 (mttt) cc_final: 0.7937 (mttt) REVERT: D 301 ASP cc_start: 0.7935 (m-30) cc_final: 0.7660 (m-30) REVERT: D 347 ARG cc_start: 0.8653 (mtp85) cc_final: 0.8434 (mtp180) REVERT: D 401 GLU cc_start: 0.7619 (tm-30) cc_final: 0.7172 (tm-30) REVERT: D 404 MET cc_start: 0.7515 (tmm) cc_final: 0.7066 (tmm) REVERT: E 165 PHE cc_start: 0.8317 (OUTLIER) cc_final: 0.8070 (t80) REVERT: E 171 ASP cc_start: 0.7921 (t0) cc_final: 0.7570 (t0) REVERT: E 265 GLN cc_start: 0.8131 (mm110) cc_final: 0.7884 (mm110) REVERT: E 286 MET cc_start: 0.6354 (mtm) cc_final: 0.6130 (mtm) REVERT: E 319 MET cc_start: 0.8811 (mtm) cc_final: 0.8526 (mtm) REVERT: E 325 ASP cc_start: 0.8737 (t70) cc_final: 0.8436 (t0) REVERT: F 30 VAL cc_start: 0.8717 (m) cc_final: 0.8467 (t) REVERT: F 132 ASP cc_start: 0.7845 (m-30) cc_final: 0.7363 (m-30) REVERT: F 135 ASP cc_start: 0.8181 (m-30) cc_final: 0.7941 (m-30) REVERT: F 206 MET cc_start: 0.8326 (OUTLIER) cc_final: 0.7930 (mmm) REVERT: G 164 LYS cc_start: 0.8592 (mppt) cc_final: 0.8360 (mppt) REVERT: G 182 GLU cc_start: 0.7990 (mm-30) cc_final: 0.7658 (mm-30) REVERT: G 197 GLN cc_start: 0.8214 (tm-30) cc_final: 0.7919 (tm-30) REVERT: H 106 MET cc_start: 0.7127 (mmt) cc_final: 0.6830 (mmt) REVERT: I 25 ARG cc_start: 0.7607 (OUTLIER) cc_final: 0.7169 (tpp80) REVERT: I 115 VAL cc_start: 0.7195 (OUTLIER) cc_final: 0.6679 (m) REVERT: I 133 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.7964 (tt) REVERT: I 154 LYS cc_start: 0.8331 (mttt) cc_final: 0.8015 (tppp) REVERT: I 177 LYS cc_start: 0.7989 (tppp) cc_final: 0.7492 (mmmm) REVERT: I 185 LYS cc_start: 0.8132 (mmpt) cc_final: 0.7743 (mmpt) REVERT: I 240 THR cc_start: 0.7922 (OUTLIER) cc_final: 0.7612 (p) REVERT: I 272 GLN cc_start: 0.8087 (tm-30) cc_final: 0.6707 (tm-30) REVERT: I 276 GLN cc_start: 0.7997 (mm110) cc_final: 0.7297 (mm110) REVERT: I 306 GLU cc_start: 0.7554 (tp30) cc_final: 0.6931 (tm-30) REVERT: I 312 ASP cc_start: 0.8825 (OUTLIER) cc_final: 0.8596 (m-30) REVERT: I 330 GLN cc_start: 0.7731 (pm20) cc_final: 0.7447 (pp30) REVERT: I 353 GLU cc_start: 0.8193 (tm-30) cc_final: 0.7766 (tm-30) REVERT: I 365 MET cc_start: 0.8386 (mmm) cc_final: 0.8117 (tmm) REVERT: I 372 ASP cc_start: 0.8003 (m-30) cc_final: 0.7675 (m-30) REVERT: I 459 LYS cc_start: 0.8289 (OUTLIER) cc_final: 0.8076 (mmmm) REVERT: I 460 ASP cc_start: 0.7921 (p0) cc_final: 0.7014 (p0) REVERT: I 461 VAL cc_start: 0.8339 (m) cc_final: 0.8081 (p) REVERT: I 463 GLN cc_start: 0.8181 (tm-30) cc_final: 0.7850 (tm-30) REVERT: I 464 LYS cc_start: 0.7921 (mmtm) cc_final: 0.7605 (mmtm) REVERT: I 522 LYS cc_start: 0.8547 (tttt) cc_final: 0.8163 (tmmt) REVERT: I 587 LYS cc_start: 0.8446 (pttm) cc_final: 0.8116 (pttt) REVERT: I 607 GLN cc_start: 0.8283 (mt0) cc_final: 0.7965 (mp10) REVERT: I 612 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8361 (tm) REVERT: L 29 THR cc_start: 0.7943 (m) cc_final: 0.7608 (p) REVERT: L 94 LYS cc_start: 0.8844 (mttm) cc_final: 0.8517 (ttmm) REVERT: M 103 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7403 (tt0) REVERT: M 106 LEU cc_start: 0.8204 (mp) cc_final: 0.7932 (mm) REVERT: M 116 GLU cc_start: 0.7470 (mt-10) cc_final: 0.7255 (mt-10) REVERT: M 125 LYS cc_start: 0.8723 (mmtp) cc_final: 0.8395 (mmtp) REVERT: M 130 LEU cc_start: 0.8389 (tp) cc_final: 0.8135 (tt) REVERT: M 168 SER cc_start: 0.8943 (t) cc_final: 0.8686 (p) REVERT: M 193 ILE cc_start: 0.8679 (OUTLIER) cc_final: 0.8241 (mt) REVERT: M 259 ASP cc_start: 0.7856 (t70) cc_final: 0.7477 (t0) REVERT: M 276 VAL cc_start: 0.8101 (t) cc_final: 0.7838 (m) REVERT: M 294 ARG cc_start: 0.8225 (OUTLIER) cc_final: 0.6822 (ptm160) REVERT: M 310 PRO cc_start: 0.8748 (Cg_endo) cc_final: 0.8324 (Cg_exo) REVERT: M 387 GLN cc_start: 0.7247 (OUTLIER) cc_final: 0.7032 (mt0) REVERT: N 20 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.8046 (ttm170) REVERT: N 71 ARG cc_start: 0.8414 (ttt-90) cc_final: 0.7974 (ttt180) outliers start: 138 outliers final: 74 residues processed: 918 average time/residue: 0.7190 time to fit residues: 762.5564 Evaluate side-chains 924 residues out of total 3383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 830 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 461 ARG Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain B residue 131 PHE Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 327 GLU Chi-restraints excluded: chain B residue 361 LYS Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain D residue 114 TYR Chi-restraints excluded: chain D residue 117 GLU Chi-restraints excluded: chain D residue 155 TYR Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain F residue 83 VAL Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 112 PHE Chi-restraints excluded: chain F residue 150 LEU Chi-restraints excluded: chain F residue 206 MET Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 65 GLN Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 151 LEU Chi-restraints excluded: chain G residue 162 ILE Chi-restraints excluded: chain G residue 165 LYS Chi-restraints excluded: chain G residue 210 GLU Chi-restraints excluded: chain G residue 216 ILE Chi-restraints excluded: chain H residue 150 GLU Chi-restraints excluded: chain H residue 157 SER Chi-restraints excluded: chain I residue 25 ARG Chi-restraints excluded: chain I residue 37 MET Chi-restraints excluded: chain I residue 47 THR Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain I residue 133 LEU Chi-restraints excluded: chain I residue 141 ASN Chi-restraints excluded: chain I residue 151 GLU Chi-restraints excluded: chain I residue 224 THR Chi-restraints excluded: chain I residue 230 GLU Chi-restraints excluded: chain I residue 239 ASP Chi-restraints excluded: chain I residue 240 THR Chi-restraints excluded: chain I residue 257 VAL Chi-restraints excluded: chain I residue 269 LEU Chi-restraints excluded: chain I residue 290 LYS Chi-restraints excluded: chain I residue 312 ASP Chi-restraints excluded: chain I residue 395 LEU Chi-restraints excluded: chain I residue 402 PHE Chi-restraints excluded: chain I residue 451 VAL Chi-restraints excluded: chain I residue 459 LYS Chi-restraints excluded: chain I residue 501 THR Chi-restraints excluded: chain I residue 502 SER Chi-restraints excluded: chain I residue 507 MET Chi-restraints excluded: chain I residue 511 ILE Chi-restraints excluded: chain I residue 555 LEU Chi-restraints excluded: chain I residue 572 SER Chi-restraints excluded: chain I residue 612 LEU Chi-restraints excluded: chain I residue 633 MET Chi-restraints excluded: chain J residue 44 ILE Chi-restraints excluded: chain J residue 104 GLN Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 131 THR Chi-restraints excluded: chain M residue 103 GLU Chi-restraints excluded: chain M residue 105 LEU Chi-restraints excluded: chain M residue 117 LEU Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain M residue 193 ILE Chi-restraints excluded: chain M residue 226 LEU Chi-restraints excluded: chain M residue 256 SER Chi-restraints excluded: chain M residue 283 GLU Chi-restraints excluded: chain M residue 294 ARG Chi-restraints excluded: chain M residue 322 MET Chi-restraints excluded: chain M residue 387 GLN Chi-restraints excluded: chain M residue 394 THR Chi-restraints excluded: chain M residue 400 THR Chi-restraints excluded: chain M residue 409 ILE Chi-restraints excluded: chain N residue 13 ASP Chi-restraints excluded: chain N residue 20 ARG Chi-restraints excluded: chain N residue 46 LEU Chi-restraints excluded: chain N residue 59 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 307 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 chunk 237 optimal weight: 4.9990 chunk 330 optimal weight: 6.9990 chunk 90 optimal weight: 0.9990 chunk 361 optimal weight: 4.9990 chunk 259 optimal weight: 0.9980 chunk 85 optimal weight: 0.5980 chunk 75 optimal weight: 0.9980 chunk 139 optimal weight: 4.9990 chunk 131 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN B 144 ASN E 158 ASN E 258 ASN E 329 ASN F 141 GLN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 304 HIS I 308 GLN I 324 ASN I 346 ASN L 64 HIS M 325 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.140624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.119683 restraints weight = 48377.112| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 2.31 r_work: 0.3461 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 31254 Z= 0.149 Angle : 0.573 14.316 42214 Z= 0.293 Chirality : 0.041 0.287 4761 Planarity : 0.004 0.057 5382 Dihedral : 5.756 58.476 4177 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 4.76 % Allowed : 23.54 % Favored : 71.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.14), residues: 3745 helix: 1.34 (0.11), residues: 2340 sheet: 0.05 (0.37), residues: 203 loop : -1.87 (0.17), residues: 1202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG I 289 TYR 0.025 0.001 TYR I 50 PHE 0.030 0.001 PHE D 48 TRP 0.021 0.001 TRP J 33 HIS 0.010 0.001 HIS A 277 Details of bonding type rmsd covalent geometry : bond 0.00341 (31240) covalent geometry : angle 0.56702 (42204) SS BOND : bond 0.01734 ( 2) SS BOND : angle 1.91331 ( 4) hydrogen bonds : bond 0.05149 ( 1704) hydrogen bonds : angle 4.01722 ( 5004) metal coordination : bond 0.01584 ( 12) metal coordination : angle 6.56423 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7490 Ramachandran restraints generated. 3745 Oldfield, 0 Emsley, 3745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7490 Ramachandran restraints generated. 3745 Oldfield, 0 Emsley, 3745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1006 residues out of total 3383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 845 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8128 (mt) REVERT: A 257 GLU cc_start: 0.8281 (mt-10) cc_final: 0.8068 (mm-30) REVERT: A 280 PHE cc_start: 0.7207 (p90) cc_final: 0.6821 (p90) REVERT: A 383 SER cc_start: 0.8999 (t) cc_final: 0.8617 (p) REVERT: A 461 ARG cc_start: 0.8586 (OUTLIER) cc_final: 0.8283 (ptp90) REVERT: B 40 LYS cc_start: 0.8158 (mmtm) cc_final: 0.7698 (mppt) REVERT: B 55 GLN cc_start: 0.7701 (OUTLIER) cc_final: 0.7376 (pp30) REVERT: B 67 TRP cc_start: 0.8068 (m-90) cc_final: 0.7856 (m-90) REVERT: B 72 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8368 (mm) REVERT: B 74 GLN cc_start: 0.7923 (tp-100) cc_final: 0.7242 (mt0) REVERT: B 75 MET cc_start: 0.8323 (mtp) cc_final: 0.7796 (mtp) REVERT: B 79 ASN cc_start: 0.8258 (t0) cc_final: 0.7850 (t0) REVERT: B 89 MET cc_start: 0.7200 (tpp) cc_final: 0.6590 (tpp) REVERT: B 93 LYS cc_start: 0.8675 (mtmt) cc_final: 0.8168 (mmmm) REVERT: B 131 PHE cc_start: 0.8137 (OUTLIER) cc_final: 0.7834 (t80) REVERT: B 204 MET cc_start: 0.8194 (tmm) cc_final: 0.7719 (tmm) REVERT: B 228 ILE cc_start: 0.8535 (mt) cc_final: 0.8174 (mp) REVERT: B 295 ASP cc_start: 0.7545 (t0) cc_final: 0.7316 (t0) REVERT: B 298 GLU cc_start: 0.8102 (mp0) cc_final: 0.7560 (mp0) REVERT: B 327 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.7781 (mp0) REVERT: B 379 ASN cc_start: 0.8344 (t0) cc_final: 0.7985 (t160) REVERT: C 75 GLU cc_start: 0.6675 (tp30) cc_final: 0.6320 (tm-30) REVERT: C 118 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8198 (tt) REVERT: C 222 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7513 (mp0) REVERT: C 266 VAL cc_start: 0.7789 (t) cc_final: 0.7470 (p) REVERT: C 388 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7695 (mm-30) REVERT: D 67 THR cc_start: 0.8431 (t) cc_final: 0.8225 (p) REVERT: D 110 LEU cc_start: 0.8378 (tp) cc_final: 0.8118 (tt) REVERT: D 114 TYR cc_start: 0.8347 (OUTLIER) cc_final: 0.8100 (m-10) REVERT: D 117 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.7798 (mp0) REVERT: D 158 ASP cc_start: 0.8135 (t70) cc_final: 0.7905 (t70) REVERT: D 159 ASP cc_start: 0.8151 (t0) cc_final: 0.7926 (t0) REVERT: D 188 LYS cc_start: 0.8168 (mttt) cc_final: 0.7924 (mttt) REVERT: D 301 ASP cc_start: 0.7982 (m-30) cc_final: 0.7688 (m-30) REVERT: D 347 ARG cc_start: 0.8661 (mtp85) cc_final: 0.8382 (mtp180) REVERT: D 401 GLU cc_start: 0.7615 (tm-30) cc_final: 0.7168 (tm-30) REVERT: D 404 MET cc_start: 0.7523 (tmm) cc_final: 0.7069 (tmm) REVERT: E 165 PHE cc_start: 0.8348 (OUTLIER) cc_final: 0.8143 (t80) REVERT: E 171 ASP cc_start: 0.7930 (t0) cc_final: 0.7613 (t0) REVERT: E 265 GLN cc_start: 0.8155 (mm110) cc_final: 0.7906 (mm110) REVERT: E 286 MET cc_start: 0.6387 (mtm) cc_final: 0.6157 (mtm) REVERT: E 319 MET cc_start: 0.8834 (mtm) cc_final: 0.8560 (mtm) REVERT: E 325 ASP cc_start: 0.8747 (t70) cc_final: 0.8454 (t0) REVERT: F 75 LYS cc_start: 0.8264 (mtmm) cc_final: 0.7935 (mtmm) REVERT: F 132 ASP cc_start: 0.7835 (m-30) cc_final: 0.7370 (m-30) REVERT: F 135 ASP cc_start: 0.8198 (m-30) cc_final: 0.7993 (m-30) REVERT: F 246 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7767 (tp30) REVERT: G 182 GLU cc_start: 0.8032 (mm-30) cc_final: 0.7706 (mm-30) REVERT: G 197 GLN cc_start: 0.8228 (tm-30) cc_final: 0.7939 (tm-30) REVERT: I 25 ARG cc_start: 0.7591 (OUTLIER) cc_final: 0.7166 (tpp80) REVERT: I 133 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.7992 (tt) REVERT: I 154 LYS cc_start: 0.8354 (mttt) cc_final: 0.8034 (tppp) REVERT: I 171 LEU cc_start: 0.7802 (OUTLIER) cc_final: 0.7468 (tm) REVERT: I 177 LYS cc_start: 0.8025 (tppp) cc_final: 0.7530 (mmmm) REVERT: I 185 LYS cc_start: 0.8211 (mmpt) cc_final: 0.8007 (mmpt) REVERT: I 186 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8698 (tt) REVERT: I 230 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.7230 (pm20) REVERT: I 240 THR cc_start: 0.8099 (OUTLIER) cc_final: 0.7775 (p) REVERT: I 272 GLN cc_start: 0.8190 (tm-30) cc_final: 0.6231 (tm-30) REVERT: I 276 GLN cc_start: 0.7878 (mm110) cc_final: 0.6945 (mm110) REVERT: I 306 GLU cc_start: 0.7506 (tp30) cc_final: 0.6858 (tm-30) REVERT: I 312 ASP cc_start: 0.8853 (OUTLIER) cc_final: 0.8617 (m-30) REVERT: I 330 GLN cc_start: 0.7755 (pm20) cc_final: 0.7471 (pp30) REVERT: I 353 GLU cc_start: 0.8200 (tm-30) cc_final: 0.7744 (tm-30) REVERT: I 365 MET cc_start: 0.8412 (mmm) cc_final: 0.8113 (tmm) REVERT: I 372 ASP cc_start: 0.8027 (m-30) cc_final: 0.7632 (m-30) REVERT: I 460 ASP cc_start: 0.7926 (p0) cc_final: 0.7402 (p0) REVERT: I 461 VAL cc_start: 0.8342 (m) cc_final: 0.8105 (p) REVERT: I 463 GLN cc_start: 0.8208 (tm-30) cc_final: 0.7865 (tm-30) REVERT: I 464 LYS cc_start: 0.7954 (mmtm) cc_final: 0.7659 (mmtm) REVERT: I 522 LYS cc_start: 0.8531 (tttt) cc_final: 0.8250 (tmmt) REVERT: I 587 LYS cc_start: 0.8435 (pttm) cc_final: 0.8116 (pttt) REVERT: I 607 GLN cc_start: 0.8299 (mt0) cc_final: 0.8007 (mp10) REVERT: I 612 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8395 (tm) REVERT: L 29 THR cc_start: 0.7932 (OUTLIER) cc_final: 0.7601 (p) REVERT: M 116 GLU cc_start: 0.7521 (mt-10) cc_final: 0.7295 (mt-10) REVERT: M 125 LYS cc_start: 0.8696 (mmtp) cc_final: 0.8371 (mmtp) REVERT: M 168 SER cc_start: 0.8962 (t) cc_final: 0.8707 (p) REVERT: M 193 ILE cc_start: 0.8706 (OUTLIER) cc_final: 0.8311 (mt) REVERT: M 259 ASP cc_start: 0.7884 (t70) cc_final: 0.7534 (t0) REVERT: M 276 VAL cc_start: 0.8120 (t) cc_final: 0.7842 (m) REVERT: M 294 ARG cc_start: 0.8263 (OUTLIER) cc_final: 0.6862 (ptm160) REVERT: M 310 PRO cc_start: 0.8766 (Cg_endo) cc_final: 0.8336 (Cg_exo) REVERT: M 387 GLN cc_start: 0.7232 (OUTLIER) cc_final: 0.6998 (mt0) REVERT: N 20 ARG cc_start: 0.8534 (OUTLIER) cc_final: 0.8058 (ttm170) REVERT: N 31 LEU cc_start: 0.8376 (mp) cc_final: 0.8080 (mp) REVERT: N 71 ARG cc_start: 0.8471 (ttt-90) cc_final: 0.8090 (ttt180) outliers start: 161 outliers final: 83 residues processed: 930 average time/residue: 0.7272 time to fit residues: 782.9657 Evaluate side-chains 947 residues out of total 3383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 839 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 363 ARG Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 461 ARG Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 131 PHE Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 327 GLU Chi-restraints excluded: chain B residue 361 LYS Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 132 GLN Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain C residue 222 GLU Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain D residue 114 TYR Chi-restraints excluded: chain D residue 117 GLU Chi-restraints excluded: chain D residue 155 TYR Chi-restraints excluded: chain D residue 160 ASP Chi-restraints excluded: chain D residue 170 ARG Chi-restraints excluded: chain D residue 179 THR Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 253 GLU Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 333 ILE Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 83 VAL Chi-restraints excluded: chain F residue 112 PHE Chi-restraints excluded: chain F residue 150 LEU Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 246 GLU Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain G residue 65 GLN Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 103 SER Chi-restraints excluded: chain G residue 151 LEU Chi-restraints excluded: chain G residue 162 ILE Chi-restraints excluded: chain G residue 165 LYS Chi-restraints excluded: chain G residue 210 GLU Chi-restraints excluded: chain G residue 216 ILE Chi-restraints excluded: chain H residue 150 GLU Chi-restraints excluded: chain I residue 25 ARG Chi-restraints excluded: chain I residue 133 LEU Chi-restraints excluded: chain I residue 141 ASN Chi-restraints excluded: chain I residue 151 GLU Chi-restraints excluded: chain I residue 171 LEU Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain I residue 230 GLU Chi-restraints excluded: chain I residue 239 ASP Chi-restraints excluded: chain I residue 240 THR Chi-restraints excluded: chain I residue 257 VAL Chi-restraints excluded: chain I residue 310 LEU Chi-restraints excluded: chain I residue 312 ASP Chi-restraints excluded: chain I residue 333 LEU Chi-restraints excluded: chain I residue 402 PHE Chi-restraints excluded: chain I residue 411 MET Chi-restraints excluded: chain I residue 416 SER Chi-restraints excluded: chain I residue 451 VAL Chi-restraints excluded: chain I residue 479 SER Chi-restraints excluded: chain I residue 483 ASP Chi-restraints excluded: chain I residue 501 THR Chi-restraints excluded: chain I residue 502 SER Chi-restraints excluded: chain I residue 507 MET Chi-restraints excluded: chain I residue 511 ILE Chi-restraints excluded: chain I residue 555 LEU Chi-restraints excluded: chain I residue 572 SER Chi-restraints excluded: chain I residue 612 LEU Chi-restraints excluded: chain I residue 633 MET Chi-restraints excluded: chain J residue 44 ILE Chi-restraints excluded: chain J residue 49 ILE Chi-restraints excluded: chain J residue 104 GLN Chi-restraints excluded: chain L residue 29 THR Chi-restraints excluded: chain L residue 131 THR Chi-restraints excluded: chain M residue 104 LEU Chi-restraints excluded: chain M residue 105 LEU Chi-restraints excluded: chain M residue 117 LEU Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain M residue 191 SER Chi-restraints excluded: chain M residue 193 ILE Chi-restraints excluded: chain M residue 226 LEU Chi-restraints excluded: chain M residue 275 GLN Chi-restraints excluded: chain M residue 283 GLU Chi-restraints excluded: chain M residue 294 ARG Chi-restraints excluded: chain M residue 361 THR Chi-restraints excluded: chain M residue 387 GLN Chi-restraints excluded: chain M residue 394 THR Chi-restraints excluded: chain M residue 400 THR Chi-restraints excluded: chain M residue 409 ILE Chi-restraints excluded: chain N residue 20 ARG Chi-restraints excluded: chain N residue 46 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 114 optimal weight: 0.6980 chunk 27 optimal weight: 0.5980 chunk 313 optimal weight: 5.9990 chunk 345 optimal weight: 3.9990 chunk 319 optimal weight: 1.9990 chunk 351 optimal weight: 0.9980 chunk 221 optimal weight: 0.7980 chunk 248 optimal weight: 2.9990 chunk 278 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 ASN D 349 ASN D 383 ASN E 158 ASN E 258 ASN F 141 GLN G 93 GLN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 304 HIS I 308 GLN I 324 ASN I 346 ASN M 325 ASN N 45 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.139661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.118716 restraints weight = 48651.470| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 2.31 r_work: 0.3456 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3296 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 31254 Z= 0.159 Angle : 0.587 14.871 42214 Z= 0.300 Chirality : 0.041 0.278 4761 Planarity : 0.004 0.057 5382 Dihedral : 5.625 58.684 4172 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 5.24 % Allowed : 23.90 % Favored : 70.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.14), residues: 3745 helix: 1.31 (0.11), residues: 2339 sheet: 0.05 (0.37), residues: 203 loop : -1.89 (0.17), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 160 TYR 0.025 0.001 TYR I 50 PHE 0.028 0.001 PHE D 48 TRP 0.023 0.001 TRP J 33 HIS 0.009 0.001 HIS B 176 Details of bonding type rmsd covalent geometry : bond 0.00367 (31240) covalent geometry : angle 0.58140 (42204) SS BOND : bond 0.01687 ( 2) SS BOND : angle 1.76600 ( 4) hydrogen bonds : bond 0.05236 ( 1704) hydrogen bonds : angle 3.99770 ( 5004) metal coordination : bond 0.02151 ( 12) metal coordination : angle 6.65686 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7490 Ramachandran restraints generated. 3745 Oldfield, 0 Emsley, 3745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7490 Ramachandran restraints generated. 3745 Oldfield, 0 Emsley, 3745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1018 residues out of total 3383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 177 poor density : 841 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 ASN cc_start: 0.8361 (OUTLIER) cc_final: 0.7835 (t0) REVERT: A 280 PHE cc_start: 0.7228 (p90) cc_final: 0.6830 (p90) REVERT: A 355 ASP cc_start: 0.8433 (t0) cc_final: 0.8166 (t70) REVERT: A 383 SER cc_start: 0.8992 (t) cc_final: 0.8576 (p) REVERT: A 461 ARG cc_start: 0.8638 (OUTLIER) cc_final: 0.8365 (ptp90) REVERT: B 55 GLN cc_start: 0.7669 (OUTLIER) cc_final: 0.7332 (pp30) REVERT: B 67 TRP cc_start: 0.8033 (m-90) cc_final: 0.7811 (m-90) REVERT: B 74 GLN cc_start: 0.7917 (OUTLIER) cc_final: 0.7265 (mt0) REVERT: B 75 MET cc_start: 0.8264 (mtp) cc_final: 0.7737 (mtp) REVERT: B 79 ASN cc_start: 0.8226 (t0) cc_final: 0.7814 (t0) REVERT: B 89 MET cc_start: 0.7244 (tpp) cc_final: 0.6169 (tpp) REVERT: B 93 LYS cc_start: 0.8668 (mtmt) cc_final: 0.7841 (mtmt) REVERT: B 131 PHE cc_start: 0.8124 (OUTLIER) cc_final: 0.7815 (t80) REVERT: B 204 MET cc_start: 0.8194 (tmm) cc_final: 0.7731 (tmm) REVERT: B 228 ILE cc_start: 0.8535 (mt) cc_final: 0.8153 (mt) REVERT: B 278 LYS cc_start: 0.8643 (mtmm) cc_final: 0.8398 (mtmm) REVERT: B 295 ASP cc_start: 0.7572 (t0) cc_final: 0.7343 (t0) REVERT: B 298 GLU cc_start: 0.8091 (mp0) cc_final: 0.7556 (mp0) REVERT: B 327 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.7769 (mp0) REVERT: B 379 ASN cc_start: 0.8370 (t0) cc_final: 0.8013 (t160) REVERT: C 75 GLU cc_start: 0.6683 (tp30) cc_final: 0.6322 (tm-30) REVERT: C 118 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8342 (tt) REVERT: C 222 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7538 (mp0) REVERT: C 266 VAL cc_start: 0.7786 (t) cc_final: 0.7464 (p) REVERT: C 388 GLU cc_start: 0.8140 (mm-30) cc_final: 0.7773 (mm-30) REVERT: D 67 THR cc_start: 0.8393 (t) cc_final: 0.8190 (p) REVERT: D 110 LEU cc_start: 0.8383 (tp) cc_final: 0.8124 (tt) REVERT: D 114 TYR cc_start: 0.8357 (OUTLIER) cc_final: 0.8127 (m-10) REVERT: D 117 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7747 (mp0) REVERT: D 159 ASP cc_start: 0.8174 (t0) cc_final: 0.7808 (t0) REVERT: D 175 GLN cc_start: 0.7307 (OUTLIER) cc_final: 0.6681 (tm130) REVERT: D 188 LYS cc_start: 0.8177 (mttt) cc_final: 0.7918 (mttt) REVERT: D 207 ARG cc_start: 0.8390 (mpt-90) cc_final: 0.8124 (mpt-90) REVERT: D 301 ASP cc_start: 0.7992 (m-30) cc_final: 0.7702 (m-30) REVERT: D 347 ARG cc_start: 0.8667 (mtp85) cc_final: 0.8437 (mtp180) REVERT: D 401 GLU cc_start: 0.7617 (tm-30) cc_final: 0.7234 (tm-30) REVERT: D 404 MET cc_start: 0.7498 (tmm) cc_final: 0.7166 (tmm) REVERT: E 265 GLN cc_start: 0.8168 (mm110) cc_final: 0.7918 (mm110) REVERT: E 286 MET cc_start: 0.6418 (mtm) cc_final: 0.6203 (mtm) REVERT: E 319 MET cc_start: 0.8831 (mtm) cc_final: 0.8573 (mtm) REVERT: E 325 ASP cc_start: 0.8735 (t70) cc_final: 0.8432 (t0) REVERT: F 75 LYS cc_start: 0.8288 (mtmm) cc_final: 0.7967 (mtmm) REVERT: F 84 MET cc_start: 0.8894 (OUTLIER) cc_final: 0.8687 (ptm) REVERT: F 122 LEU cc_start: 0.8694 (mt) cc_final: 0.8470 (mt) REVERT: F 132 ASP cc_start: 0.7873 (m-30) cc_final: 0.7426 (m-30) REVERT: F 135 ASP cc_start: 0.8206 (m-30) cc_final: 0.7991 (m-30) REVERT: F 206 MET cc_start: 0.8311 (OUTLIER) cc_final: 0.7903 (mmm) REVERT: F 246 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7797 (tp30) REVERT: G 82 LYS cc_start: 0.8205 (OUTLIER) cc_final: 0.7905 (tppp) REVERT: G 182 GLU cc_start: 0.8022 (mm-30) cc_final: 0.7710 (mm-30) REVERT: G 197 GLN cc_start: 0.8244 (tm-30) cc_final: 0.7950 (tm-30) REVERT: I 20 ILE cc_start: 0.8540 (mm) cc_final: 0.8239 (tp) REVERT: I 25 ARG cc_start: 0.7628 (OUTLIER) cc_final: 0.7210 (tpp80) REVERT: I 133 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.7980 (tt) REVERT: I 154 LYS cc_start: 0.8345 (mttt) cc_final: 0.8022 (tppp) REVERT: I 165 VAL cc_start: 0.9107 (OUTLIER) cc_final: 0.8774 (m) REVERT: I 176 ASN cc_start: 0.7785 (t0) cc_final: 0.7442 (t0) REVERT: I 177 LYS cc_start: 0.8104 (tppp) cc_final: 0.7577 (mmmm) REVERT: I 185 LYS cc_start: 0.8193 (mmpt) cc_final: 0.7907 (mmpt) REVERT: I 230 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.7204 (pm20) REVERT: I 240 THR cc_start: 0.8114 (OUTLIER) cc_final: 0.7786 (p) REVERT: I 272 GLN cc_start: 0.8247 (tm-30) cc_final: 0.7709 (tm-30) REVERT: I 290 LYS cc_start: 0.8628 (mmtm) cc_final: 0.8364 (mmmm) REVERT: I 306 GLU cc_start: 0.7506 (tp30) cc_final: 0.6852 (tm-30) REVERT: I 330 GLN cc_start: 0.7781 (pm20) cc_final: 0.7514 (pp30) REVERT: I 365 MET cc_start: 0.8383 (mmm) cc_final: 0.8087 (tmm) REVERT: I 372 ASP cc_start: 0.8038 (m-30) cc_final: 0.7646 (m-30) REVERT: I 460 ASP cc_start: 0.7942 (p0) cc_final: 0.7402 (p0) REVERT: I 461 VAL cc_start: 0.8398 (m) cc_final: 0.8150 (p) REVERT: I 463 GLN cc_start: 0.8210 (tm-30) cc_final: 0.7866 (tm-30) REVERT: I 464 LYS cc_start: 0.7959 (mmtm) cc_final: 0.7663 (mmtm) REVERT: I 472 LYS cc_start: 0.8748 (mttt) cc_final: 0.8407 (mmmm) REVERT: I 522 LYS cc_start: 0.8537 (tttt) cc_final: 0.8244 (tmmt) REVERT: I 587 LYS cc_start: 0.8427 (pttm) cc_final: 0.8111 (pttt) REVERT: I 607 GLN cc_start: 0.8309 (mt0) cc_final: 0.8025 (mp10) REVERT: I 612 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8399 (tm) REVERT: J 45 CYS cc_start: 0.7361 (OUTLIER) cc_final: 0.6940 (m) REVERT: L 29 THR cc_start: 0.7944 (OUTLIER) cc_final: 0.7608 (p) REVERT: L 94 LYS cc_start: 0.8808 (OUTLIER) cc_final: 0.8569 (mmmm) REVERT: M 106 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8066 (mm) REVERT: M 116 GLU cc_start: 0.7519 (mt-10) cc_final: 0.7295 (mt-10) REVERT: M 125 LYS cc_start: 0.8672 (mmtp) cc_final: 0.8293 (mmtp) REVERT: M 168 SER cc_start: 0.8961 (t) cc_final: 0.8706 (p) REVERT: M 193 ILE cc_start: 0.8725 (OUTLIER) cc_final: 0.8395 (mt) REVERT: M 259 ASP cc_start: 0.7858 (t70) cc_final: 0.7460 (t0) REVERT: M 276 VAL cc_start: 0.8156 (OUTLIER) cc_final: 0.7841 (m) REVERT: M 294 ARG cc_start: 0.8300 (OUTLIER) cc_final: 0.6886 (ptm160) REVERT: M 310 PRO cc_start: 0.8752 (Cg_endo) cc_final: 0.8327 (Cg_exo) REVERT: M 387 GLN cc_start: 0.7239 (OUTLIER) cc_final: 0.6990 (mt0) REVERT: N 20 ARG cc_start: 0.8533 (OUTLIER) cc_final: 0.8055 (ttm170) REVERT: N 31 LEU cc_start: 0.8373 (mp) cc_final: 0.8059 (mp) REVERT: N 71 ARG cc_start: 0.8481 (ttt-90) cc_final: 0.8096 (ttt180) outliers start: 177 outliers final: 90 residues processed: 930 average time/residue: 0.7366 time to fit residues: 791.3702 Evaluate side-chains 943 residues out of total 3383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 823 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 151 ASN Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 410 GLU Chi-restraints excluded: chain A residue 461 ARG Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain B residue 74 GLN Chi-restraints excluded: chain B residue 131 PHE Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 327 GLU Chi-restraints excluded: chain B residue 361 LYS Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 396 ASN Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 222 GLU Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 247 GLN Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 114 TYR Chi-restraints excluded: chain D residue 117 GLU Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 155 TYR Chi-restraints excluded: chain D residue 160 ASP Chi-restraints excluded: chain D residue 175 GLN Chi-restraints excluded: chain D residue 179 THR Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 333 ILE Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 83 VAL Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 112 PHE Chi-restraints excluded: chain F residue 136 ILE Chi-restraints excluded: chain F residue 145 ILE Chi-restraints excluded: chain F residue 150 LEU Chi-restraints excluded: chain F residue 206 MET Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 246 GLU Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 65 GLN Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 82 LYS Chi-restraints excluded: chain G residue 103 SER Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 162 ILE Chi-restraints excluded: chain G residue 165 LYS Chi-restraints excluded: chain G residue 216 ILE Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 150 GLU Chi-restraints excluded: chain I residue 25 ARG Chi-restraints excluded: chain I residue 133 LEU Chi-restraints excluded: chain I residue 141 ASN Chi-restraints excluded: chain I residue 149 CYS Chi-restraints excluded: chain I residue 151 GLU Chi-restraints excluded: chain I residue 165 VAL Chi-restraints excluded: chain I residue 230 GLU Chi-restraints excluded: chain I residue 239 ASP Chi-restraints excluded: chain I residue 240 THR Chi-restraints excluded: chain I residue 257 VAL Chi-restraints excluded: chain I residue 269 LEU Chi-restraints excluded: chain I residue 295 LEU Chi-restraints excluded: chain I residue 312 ASP Chi-restraints excluded: chain I residue 333 LEU Chi-restraints excluded: chain I residue 402 PHE Chi-restraints excluded: chain I residue 411 MET Chi-restraints excluded: chain I residue 416 SER Chi-restraints excluded: chain I residue 451 VAL Chi-restraints excluded: chain I residue 498 PHE Chi-restraints excluded: chain I residue 501 THR Chi-restraints excluded: chain I residue 507 MET Chi-restraints excluded: chain I residue 511 ILE Chi-restraints excluded: chain I residue 555 LEU Chi-restraints excluded: chain I residue 572 SER Chi-restraints excluded: chain I residue 612 LEU Chi-restraints excluded: chain I residue 633 MET Chi-restraints excluded: chain J residue 44 ILE Chi-restraints excluded: chain J residue 45 CYS Chi-restraints excluded: chain J residue 104 GLN Chi-restraints excluded: chain L residue 29 THR Chi-restraints excluded: chain L residue 94 LYS Chi-restraints excluded: chain L residue 131 THR Chi-restraints excluded: chain M residue 104 LEU Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain M residue 132 SER Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain M residue 191 SER Chi-restraints excluded: chain M residue 193 ILE Chi-restraints excluded: chain M residue 226 LEU Chi-restraints excluded: chain M residue 276 VAL Chi-restraints excluded: chain M residue 283 GLU Chi-restraints excluded: chain M residue 294 ARG Chi-restraints excluded: chain M residue 299 LYS Chi-restraints excluded: chain M residue 322 MET Chi-restraints excluded: chain M residue 361 THR Chi-restraints excluded: chain M residue 387 GLN Chi-restraints excluded: chain M residue 394 THR Chi-restraints excluded: chain M residue 400 THR Chi-restraints excluded: chain M residue 409 ILE Chi-restraints excluded: chain N residue 20 ARG Chi-restraints excluded: chain N residue 38 MET Chi-restraints excluded: chain N residue 46 LEU Chi-restraints excluded: chain N residue 61 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 244 optimal weight: 2.9990 chunk 315 optimal weight: 0.7980 chunk 109 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 105 optimal weight: 0.8980 chunk 363 optimal weight: 1.9990 chunk 17 optimal weight: 7.9990 chunk 177 optimal weight: 1.9990 chunk 67 optimal weight: 0.2980 chunk 161 optimal weight: 0.9990 chunk 305 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 ASN D 349 ASN D 383 ASN E 258 ASN F 141 GLN G 93 GLN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 304 HIS I 308 GLN I 324 ASN I 346 ASN M 172 GLN M 325 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.140798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.119846 restraints weight = 48472.629| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 2.32 r_work: 0.3473 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3311 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.137 31254 Z= 0.137 Angle : 0.610 19.511 42214 Z= 0.309 Chirality : 0.041 0.706 4761 Planarity : 0.004 0.057 5382 Dihedral : 5.636 58.738 4172 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 4.85 % Allowed : 24.79 % Favored : 70.36 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % 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: 0.44 (0.14), residues: 3745 helix: 1.36 (0.11), residues: 2336 sheet: 0.06 (0.37), residues: 203 loop : -1.85 (0.17), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 160 TYR 0.027 0.001 TYR I 50 PHE 0.024 0.001 PHE D 48 TRP 0.025 0.001 TRP J 33 HIS 0.008 0.001 HIS B 176 Details of bonding type rmsd covalent geometry : bond 0.00316 (31240) covalent geometry : angle 0.59814 (42204) SS BOND : bond 0.00755 ( 2) SS BOND : angle 9.80955 ( 4) hydrogen bonds : bond 0.04875 ( 1704) hydrogen bonds : angle 3.98438 ( 5004) metal coordination : bond 0.01449 ( 12) metal coordination : angle 6.02324 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7490 Ramachandran restraints generated. 3745 Oldfield, 0 Emsley, 3745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7490 Ramachandran restraints generated. 3745 Oldfield, 0 Emsley, 3745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 997 residues out of total 3383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 833 time to evaluate : 1.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 MET cc_start: 0.8064 (ttp) cc_final: 0.7484 (ttp) REVERT: A 151 ASN cc_start: 0.8393 (OUTLIER) cc_final: 0.7954 (t0) REVERT: A 257 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.8057 (mm-30) REVERT: A 280 PHE cc_start: 0.7208 (p90) cc_final: 0.6791 (p90) REVERT: A 284 LEU cc_start: 0.7619 (mm) cc_final: 0.7377 (mm) REVERT: A 383 SER cc_start: 0.8991 (t) cc_final: 0.8593 (p) REVERT: A 461 ARG cc_start: 0.8583 (OUTLIER) cc_final: 0.8294 (ptp90) REVERT: B 55 GLN cc_start: 0.7685 (OUTLIER) cc_final: 0.7343 (pp30) REVERT: B 74 GLN cc_start: 0.7903 (OUTLIER) cc_final: 0.7247 (mt0) REVERT: B 75 MET cc_start: 0.8293 (mtp) cc_final: 0.7762 (mtp) REVERT: B 79 ASN cc_start: 0.8219 (t0) cc_final: 0.7859 (t0) REVERT: B 89 MET cc_start: 0.7259 (tpp) cc_final: 0.6206 (tpp) REVERT: B 93 LYS cc_start: 0.8666 (mtmt) cc_final: 0.7975 (mtmt) REVERT: B 109 GLU cc_start: 0.8317 (mt-10) cc_final: 0.8096 (mt-10) REVERT: B 131 PHE cc_start: 0.8110 (OUTLIER) cc_final: 0.7831 (t80) REVERT: B 150 LYS cc_start: 0.8853 (mtmt) cc_final: 0.8474 (mtmt) REVERT: B 204 MET cc_start: 0.8218 (tmm) cc_final: 0.7728 (tmm) REVERT: B 228 ILE cc_start: 0.8528 (mt) cc_final: 0.8147 (mt) REVERT: B 243 LYS cc_start: 0.8291 (OUTLIER) cc_final: 0.7830 (ttmt) REVERT: B 278 LYS cc_start: 0.8659 (mtmm) cc_final: 0.8405 (mtmm) REVERT: B 295 ASP cc_start: 0.7550 (t0) cc_final: 0.7318 (t0) REVERT: B 298 GLU cc_start: 0.8137 (mp0) cc_final: 0.7593 (mp0) REVERT: B 327 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.7811 (mp0) REVERT: B 379 ASN cc_start: 0.8369 (t0) cc_final: 0.8022 (t0) REVERT: C 75 GLU cc_start: 0.6656 (tp30) cc_final: 0.6297 (tm-30) REVERT: C 118 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8175 (tt) REVERT: C 222 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7542 (mp0) REVERT: C 266 VAL cc_start: 0.7871 (t) cc_final: 0.7538 (p) REVERT: C 388 GLU cc_start: 0.8127 (mm-30) cc_final: 0.7750 (mm-30) REVERT: D 67 THR cc_start: 0.8387 (t) cc_final: 0.8187 (p) REVERT: D 110 LEU cc_start: 0.8376 (tp) cc_final: 0.8115 (tt) REVERT: D 114 TYR cc_start: 0.8336 (OUTLIER) cc_final: 0.8113 (m-10) REVERT: D 117 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7685 (mp0) REVERT: D 121 ARG cc_start: 0.8086 (tpp80) cc_final: 0.7865 (tpp80) REVERT: D 159 ASP cc_start: 0.8191 (t0) cc_final: 0.7799 (t0) REVERT: D 188 LYS cc_start: 0.8171 (mttt) cc_final: 0.7913 (mttt) REVERT: D 301 ASP cc_start: 0.7966 (m-30) cc_final: 0.7669 (m-30) REVERT: D 347 ARG cc_start: 0.8658 (mtp85) cc_final: 0.8446 (mtp180) REVERT: D 382 ASN cc_start: 0.8788 (m-40) cc_final: 0.8546 (m110) REVERT: D 401 GLU cc_start: 0.7617 (tm-30) cc_final: 0.7161 (tm-30) REVERT: D 404 MET cc_start: 0.7493 (tmm) cc_final: 0.7037 (tmm) REVERT: E 265 GLN cc_start: 0.8152 (mm110) cc_final: 0.7900 (mm110) REVERT: E 286 MET cc_start: 0.6414 (mtm) cc_final: 0.6180 (mtm) REVERT: E 319 MET cc_start: 0.8796 (mtm) cc_final: 0.8549 (mtm) REVERT: E 325 ASP cc_start: 0.8742 (t70) cc_final: 0.8441 (t0) REVERT: F 122 LEU cc_start: 0.8690 (mt) cc_final: 0.8461 (mt) REVERT: F 132 ASP cc_start: 0.7856 (m-30) cc_final: 0.7409 (m-30) REVERT: F 135 ASP cc_start: 0.8175 (m-30) cc_final: 0.7968 (m-30) REVERT: F 206 MET cc_start: 0.8307 (OUTLIER) cc_final: 0.7906 (mmm) REVERT: F 236 LYS cc_start: 0.8644 (ttmt) cc_final: 0.8180 (mmtm) REVERT: F 246 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7782 (tp30) REVERT: G 82 LYS cc_start: 0.8193 (tppp) cc_final: 0.7895 (tppp) REVERT: G 197 GLN cc_start: 0.8254 (tm-30) cc_final: 0.7961 (tm-30) REVERT: I 133 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.7981 (tt) REVERT: I 154 LYS cc_start: 0.8320 (mttt) cc_final: 0.8002 (tppp) REVERT: I 171 LEU cc_start: 0.7660 (OUTLIER) cc_final: 0.7414 (tm) REVERT: I 177 LYS cc_start: 0.8066 (tppp) cc_final: 0.7549 (mmmm) REVERT: I 185 LYS cc_start: 0.8189 (mmpt) cc_final: 0.7951 (mmpt) REVERT: I 186 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8705 (tt) REVERT: I 230 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.7227 (pm20) REVERT: I 240 THR cc_start: 0.8109 (OUTLIER) cc_final: 0.7767 (p) REVERT: I 272 GLN cc_start: 0.8221 (tm-30) cc_final: 0.7687 (tm-30) REVERT: I 290 LYS cc_start: 0.8736 (mmtm) cc_final: 0.8279 (mmmm) REVERT: I 306 GLU cc_start: 0.7490 (tp30) cc_final: 0.6847 (tm-30) REVERT: I 312 ASP cc_start: 0.8849 (OUTLIER) cc_final: 0.8607 (m-30) REVERT: I 330 GLN cc_start: 0.7773 (pm20) cc_final: 0.7514 (pp30) REVERT: I 365 MET cc_start: 0.8412 (mmm) cc_final: 0.8095 (tmm) REVERT: I 372 ASP cc_start: 0.8055 (m-30) cc_final: 0.7652 (m-30) REVERT: I 460 ASP cc_start: 0.7908 (p0) cc_final: 0.7094 (p0) REVERT: I 461 VAL cc_start: 0.8353 (m) cc_final: 0.8090 (p) REVERT: I 463 GLN cc_start: 0.8191 (tm-30) cc_final: 0.7859 (tm-30) REVERT: I 464 LYS cc_start: 0.7938 (mmtm) cc_final: 0.7649 (mmtm) REVERT: I 472 LYS cc_start: 0.8731 (mttt) cc_final: 0.8396 (mmmm) REVERT: I 522 LYS cc_start: 0.8523 (tttt) cc_final: 0.8231 (tmmt) REVERT: I 587 LYS cc_start: 0.8443 (pttm) cc_final: 0.8116 (pttt) REVERT: I 607 GLN cc_start: 0.8278 (mt0) cc_final: 0.7996 (mp10) REVERT: I 612 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8409 (tm) REVERT: J 45 CYS cc_start: 0.7370 (OUTLIER) cc_final: 0.6929 (m) REVERT: L 29 THR cc_start: 0.7977 (OUTLIER) cc_final: 0.7687 (p) REVERT: L 94 LYS cc_start: 0.8814 (mmmm) cc_final: 0.8255 (mmmm) REVERT: M 116 GLU cc_start: 0.7514 (mt-10) cc_final: 0.7289 (mt-10) REVERT: M 125 LYS cc_start: 0.8693 (mmtp) cc_final: 0.8304 (mmtp) REVERT: M 168 SER cc_start: 0.8972 (t) cc_final: 0.8714 (p) REVERT: M 259 ASP cc_start: 0.7890 (t70) cc_final: 0.7499 (t0) REVERT: M 276 VAL cc_start: 0.8127 (OUTLIER) cc_final: 0.7866 (m) REVERT: M 294 ARG cc_start: 0.8280 (OUTLIER) cc_final: 0.6861 (ptm160) REVERT: M 310 PRO cc_start: 0.8719 (Cg_endo) cc_final: 0.8284 (Cg_exo) REVERT: N 20 ARG cc_start: 0.8511 (OUTLIER) cc_final: 0.7865 (ttm170) REVERT: N 31 LEU cc_start: 0.8387 (mp) cc_final: 0.8068 (mp) REVERT: N 71 ARG cc_start: 0.8447 (ttt-90) cc_final: 0.8089 (ttt180) outliers start: 164 outliers final: 95 residues processed: 923 average time/residue: 0.7301 time to fit residues: 779.5426 Evaluate side-chains 934 residues out of total 3383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 813 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 151 ASN Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 461 ARG Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain B residue 74 GLN Chi-restraints excluded: chain B residue 131 PHE Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 243 LYS Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 327 GLU Chi-restraints excluded: chain B residue 361 LYS Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 222 GLU Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 247 GLN Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 357 MET Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 114 TYR Chi-restraints excluded: chain D residue 117 GLU Chi-restraints excluded: chain D residue 155 TYR Chi-restraints excluded: chain D residue 160 ASP Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 170 ARG Chi-restraints excluded: chain D residue 179 THR Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 333 ILE Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 83 VAL Chi-restraints excluded: chain F residue 112 PHE Chi-restraints excluded: chain F residue 136 ILE Chi-restraints excluded: chain F residue 145 ILE Chi-restraints excluded: chain F residue 150 LEU Chi-restraints excluded: chain F residue 206 MET Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 246 GLU Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 103 SER Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 151 LEU Chi-restraints excluded: chain G residue 162 ILE Chi-restraints excluded: chain G residue 210 GLU Chi-restraints excluded: chain G residue 216 ILE Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 70 GLU Chi-restraints excluded: chain H residue 157 SER Chi-restraints excluded: chain I residue 133 LEU Chi-restraints excluded: chain I residue 141 ASN Chi-restraints excluded: chain I residue 149 CYS Chi-restraints excluded: chain I residue 151 GLU Chi-restraints excluded: chain I residue 170 CYS Chi-restraints excluded: chain I residue 171 LEU Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain I residue 230 GLU Chi-restraints excluded: chain I residue 239 ASP Chi-restraints excluded: chain I residue 240 THR Chi-restraints excluded: chain I residue 252 LEU Chi-restraints excluded: chain I residue 257 VAL Chi-restraints excluded: chain I residue 312 ASP Chi-restraints excluded: chain I residue 333 LEU Chi-restraints excluded: chain I residue 402 PHE Chi-restraints excluded: chain I residue 411 MET Chi-restraints excluded: chain I residue 416 SER Chi-restraints excluded: chain I residue 451 VAL Chi-restraints excluded: chain I residue 483 ASP Chi-restraints excluded: chain I residue 501 THR Chi-restraints excluded: chain I residue 507 MET Chi-restraints excluded: chain I residue 511 ILE Chi-restraints excluded: chain I residue 536 SER Chi-restraints excluded: chain I residue 555 LEU Chi-restraints excluded: chain I residue 572 SER Chi-restraints excluded: chain I residue 591 VAL Chi-restraints excluded: chain I residue 612 LEU Chi-restraints excluded: chain I residue 633 MET Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 44 ILE Chi-restraints excluded: chain J residue 45 CYS Chi-restraints excluded: chain J residue 104 GLN Chi-restraints excluded: chain L residue 29 THR Chi-restraints excluded: chain L residue 131 THR Chi-restraints excluded: chain M residue 104 LEU Chi-restraints excluded: chain M residue 132 SER Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain M residue 226 LEU Chi-restraints excluded: chain M residue 276 VAL Chi-restraints excluded: chain M residue 283 GLU Chi-restraints excluded: chain M residue 294 ARG Chi-restraints excluded: chain M residue 299 LYS Chi-restraints excluded: chain M residue 322 MET Chi-restraints excluded: chain M residue 323 LEU Chi-restraints excluded: chain M residue 355 GLU Chi-restraints excluded: chain M residue 361 THR Chi-restraints excluded: chain M residue 394 THR Chi-restraints excluded: chain M residue 400 THR Chi-restraints excluded: chain M residue 409 ILE Chi-restraints excluded: chain N residue 20 ARG Chi-restraints excluded: chain N residue 46 LEU Chi-restraints excluded: chain N residue 59 ILE Chi-restraints excluded: chain N residue 61 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 233 optimal weight: 0.5980 chunk 364 optimal weight: 0.2980 chunk 141 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 216 optimal weight: 0.0470 chunk 74 optimal weight: 0.9980 chunk 203 optimal weight: 3.9990 chunk 343 optimal weight: 3.9990 chunk 177 optimal weight: 0.6980 chunk 143 optimal weight: 0.1980 chunk 251 optimal weight: 5.9990 overall best weight: 0.3678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 ASN C 38 ASN D 175 GLN D 349 ASN D 383 ASN E 158 ASN E 258 ASN F 141 GLN G 93 GLN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 304 HIS I 324 ASN I 346 ASN ** I 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 158 GLN M 325 ASN N 45 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.142502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.121617 restraints weight = 48617.416| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 2.32 r_work: 0.3494 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3335 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.137 31254 Z= 0.122 Angle : 0.614 21.393 42214 Z= 0.308 Chirality : 0.040 0.661 4761 Planarity : 0.004 0.062 5382 Dihedral : 5.545 60.034 4172 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 4.41 % Allowed : 25.85 % Favored : 69.74 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % 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: 0.53 (0.14), residues: 3745 helix: 1.45 (0.11), residues: 2330 sheet: 0.06 (0.38), residues: 198 loop : -1.83 (0.17), residues: 1217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 424 TYR 0.036 0.001 TYR I 366 PHE 0.022 0.001 PHE D 48 TRP 0.028 0.001 TRP J 33 HIS 0.011 0.001 HIS B 176 Details of bonding type rmsd covalent geometry : bond 0.00275 (31240) covalent geometry : angle 0.60225 (42204) SS BOND : bond 0.00869 ( 2) SS BOND : angle 10.78210 ( 4) hydrogen bonds : bond 0.04262 ( 1704) hydrogen bonds : angle 3.90025 ( 5004) metal coordination : bond 0.00860 ( 12) metal coordination : angle 5.17610 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7490 Ramachandran restraints generated. 3745 Oldfield, 0 Emsley, 3745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7490 Ramachandran restraints generated. 3745 Oldfield, 0 Emsley, 3745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 999 residues out of total 3383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 850 time to evaluate : 1.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 MET cc_start: 0.8045 (ttp) cc_final: 0.7534 (ttp) REVERT: A 151 ASN cc_start: 0.8327 (OUTLIER) cc_final: 0.7895 (t0) REVERT: A 203 LEU cc_start: 0.8606 (mp) cc_final: 0.8354 (mt) REVERT: A 219 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.8079 (mt) REVERT: A 257 GLU cc_start: 0.8280 (mt-10) cc_final: 0.8075 (mm-30) REVERT: A 355 ASP cc_start: 0.8338 (t0) cc_final: 0.8058 (t70) REVERT: A 383 SER cc_start: 0.8980 (t) cc_final: 0.8582 (p) REVERT: B 40 LYS cc_start: 0.7880 (tppp) cc_final: 0.7496 (mmtp) REVERT: B 55 GLN cc_start: 0.7603 (OUTLIER) cc_final: 0.7270 (pp30) REVERT: B 72 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8110 (mm) REVERT: B 75 MET cc_start: 0.8280 (mtp) cc_final: 0.7796 (mtp) REVERT: B 79 ASN cc_start: 0.8158 (t0) cc_final: 0.7828 (t0) REVERT: B 89 MET cc_start: 0.7235 (tpp) cc_final: 0.6119 (tpp) REVERT: B 93 LYS cc_start: 0.8668 (mtmt) cc_final: 0.7918 (mtmt) REVERT: B 109 GLU cc_start: 0.8280 (mt-10) cc_final: 0.8047 (mt-10) REVERT: B 129 GLN cc_start: 0.8625 (tp40) cc_final: 0.8398 (tm130) REVERT: B 131 PHE cc_start: 0.8108 (OUTLIER) cc_final: 0.7815 (t80) REVERT: B 150 LYS cc_start: 0.8848 (mtmt) cc_final: 0.8441 (mtmt) REVERT: B 204 MET cc_start: 0.8200 (tmm) cc_final: 0.7708 (tmm) REVERT: B 243 LYS cc_start: 0.8257 (OUTLIER) cc_final: 0.7830 (ttmt) REVERT: B 278 LYS cc_start: 0.8678 (mtmm) cc_final: 0.8411 (mtmm) REVERT: B 295 ASP cc_start: 0.7502 (t0) cc_final: 0.7261 (t0) REVERT: B 298 GLU cc_start: 0.8108 (mp0) cc_final: 0.7566 (mp0) REVERT: B 327 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.7840 (mp0) REVERT: B 368 ARG cc_start: 0.8864 (mtm180) cc_final: 0.8631 (mtm180) REVERT: B 379 ASN cc_start: 0.8334 (t0) cc_final: 0.7997 (t0) REVERT: B 404 GLN cc_start: 0.8196 (tt0) cc_final: 0.7969 (tt0) REVERT: C 38 ASN cc_start: 0.7543 (OUTLIER) cc_final: 0.6977 (p0) REVERT: C 75 GLU cc_start: 0.6520 (tp30) cc_final: 0.6186 (tm-30) REVERT: C 118 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8146 (tt) REVERT: C 222 GLU cc_start: 0.7761 (mp0) cc_final: 0.7459 (mp0) REVERT: C 262 GLU cc_start: 0.7469 (mt-10) cc_final: 0.7268 (tt0) REVERT: C 266 VAL cc_start: 0.7825 (t) cc_final: 0.7504 (p) REVERT: C 388 GLU cc_start: 0.8136 (mm-30) cc_final: 0.7748 (mm-30) REVERT: D 110 LEU cc_start: 0.8357 (tp) cc_final: 0.8088 (tt) REVERT: D 114 TYR cc_start: 0.8304 (OUTLIER) cc_final: 0.8064 (m-10) REVERT: D 117 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7574 (mp0) REVERT: D 159 ASP cc_start: 0.8170 (t0) cc_final: 0.7831 (t0) REVERT: D 188 LYS cc_start: 0.8214 (mttt) cc_final: 0.7980 (mttt) REVERT: D 347 ARG cc_start: 0.8612 (mtp85) cc_final: 0.8370 (mtp180) REVERT: D 401 GLU cc_start: 0.7623 (tm-30) cc_final: 0.7232 (tm-30) REVERT: D 404 MET cc_start: 0.7394 (tmm) cc_final: 0.7065 (tmm) REVERT: E 265 GLN cc_start: 0.8119 (mm110) cc_final: 0.7886 (mm110) REVERT: E 286 MET cc_start: 0.6372 (mtm) cc_final: 0.6168 (mtm) REVERT: E 319 MET cc_start: 0.8793 (mtm) cc_final: 0.8523 (mtm) REVERT: E 325 ASP cc_start: 0.8719 (t70) cc_final: 0.8413 (t0) REVERT: F 30 VAL cc_start: 0.8723 (m) cc_final: 0.8476 (t) REVERT: F 122 LEU cc_start: 0.8671 (mt) cc_final: 0.8434 (mt) REVERT: F 132 ASP cc_start: 0.7836 (m-30) cc_final: 0.7367 (m-30) REVERT: F 135 ASP cc_start: 0.8159 (m-30) cc_final: 0.7942 (m-30) REVERT: F 206 MET cc_start: 0.8196 (OUTLIER) cc_final: 0.7801 (mmm) REVERT: F 236 LYS cc_start: 0.8655 (ttmt) cc_final: 0.8185 (mmtm) REVERT: F 246 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7683 (tp30) REVERT: G 82 LYS cc_start: 0.8147 (tppp) cc_final: 0.7858 (tppp) REVERT: G 197 GLN cc_start: 0.8238 (tm-30) cc_final: 0.7938 (tm-30) REVERT: I 20 ILE cc_start: 0.8449 (OUTLIER) cc_final: 0.8173 (tp) REVERT: I 47 THR cc_start: 0.8212 (OUTLIER) cc_final: 0.7906 (m) REVERT: I 133 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.7970 (tt) REVERT: I 141 ASN cc_start: 0.7669 (OUTLIER) cc_final: 0.7230 (t0) REVERT: I 149 CYS cc_start: 0.8621 (OUTLIER) cc_final: 0.8241 (m) REVERT: I 154 LYS cc_start: 0.8317 (mttt) cc_final: 0.7993 (tppp) REVERT: I 165 VAL cc_start: 0.9045 (OUTLIER) cc_final: 0.8769 (m) REVERT: I 177 LYS cc_start: 0.8076 (tppp) cc_final: 0.7547 (mmmm) REVERT: I 186 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8682 (tt) REVERT: I 230 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.7203 (pm20) REVERT: I 240 THR cc_start: 0.8018 (m) cc_final: 0.7684 (p) REVERT: I 290 LYS cc_start: 0.8711 (mmtm) cc_final: 0.8280 (mmmm) REVERT: I 306 GLU cc_start: 0.7495 (tp30) cc_final: 0.6855 (tm-30) REVERT: I 312 ASP cc_start: 0.8825 (OUTLIER) cc_final: 0.8589 (m-30) REVERT: I 330 GLN cc_start: 0.7841 (pm20) cc_final: 0.7576 (pp30) REVERT: I 353 GLU cc_start: 0.8123 (tm-30) cc_final: 0.7624 (tm-30) REVERT: I 365 MET cc_start: 0.8374 (mmm) cc_final: 0.8099 (tmm) REVERT: I 372 ASP cc_start: 0.8004 (m-30) cc_final: 0.7717 (m-30) REVERT: I 460 ASP cc_start: 0.7877 (p0) cc_final: 0.7392 (p0) REVERT: I 463 GLN cc_start: 0.8155 (tm-30) cc_final: 0.7804 (tm-30) REVERT: I 464 LYS cc_start: 0.7880 (mmtm) cc_final: 0.7593 (mmtm) REVERT: I 472 LYS cc_start: 0.8701 (mttt) cc_final: 0.8421 (mmmm) REVERT: I 515 LYS cc_start: 0.8769 (tptp) cc_final: 0.8473 (tptp) REVERT: I 522 LYS cc_start: 0.8495 (tttt) cc_final: 0.8230 (tmmt) REVERT: I 587 LYS cc_start: 0.8482 (pttm) cc_final: 0.8149 (pttt) REVERT: I 607 GLN cc_start: 0.8248 (mt0) cc_final: 0.7992 (mp10) REVERT: I 612 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8406 (tm) REVERT: I 636 LEU cc_start: 0.8661 (tm) cc_final: 0.8163 (pp) REVERT: L 29 THR cc_start: 0.7959 (OUTLIER) cc_final: 0.7661 (p) REVERT: L 94 LYS cc_start: 0.8790 (mmmm) cc_final: 0.8302 (mmmm) REVERT: L 146 THR cc_start: 0.7130 (OUTLIER) cc_final: 0.6716 (p) REVERT: M 112 LEU cc_start: 0.7572 (OUTLIER) cc_final: 0.7319 (pp) REVERT: M 125 LYS cc_start: 0.8669 (mmtp) cc_final: 0.8299 (mmtp) REVERT: M 168 SER cc_start: 0.8941 (t) cc_final: 0.8538 (p) REVERT: M 208 LEU cc_start: 0.8952 (mt) cc_final: 0.8737 (mm) REVERT: M 259 ASP cc_start: 0.7871 (t70) cc_final: 0.7381 (t0) REVERT: M 276 VAL cc_start: 0.8065 (OUTLIER) cc_final: 0.7847 (m) REVERT: M 294 ARG cc_start: 0.8232 (OUTLIER) cc_final: 0.6790 (ptm160) REVERT: N 20 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.7833 (ttm170) REVERT: N 31 LEU cc_start: 0.8401 (mp) cc_final: 0.8091 (mp) REVERT: N 71 ARG cc_start: 0.8399 (ttt-90) cc_final: 0.8074 (ttt180) outliers start: 149 outliers final: 75 residues processed: 937 average time/residue: 0.7213 time to fit residues: 780.0676 Evaluate side-chains 925 residues out of total 3383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 821 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 151 ASN Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 363 ARG Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 74 GLN Chi-restraints excluded: chain B residue 131 PHE Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 243 LYS Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 327 GLU Chi-restraints excluded: chain B residue 361 LYS Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 114 TYR Chi-restraints excluded: chain D residue 117 GLU Chi-restraints excluded: chain D residue 155 TYR Chi-restraints excluded: chain D residue 160 ASP Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 170 ARG Chi-restraints excluded: chain D residue 179 THR Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain D residue 253 GLU Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 333 ILE Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 83 VAL Chi-restraints excluded: chain F residue 112 PHE Chi-restraints excluded: chain F residue 136 ILE Chi-restraints excluded: chain F residue 145 ILE Chi-restraints excluded: chain F residue 150 LEU Chi-restraints excluded: chain F residue 206 MET Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 246 GLU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 162 ILE Chi-restraints excluded: chain G residue 175 HIS Chi-restraints excluded: chain G residue 210 GLU Chi-restraints excluded: chain G residue 216 ILE Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 44 TYR Chi-restraints excluded: chain H residue 157 SER Chi-restraints excluded: chain I residue 20 ILE Chi-restraints excluded: chain I residue 47 THR Chi-restraints excluded: chain I residue 103 LEU Chi-restraints excluded: chain I residue 133 LEU Chi-restraints excluded: chain I residue 141 ASN Chi-restraints excluded: chain I residue 149 CYS Chi-restraints excluded: chain I residue 151 GLU Chi-restraints excluded: chain I residue 165 VAL Chi-restraints excluded: chain I residue 170 CYS Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain I residue 230 GLU Chi-restraints excluded: chain I residue 239 ASP Chi-restraints excluded: chain I residue 312 ASP Chi-restraints excluded: chain I residue 402 PHE Chi-restraints excluded: chain I residue 451 VAL Chi-restraints excluded: chain I residue 483 ASP Chi-restraints excluded: chain I residue 501 THR Chi-restraints excluded: chain I residue 507 MET Chi-restraints excluded: chain I residue 555 LEU Chi-restraints excluded: chain I residue 572 SER Chi-restraints excluded: chain I residue 591 VAL Chi-restraints excluded: chain I residue 612 LEU Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 104 GLN Chi-restraints excluded: chain L residue 29 THR Chi-restraints excluded: chain L residue 131 THR Chi-restraints excluded: chain L residue 146 THR Chi-restraints excluded: chain M residue 112 LEU Chi-restraints excluded: chain M residue 132 SER Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain M residue 256 SER Chi-restraints excluded: chain M residue 276 VAL Chi-restraints excluded: chain M residue 283 GLU Chi-restraints excluded: chain M residue 294 ARG Chi-restraints excluded: chain M residue 299 LYS Chi-restraints excluded: chain M residue 355 GLU Chi-restraints excluded: chain M residue 394 THR Chi-restraints excluded: chain M residue 409 ILE Chi-restraints excluded: chain N residue 13 ASP Chi-restraints excluded: chain N residue 20 ARG Chi-restraints excluded: chain N residue 46 LEU Chi-restraints excluded: chain N residue 59 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 15 optimal weight: 0.9980 chunk 162 optimal weight: 1.9990 chunk 353 optimal weight: 0.5980 chunk 94 optimal weight: 0.4980 chunk 330 optimal weight: 2.9990 chunk 321 optimal weight: 0.6980 chunk 170 optimal weight: 0.2980 chunk 208 optimal weight: 3.9990 chunk 238 optimal weight: 0.7980 chunk 293 optimal weight: 0.9990 chunk 247 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN B 144 ASN B 208 GLN C 38 ASN D 288 HIS D 349 ASN D 383 ASN E 158 ASN E 258 ASN E 329 ASN F 141 GLN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 143 HIS I 304 HIS I 308 GLN I 324 ASN M 325 ASN M 389 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.142033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.121158 restraints weight = 48586.249| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 2.31 r_work: 0.3489 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.149 31254 Z= 0.134 Angle : 0.651 24.005 42214 Z= 0.324 Chirality : 0.041 0.627 4761 Planarity : 0.004 0.060 5382 Dihedral : 5.485 60.660 4170 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 3.96 % Allowed : 27.15 % Favored : 68.88 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.55 (0.14), residues: 3745 helix: 1.45 (0.11), residues: 2338 sheet: 0.00 (0.37), residues: 212 loop : -1.80 (0.17), residues: 1195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 424 TYR 0.029 0.001 TYR I 50 PHE 0.021 0.001 PHE D 48 TRP 0.028 0.001 TRP J 33 HIS 0.017 0.001 HIS I 143 Details of bonding type rmsd covalent geometry : bond 0.00311 (31240) covalent geometry : angle 0.63930 (42204) SS BOND : bond 0.00461 ( 2) SS BOND : angle 11.14720 ( 4) hydrogen bonds : bond 0.04464 ( 1704) hydrogen bonds : angle 3.90808 ( 5004) metal coordination : bond 0.01029 ( 12) metal coordination : angle 5.14908 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7490 Ramachandran restraints generated. 3745 Oldfield, 0 Emsley, 3745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7490 Ramachandran restraints generated. 3745 Oldfield, 0 Emsley, 3745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 962 residues out of total 3383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 828 time to evaluate : 1.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 LEU cc_start: 0.7143 (OUTLIER) cc_final: 0.6921 (mt) REVERT: A 77 MET cc_start: 0.8048 (ttp) cc_final: 0.7702 (ttm) REVERT: A 151 ASN cc_start: 0.8298 (OUTLIER) cc_final: 0.7903 (t0) REVERT: A 203 LEU cc_start: 0.8613 (mp) cc_final: 0.8353 (mt) REVERT: A 219 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.8083 (mt) REVERT: A 257 GLU cc_start: 0.8266 (mt-10) cc_final: 0.8056 (mm-30) REVERT: A 280 PHE cc_start: 0.7001 (p90) cc_final: 0.6686 (p90) REVERT: A 383 SER cc_start: 0.8977 (t) cc_final: 0.8583 (p) REVERT: A 461 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.8258 (ttp80) REVERT: B 40 LYS cc_start: 0.7970 (tppp) cc_final: 0.7613 (mmtp) REVERT: B 55 GLN cc_start: 0.7619 (OUTLIER) cc_final: 0.7283 (pp30) REVERT: B 72 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8149 (mm) REVERT: B 74 GLN cc_start: 0.7884 (OUTLIER) cc_final: 0.7231 (mt0) REVERT: B 75 MET cc_start: 0.8281 (mtp) cc_final: 0.7763 (mtp) REVERT: B 79 ASN cc_start: 0.8149 (t0) cc_final: 0.7817 (t0) REVERT: B 89 MET cc_start: 0.7214 (tpp) cc_final: 0.5924 (tpp) REVERT: B 93 LYS cc_start: 0.8666 (mtmt) cc_final: 0.7901 (mtmt) REVERT: B 131 PHE cc_start: 0.8066 (OUTLIER) cc_final: 0.7816 (t80) REVERT: B 204 MET cc_start: 0.8222 (tmm) cc_final: 0.7736 (tmm) REVERT: B 228 ILE cc_start: 0.8509 (mt) cc_final: 0.8125 (mt) REVERT: B 243 LYS cc_start: 0.8276 (OUTLIER) cc_final: 0.7882 (ttmt) REVERT: B 278 LYS cc_start: 0.8689 (mtmm) cc_final: 0.8410 (mtmm) REVERT: B 295 ASP cc_start: 0.7467 (t0) cc_final: 0.7219 (t0) REVERT: B 298 GLU cc_start: 0.8125 (mp0) cc_final: 0.7601 (mp0) REVERT: B 327 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.7829 (mp0) REVERT: B 379 ASN cc_start: 0.8343 (t0) cc_final: 0.8005 (t0) REVERT: C 38 ASN cc_start: 0.7214 (OUTLIER) cc_final: 0.6850 (p0) REVERT: C 75 GLU cc_start: 0.6523 (tp30) cc_final: 0.6170 (tm-30) REVERT: C 118 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8138 (tt) REVERT: C 222 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7446 (mp0) REVERT: C 262 GLU cc_start: 0.7461 (mt-10) cc_final: 0.7248 (tt0) REVERT: C 266 VAL cc_start: 0.7816 (t) cc_final: 0.7488 (p) REVERT: C 388 GLU cc_start: 0.8141 (mm-30) cc_final: 0.7731 (mm-30) REVERT: D 110 LEU cc_start: 0.8371 (tp) cc_final: 0.8103 (tt) REVERT: D 114 TYR cc_start: 0.8306 (OUTLIER) cc_final: 0.8067 (m-10) REVERT: D 117 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7501 (mp0) REVERT: D 121 ARG cc_start: 0.8036 (tpp80) cc_final: 0.7829 (tpp80) REVERT: D 159 ASP cc_start: 0.8203 (t0) cc_final: 0.7852 (t0) REVERT: D 188 LYS cc_start: 0.8246 (mttt) cc_final: 0.7996 (mttt) REVERT: D 301 ASP cc_start: 0.7940 (m-30) cc_final: 0.7635 (m-30) REVERT: D 401 GLU cc_start: 0.7624 (tm-30) cc_final: 0.7233 (tm-30) REVERT: D 404 MET cc_start: 0.7420 (tmm) cc_final: 0.7091 (tmm) REVERT: E 265 GLN cc_start: 0.8133 (mm110) cc_final: 0.7893 (mm110) REVERT: E 286 MET cc_start: 0.6376 (mtm) cc_final: 0.6155 (mtm) REVERT: E 319 MET cc_start: 0.8803 (mtm) cc_final: 0.8527 (mtm) REVERT: E 325 ASP cc_start: 0.8735 (t70) cc_final: 0.8430 (t0) REVERT: F 122 LEU cc_start: 0.8704 (mt) cc_final: 0.8453 (mt) REVERT: F 132 ASP cc_start: 0.7845 (m-30) cc_final: 0.7379 (m-30) REVERT: F 135 ASP cc_start: 0.8165 (m-30) cc_final: 0.7950 (m-30) REVERT: F 206 MET cc_start: 0.8212 (OUTLIER) cc_final: 0.7823 (mmm) REVERT: F 236 LYS cc_start: 0.8655 (ttmt) cc_final: 0.8189 (mmtm) REVERT: F 246 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7690 (tp30) REVERT: G 82 LYS cc_start: 0.8158 (tppp) cc_final: 0.7870 (tppp) REVERT: G 197 GLN cc_start: 0.8249 (tm-30) cc_final: 0.7949 (tm-30) REVERT: I 20 ILE cc_start: 0.8506 (OUTLIER) cc_final: 0.8208 (tp) REVERT: I 29 GLN cc_start: 0.8109 (OUTLIER) cc_final: 0.7858 (tt0) REVERT: I 47 THR cc_start: 0.8290 (OUTLIER) cc_final: 0.7986 (m) REVERT: I 141 ASN cc_start: 0.7684 (OUTLIER) cc_final: 0.7368 (t0) REVERT: I 149 CYS cc_start: 0.8639 (OUTLIER) cc_final: 0.8296 (m) REVERT: I 154 LYS cc_start: 0.8321 (mttt) cc_final: 0.8031 (tppp) REVERT: I 165 VAL cc_start: 0.9047 (OUTLIER) cc_final: 0.8765 (m) REVERT: I 186 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8682 (tt) REVERT: I 230 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.7208 (pm20) REVERT: I 240 THR cc_start: 0.8003 (m) cc_final: 0.7670 (p) REVERT: I 260 TYR cc_start: 0.7504 (t80) cc_final: 0.6824 (t80) REVERT: I 306 GLU cc_start: 0.7464 (tp30) cc_final: 0.6866 (tm-30) REVERT: I 312 ASP cc_start: 0.8838 (OUTLIER) cc_final: 0.8607 (m-30) REVERT: I 330 GLN cc_start: 0.7861 (pm20) cc_final: 0.7459 (pp30) REVERT: I 331 ASP cc_start: 0.7072 (m-30) cc_final: 0.6413 (m-30) REVERT: I 353 GLU cc_start: 0.8101 (tm-30) cc_final: 0.7583 (tm-30) REVERT: I 365 MET cc_start: 0.8382 (mmm) cc_final: 0.8097 (tmm) REVERT: I 367 VAL cc_start: 0.8645 (p) cc_final: 0.8357 (m) REVERT: I 372 ASP cc_start: 0.7978 (m-30) cc_final: 0.7693 (m-30) REVERT: I 460 ASP cc_start: 0.7904 (p0) cc_final: 0.6575 (p0) REVERT: I 461 VAL cc_start: 0.8255 (m) cc_final: 0.7906 (p) REVERT: I 463 GLN cc_start: 0.8152 (tm-30) cc_final: 0.7755 (tm-30) REVERT: I 464 LYS cc_start: 0.7894 (mmtm) cc_final: 0.7655 (mmtm) REVERT: I 472 LYS cc_start: 0.8697 (mttt) cc_final: 0.8371 (mmmm) REVERT: I 500 TYR cc_start: 0.8275 (t80) cc_final: 0.8000 (t80) REVERT: I 522 LYS cc_start: 0.8524 (tttt) cc_final: 0.8231 (tmmt) REVERT: I 587 LYS cc_start: 0.8512 (pttm) cc_final: 0.8211 (pttt) REVERT: I 607 GLN cc_start: 0.8267 (mt0) cc_final: 0.8013 (mp10) REVERT: I 612 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8416 (tm) REVERT: I 636 LEU cc_start: 0.8652 (tm) cc_final: 0.8188 (pp) REVERT: J 45 CYS cc_start: 0.7372 (OUTLIER) cc_final: 0.6905 (m) REVERT: L 29 THR cc_start: 0.7977 (OUTLIER) cc_final: 0.7676 (p) REVERT: L 94 LYS cc_start: 0.8800 (mmmm) cc_final: 0.8302 (mmmm) REVERT: M 102 ASP cc_start: 0.7773 (p0) cc_final: 0.7478 (p0) REVERT: M 112 LEU cc_start: 0.7597 (OUTLIER) cc_final: 0.7347 (pp) REVERT: M 125 LYS cc_start: 0.8696 (mmtp) cc_final: 0.8315 (mmtp) REVERT: M 168 SER cc_start: 0.8978 (t) cc_final: 0.8660 (p) REVERT: M 208 LEU cc_start: 0.8962 (mt) cc_final: 0.8761 (mm) REVERT: M 276 VAL cc_start: 0.8093 (t) cc_final: 0.7826 (m) REVERT: M 294 ARG cc_start: 0.8242 (OUTLIER) cc_final: 0.6819 (ptm160) REVERT: M 310 PRO cc_start: 0.8687 (Cg_endo) cc_final: 0.8233 (Cg_exo) REVERT: N 20 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.7835 (ttm170) REVERT: N 31 LEU cc_start: 0.8392 (mp) cc_final: 0.8085 (mp) REVERT: N 37 LEU cc_start: 0.9036 (mp) cc_final: 0.8799 (mt) REVERT: N 71 ARG cc_start: 0.8435 (ttt-90) cc_final: 0.8094 (ttt180) outliers start: 134 outliers final: 73 residues processed: 906 average time/residue: 0.7212 time to fit residues: 754.2105 Evaluate side-chains 935 residues out of total 3383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 830 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 151 ASN Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 363 ARG Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 461 ARG Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 74 GLN Chi-restraints excluded: chain B residue 131 PHE Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 243 LYS Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 327 GLU Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain C residue 222 GLU Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 114 TYR Chi-restraints excluded: chain D residue 117 GLU Chi-restraints excluded: chain D residue 155 TYR Chi-restraints excluded: chain D residue 160 ASP Chi-restraints excluded: chain D residue 170 ARG Chi-restraints excluded: chain D residue 179 THR Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 253 GLU Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain E residue 333 ILE Chi-restraints excluded: chain F residue 83 VAL Chi-restraints excluded: chain F residue 112 PHE Chi-restraints excluded: chain F residue 136 ILE Chi-restraints excluded: chain F residue 145 ILE Chi-restraints excluded: chain F residue 150 LEU Chi-restraints excluded: chain F residue 206 MET Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 246 GLU Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 65 GLN Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 162 ILE Chi-restraints excluded: chain G residue 175 HIS Chi-restraints excluded: chain G residue 210 GLU Chi-restraints excluded: chain G residue 216 ILE Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 157 SER Chi-restraints excluded: chain I residue 20 ILE Chi-restraints excluded: chain I residue 29 GLN Chi-restraints excluded: chain I residue 47 THR Chi-restraints excluded: chain I residue 103 LEU Chi-restraints excluded: chain I residue 141 ASN Chi-restraints excluded: chain I residue 149 CYS Chi-restraints excluded: chain I residue 151 GLU Chi-restraints excluded: chain I residue 165 VAL Chi-restraints excluded: chain I residue 170 CYS Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain I residue 230 GLU Chi-restraints excluded: chain I residue 239 ASP Chi-restraints excluded: chain I residue 257 VAL Chi-restraints excluded: chain I residue 312 ASP Chi-restraints excluded: chain I residue 333 LEU Chi-restraints excluded: chain I residue 402 PHE Chi-restraints excluded: chain I residue 451 VAL Chi-restraints excluded: chain I residue 501 THR Chi-restraints excluded: chain I residue 555 LEU Chi-restraints excluded: chain I residue 572 SER Chi-restraints excluded: chain I residue 591 VAL Chi-restraints excluded: chain I residue 612 LEU Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 45 CYS Chi-restraints excluded: chain J residue 104 GLN Chi-restraints excluded: chain L residue 29 THR Chi-restraints excluded: chain L residue 131 THR Chi-restraints excluded: chain L residue 146 THR Chi-restraints excluded: chain M residue 105 LEU Chi-restraints excluded: chain M residue 112 LEU Chi-restraints excluded: chain M residue 132 SER Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain M residue 256 SER Chi-restraints excluded: chain M residue 283 GLU Chi-restraints excluded: chain M residue 294 ARG Chi-restraints excluded: chain M residue 355 GLU Chi-restraints excluded: chain M residue 361 THR Chi-restraints excluded: chain M residue 394 THR Chi-restraints excluded: chain M residue 409 ILE Chi-restraints excluded: chain N residue 13 ASP Chi-restraints excluded: chain N residue 20 ARG Chi-restraints excluded: chain N residue 46 LEU Chi-restraints excluded: chain N residue 59 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 353 optimal weight: 0.5980 chunk 45 optimal weight: 0.9980 chunk 232 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 chunk 176 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 260 optimal weight: 5.9990 chunk 289 optimal weight: 0.6980 chunk 238 optimal weight: 0.9990 chunk 321 optimal weight: 3.9990 chunk 147 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 463 GLN B 208 GLN C 38 ASN C 400 ASN D 349 ASN E 258 ASN E 329 ASN F 141 GLN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 284 GLN I 304 HIS I 308 GLN I 324 ASN I 346 ASN ** I 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 158 GLN M 325 ASN N 45 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.140779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.119789 restraints weight = 48587.105| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 2.32 r_work: 0.3469 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.144 31254 Z= 0.155 Angle : 0.672 23.387 42214 Z= 0.337 Chirality : 0.042 0.630 4761 Planarity : 0.004 0.060 5382 Dihedral : 5.436 60.305 4164 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 4.20 % Allowed : 27.21 % Favored : 68.59 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % 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: 0.50 (0.14), residues: 3745 helix: 1.40 (0.11), residues: 2342 sheet: 0.01 (0.36), residues: 212 loop : -1.82 (0.17), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 160 TYR 0.049 0.001 TYR B 132 PHE 0.021 0.001 PHE D 48 TRP 0.030 0.001 TRP J 33 HIS 0.012 0.001 HIS A 277 Details of bonding type rmsd covalent geometry : bond 0.00365 (31240) covalent geometry : angle 0.65965 (42204) SS BOND : bond 0.00580 ( 2) SS BOND : angle 11.06571 ( 4) hydrogen bonds : bond 0.04933 ( 1704) hydrogen bonds : angle 3.95163 ( 5004) metal coordination : bond 0.01484 ( 12) metal coordination : angle 5.68021 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7490 Ramachandran restraints generated. 3745 Oldfield, 0 Emsley, 3745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7490 Ramachandran restraints generated. 3745 Oldfield, 0 Emsley, 3745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 992 residues out of total 3383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 850 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 MET cc_start: 0.8046 (ttp) cc_final: 0.7681 (ttm) REVERT: A 151 ASN cc_start: 0.8327 (OUTLIER) cc_final: 0.7927 (t0) REVERT: A 219 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.8109 (mt) REVERT: A 257 GLU cc_start: 0.8303 (mt-10) cc_final: 0.8095 (mm-30) REVERT: A 280 PHE cc_start: 0.7021 (p90) cc_final: 0.6698 (p90) REVERT: A 355 ASP cc_start: 0.8447 (t0) cc_final: 0.8171 (t70) REVERT: A 383 SER cc_start: 0.8984 (t) cc_final: 0.8594 (p) REVERT: A 461 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.8314 (ttp80) REVERT: B 40 LYS cc_start: 0.8000 (tppp) cc_final: 0.7721 (mmtp) REVERT: B 55 GLN cc_start: 0.7619 (OUTLIER) cc_final: 0.7255 (pp30) REVERT: B 72 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8140 (mm) REVERT: B 75 MET cc_start: 0.8320 (mtp) cc_final: 0.7832 (mtp) REVERT: B 79 ASN cc_start: 0.8157 (t0) cc_final: 0.7866 (t0) REVERT: B 89 MET cc_start: 0.7382 (tpp) cc_final: 0.6083 (tpp) REVERT: B 93 LYS cc_start: 0.8668 (mtmt) cc_final: 0.7918 (mtmt) REVERT: B 129 GLN cc_start: 0.8562 (tp40) cc_final: 0.8293 (tm130) REVERT: B 204 MET cc_start: 0.8241 (tmm) cc_final: 0.7759 (tmm) REVERT: B 228 ILE cc_start: 0.8528 (mt) cc_final: 0.8153 (mt) REVERT: B 243 LYS cc_start: 0.8290 (OUTLIER) cc_final: 0.7902 (ttmt) REVERT: B 278 LYS cc_start: 0.8684 (mtmm) cc_final: 0.8414 (mtmm) REVERT: B 295 ASP cc_start: 0.7487 (t0) cc_final: 0.7246 (t0) REVERT: B 298 GLU cc_start: 0.8134 (mp0) cc_final: 0.7631 (mp0) REVERT: B 327 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.7804 (mp0) REVERT: B 379 ASN cc_start: 0.8372 (t0) cc_final: 0.8024 (t0) REVERT: C 38 ASN cc_start: 0.7115 (OUTLIER) cc_final: 0.6727 (p0) REVERT: C 75 GLU cc_start: 0.6558 (tp30) cc_final: 0.6213 (tm-30) REVERT: C 118 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8293 (tt) REVERT: C 222 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7479 (mp0) REVERT: C 262 GLU cc_start: 0.7479 (mt-10) cc_final: 0.7267 (tt0) REVERT: C 266 VAL cc_start: 0.7842 (t) cc_final: 0.7543 (p) REVERT: C 388 GLU cc_start: 0.8121 (mm-30) cc_final: 0.7729 (mm-30) REVERT: D 110 LEU cc_start: 0.8385 (tp) cc_final: 0.8119 (tt) REVERT: D 114 TYR cc_start: 0.8345 (OUTLIER) cc_final: 0.8119 (m-10) REVERT: D 117 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7461 (mp0) REVERT: D 159 ASP cc_start: 0.8215 (t0) cc_final: 0.7912 (t0) REVERT: D 188 LYS cc_start: 0.8189 (mttt) cc_final: 0.7940 (mttt) REVERT: D 207 ARG cc_start: 0.8339 (mpt-90) cc_final: 0.8135 (mmt-90) REVERT: D 301 ASP cc_start: 0.7968 (m-30) cc_final: 0.7655 (m-30) REVERT: D 401 GLU cc_start: 0.7617 (tm-30) cc_final: 0.7230 (tm-30) REVERT: D 404 MET cc_start: 0.7426 (tmm) cc_final: 0.7091 (tmm) REVERT: E 265 GLN cc_start: 0.8152 (mm110) cc_final: 0.7901 (mm110) REVERT: E 286 MET cc_start: 0.6420 (mtm) cc_final: 0.6196 (mtm) REVERT: E 319 MET cc_start: 0.8811 (mtm) cc_final: 0.8552 (mtm) REVERT: E 325 ASP cc_start: 0.8729 (t70) cc_final: 0.8425 (t0) REVERT: F 75 LYS cc_start: 0.8286 (mtmm) cc_final: 0.7971 (mtmm) REVERT: F 122 LEU cc_start: 0.8717 (mt) cc_final: 0.8464 (mt) REVERT: F 132 ASP cc_start: 0.7860 (m-30) cc_final: 0.7386 (m-30) REVERT: F 135 ASP cc_start: 0.8195 (m-30) cc_final: 0.7950 (m-30) REVERT: F 206 MET cc_start: 0.8335 (OUTLIER) cc_final: 0.7920 (mmm) REVERT: F 219 GLU cc_start: 0.7132 (tp30) cc_final: 0.6728 (tp30) REVERT: F 236 LYS cc_start: 0.8660 (ttmt) cc_final: 0.8202 (mmtm) REVERT: F 246 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7746 (tp30) REVERT: G 82 LYS cc_start: 0.8172 (tppp) cc_final: 0.7901 (tppp) REVERT: G 197 GLN cc_start: 0.8252 (tm-30) cc_final: 0.7960 (tm-30) REVERT: I 20 ILE cc_start: 0.8504 (OUTLIER) cc_final: 0.8215 (tp) REVERT: I 149 CYS cc_start: 0.8651 (OUTLIER) cc_final: 0.8327 (m) REVERT: I 154 LYS cc_start: 0.8309 (mttt) cc_final: 0.8029 (tppp) REVERT: I 165 VAL cc_start: 0.9039 (OUTLIER) cc_final: 0.8751 (m) REVERT: I 186 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8687 (tt) REVERT: I 188 GLU cc_start: 0.8125 (tp30) cc_final: 0.7538 (mm-30) REVERT: I 230 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.7193 (pm20) REVERT: I 240 THR cc_start: 0.7987 (m) cc_final: 0.7665 (p) REVERT: I 260 TYR cc_start: 0.7611 (t80) cc_final: 0.6572 (t80) REVERT: I 284 GLN cc_start: 0.8603 (tp-100) cc_final: 0.8377 (tp-100) REVERT: I 290 LYS cc_start: 0.8789 (tppt) cc_final: 0.8346 (mmmm) REVERT: I 306 GLU cc_start: 0.7489 (tp30) cc_final: 0.6860 (tm-30) REVERT: I 312 ASP cc_start: 0.8855 (OUTLIER) cc_final: 0.8619 (m-30) REVERT: I 330 GLN cc_start: 0.7855 (pm20) cc_final: 0.7617 (pp30) REVERT: I 353 GLU cc_start: 0.8115 (tm-30) cc_final: 0.7593 (tm-30) REVERT: I 365 MET cc_start: 0.8419 (mmm) cc_final: 0.8146 (tmm) REVERT: I 367 VAL cc_start: 0.8660 (p) cc_final: 0.8373 (m) REVERT: I 372 ASP cc_start: 0.7987 (m-30) cc_final: 0.7718 (m-30) REVERT: I 460 ASP cc_start: 0.7913 (p0) cc_final: 0.6620 (p0) REVERT: I 461 VAL cc_start: 0.8325 (m) cc_final: 0.7962 (p) REVERT: I 463 GLN cc_start: 0.8172 (tm-30) cc_final: 0.7826 (tm-30) REVERT: I 464 LYS cc_start: 0.7934 (mmtm) cc_final: 0.7668 (mmtm) REVERT: I 472 LYS cc_start: 0.8708 (mttt) cc_final: 0.8387 (mmmm) REVERT: I 519 GLU cc_start: 0.7830 (tm-30) cc_final: 0.7532 (tp30) REVERT: I 522 LYS cc_start: 0.8518 (tttt) cc_final: 0.8232 (tmmt) REVERT: I 587 LYS cc_start: 0.8508 (pttm) cc_final: 0.8205 (pttt) REVERT: I 607 GLN cc_start: 0.8281 (mt0) cc_final: 0.7998 (mp10) REVERT: I 612 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8426 (tm) REVERT: I 636 LEU cc_start: 0.8641 (tm) cc_final: 0.8214 (pp) REVERT: J 45 CYS cc_start: 0.7433 (OUTLIER) cc_final: 0.6984 (m) REVERT: L 29 THR cc_start: 0.7967 (OUTLIER) cc_final: 0.7636 (p) REVERT: L 94 LYS cc_start: 0.8822 (mmmm) cc_final: 0.8321 (mmmm) REVERT: M 102 ASP cc_start: 0.7871 (p0) cc_final: 0.7631 (p0) REVERT: M 112 LEU cc_start: 0.7676 (OUTLIER) cc_final: 0.7401 (pp) REVERT: M 125 LYS cc_start: 0.8691 (mmtp) cc_final: 0.8328 (mmtp) REVERT: M 168 SER cc_start: 0.8980 (t) cc_final: 0.8659 (p) REVERT: M 276 VAL cc_start: 0.8126 (OUTLIER) cc_final: 0.7857 (m) REVERT: M 294 ARG cc_start: 0.8280 (OUTLIER) cc_final: 0.6870 (ptm160) REVERT: M 370 ILE cc_start: 0.8632 (pt) cc_final: 0.8401 (pp) REVERT: N 20 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.8027 (ttm170) REVERT: N 31 LEU cc_start: 0.8404 (mp) cc_final: 0.8082 (mp) REVERT: N 37 LEU cc_start: 0.9022 (mp) cc_final: 0.8794 (mt) REVERT: N 71 ARG cc_start: 0.8468 (ttt-90) cc_final: 0.8133 (ttt180) outliers start: 142 outliers final: 84 residues processed: 928 average time/residue: 0.7236 time to fit residues: 775.8409 Evaluate side-chains 936 residues out of total 3383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 825 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 151 ASN Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 461 ARG Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 74 GLN Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 243 LYS Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 327 GLU Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 222 GLU Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 114 TYR Chi-restraints excluded: chain D residue 117 GLU Chi-restraints excluded: chain D residue 155 TYR Chi-restraints excluded: chain D residue 160 ASP Chi-restraints excluded: chain D residue 170 ARG Chi-restraints excluded: chain D residue 177 GLU Chi-restraints excluded: chain D residue 179 THR Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 333 ILE Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 83 VAL Chi-restraints excluded: chain F residue 112 PHE Chi-restraints excluded: chain F residue 136 ILE Chi-restraints excluded: chain F residue 145 ILE Chi-restraints excluded: chain F residue 150 LEU Chi-restraints excluded: chain F residue 206 MET Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 246 GLU Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 65 GLN Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 103 SER Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 162 ILE Chi-restraints excluded: chain G residue 165 LYS Chi-restraints excluded: chain G residue 175 HIS Chi-restraints excluded: chain G residue 210 GLU Chi-restraints excluded: chain G residue 216 ILE Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 157 SER Chi-restraints excluded: chain I residue 20 ILE Chi-restraints excluded: chain I residue 47 THR Chi-restraints excluded: chain I residue 149 CYS Chi-restraints excluded: chain I residue 151 GLU Chi-restraints excluded: chain I residue 165 VAL Chi-restraints excluded: chain I residue 170 CYS Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain I residue 230 GLU Chi-restraints excluded: chain I residue 239 ASP Chi-restraints excluded: chain I residue 257 VAL Chi-restraints excluded: chain I residue 312 ASP Chi-restraints excluded: chain I residue 333 LEU Chi-restraints excluded: chain I residue 402 PHE Chi-restraints excluded: chain I residue 416 SER Chi-restraints excluded: chain I residue 451 VAL Chi-restraints excluded: chain I residue 501 THR Chi-restraints excluded: chain I residue 507 MET Chi-restraints excluded: chain I residue 555 LEU Chi-restraints excluded: chain I residue 572 SER Chi-restraints excluded: chain I residue 591 VAL Chi-restraints excluded: chain I residue 612 LEU Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 45 CYS Chi-restraints excluded: chain J residue 104 GLN Chi-restraints excluded: chain L residue 29 THR Chi-restraints excluded: chain L residue 131 THR Chi-restraints excluded: chain L residue 146 THR Chi-restraints excluded: chain M residue 105 LEU Chi-restraints excluded: chain M residue 112 LEU Chi-restraints excluded: chain M residue 132 SER Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain M residue 256 SER Chi-restraints excluded: chain M residue 276 VAL Chi-restraints excluded: chain M residue 283 GLU Chi-restraints excluded: chain M residue 294 ARG Chi-restraints excluded: chain M residue 299 LYS Chi-restraints excluded: chain M residue 323 LEU Chi-restraints excluded: chain M residue 355 GLU Chi-restraints excluded: chain M residue 361 THR Chi-restraints excluded: chain M residue 394 THR Chi-restraints excluded: chain M residue 409 ILE Chi-restraints excluded: chain N residue 13 ASP Chi-restraints excluded: chain N residue 20 ARG Chi-restraints excluded: chain N residue 46 LEU Chi-restraints excluded: chain N residue 59 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 368 optimal weight: 0.6980 chunk 309 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 252 optimal weight: 0.9990 chunk 161 optimal weight: 0.9980 chunk 143 optimal weight: 1.9990 chunk 136 optimal weight: 0.8980 chunk 122 optimal weight: 7.9990 chunk 74 optimal weight: 0.5980 chunk 210 optimal weight: 0.9990 chunk 208 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 463 GLN B 208 GLN B 404 GLN C 38 ASN D 349 ASN E 258 ASN F 141 GLN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 304 HIS I 324 ASN ** I 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 325 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.141005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.120091 restraints weight = 48389.905| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 2.31 r_work: 0.3472 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3312 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.143 31254 Z= 0.155 Angle : 0.685 23.066 42214 Z= 0.342 Chirality : 0.042 0.630 4761 Planarity : 0.004 0.060 5382 Dihedral : 5.389 60.143 4162 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 3.52 % Allowed : 28.10 % Favored : 68.38 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % 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: 0.47 (0.14), residues: 3745 helix: 1.38 (0.11), residues: 2340 sheet: 0.02 (0.36), residues: 212 loop : -1.83 (0.17), residues: 1193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 160 TYR 0.045 0.001 TYR B 132 PHE 0.021 0.001 PHE D 48 TRP 0.031 0.001 TRP J 33 HIS 0.011 0.001 HIS A 277 Details of bonding type rmsd covalent geometry : bond 0.00367 (31240) covalent geometry : angle 0.67336 (42204) SS BOND : bond 0.00598 ( 2) SS BOND : angle 11.00290 ( 4) hydrogen bonds : bond 0.04927 ( 1704) hydrogen bonds : angle 3.95289 ( 5004) metal coordination : bond 0.01461 ( 12) metal coordination : angle 5.69421 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7490 Ramachandran restraints generated. 3745 Oldfield, 0 Emsley, 3745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7490 Ramachandran restraints generated. 3745 Oldfield, 0 Emsley, 3745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 955 residues out of total 3383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 836 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 ASN cc_start: 0.8344 (OUTLIER) cc_final: 0.7992 (t0) REVERT: A 203 LEU cc_start: 0.8621 (mp) cc_final: 0.8397 (mt) REVERT: A 219 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.8102 (mt) REVERT: A 257 GLU cc_start: 0.8298 (mt-10) cc_final: 0.8094 (mm-30) REVERT: A 280 PHE cc_start: 0.7023 (p90) cc_final: 0.6696 (p90) REVERT: A 383 SER cc_start: 0.8993 (t) cc_final: 0.8600 (p) REVERT: B 40 LYS cc_start: 0.8016 (tppp) cc_final: 0.7737 (mmtp) REVERT: B 55 GLN cc_start: 0.7616 (OUTLIER) cc_final: 0.7252 (pp30) REVERT: B 72 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8137 (mm) REVERT: B 75 MET cc_start: 0.8328 (mtp) cc_final: 0.7833 (mtp) REVERT: B 79 ASN cc_start: 0.8157 (t0) cc_final: 0.7876 (t0) REVERT: B 89 MET cc_start: 0.7376 (tpp) cc_final: 0.6070 (tpp) REVERT: B 93 LYS cc_start: 0.8661 (mtmt) cc_final: 0.7907 (mtmt) REVERT: B 112 ILE cc_start: 0.9151 (mm) cc_final: 0.8773 (tp) REVERT: B 129 GLN cc_start: 0.8575 (tp40) cc_final: 0.8295 (tm130) REVERT: B 204 MET cc_start: 0.8234 (tmm) cc_final: 0.7748 (tmm) REVERT: B 228 ILE cc_start: 0.8543 (mt) cc_final: 0.8161 (mt) REVERT: B 278 LYS cc_start: 0.8672 (mtmm) cc_final: 0.8399 (mtmm) REVERT: B 295 ASP cc_start: 0.7482 (t0) cc_final: 0.7230 (t0) REVERT: B 298 GLU cc_start: 0.8180 (mp0) cc_final: 0.7687 (mp0) REVERT: B 327 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.7811 (mp0) REVERT: B 379 ASN cc_start: 0.8355 (t0) cc_final: 0.8027 (t0) REVERT: C 75 GLU cc_start: 0.6579 (tp30) cc_final: 0.6231 (tm-30) REVERT: C 118 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8298 (tt) REVERT: C 222 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7472 (mp0) REVERT: C 262 GLU cc_start: 0.7467 (mt-10) cc_final: 0.7248 (tt0) REVERT: C 266 VAL cc_start: 0.7837 (t) cc_final: 0.7524 (p) REVERT: C 388 GLU cc_start: 0.8123 (mm-30) cc_final: 0.7744 (mm-30) REVERT: D 110 LEU cc_start: 0.8391 (tp) cc_final: 0.8125 (tt) REVERT: D 114 TYR cc_start: 0.8338 (OUTLIER) cc_final: 0.8120 (m-10) REVERT: D 117 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7425 (mp0) REVERT: D 159 ASP cc_start: 0.8202 (t0) cc_final: 0.7896 (t0) REVERT: D 188 LYS cc_start: 0.8178 (mttt) cc_final: 0.7932 (mttt) REVERT: D 301 ASP cc_start: 0.7979 (m-30) cc_final: 0.7663 (m-30) REVERT: D 394 GLU cc_start: 0.8396 (pm20) cc_final: 0.8133 (pm20) REVERT: D 401 GLU cc_start: 0.7618 (tm-30) cc_final: 0.7162 (tm-30) REVERT: D 404 MET cc_start: 0.7430 (tmm) cc_final: 0.6982 (tmm) REVERT: E 265 GLN cc_start: 0.8136 (mm110) cc_final: 0.7881 (mm110) REVERT: E 286 MET cc_start: 0.6378 (mtm) cc_final: 0.6173 (mtm) REVERT: E 319 MET cc_start: 0.8817 (mtm) cc_final: 0.8562 (mtm) REVERT: E 325 ASP cc_start: 0.8740 (t70) cc_final: 0.8435 (t0) REVERT: F 75 LYS cc_start: 0.8290 (mtmm) cc_final: 0.7980 (mtmm) REVERT: F 122 LEU cc_start: 0.8711 (mt) cc_final: 0.8456 (mt) REVERT: F 132 ASP cc_start: 0.7868 (m-30) cc_final: 0.7398 (m-30) REVERT: F 135 ASP cc_start: 0.8205 (m-30) cc_final: 0.7962 (m-30) REVERT: F 206 MET cc_start: 0.8325 (OUTLIER) cc_final: 0.7914 (mmm) REVERT: F 219 GLU cc_start: 0.7171 (tp30) cc_final: 0.6771 (tp30) REVERT: F 236 LYS cc_start: 0.8657 (ttmt) cc_final: 0.8198 (mmtm) REVERT: F 246 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7759 (tp30) REVERT: G 82 LYS cc_start: 0.8190 (tppp) cc_final: 0.7917 (tppp) REVERT: G 165 LYS cc_start: 0.8735 (OUTLIER) cc_final: 0.8506 (ptpp) REVERT: G 197 GLN cc_start: 0.8272 (tm-30) cc_final: 0.7975 (tm-30) REVERT: I 20 ILE cc_start: 0.8504 (OUTLIER) cc_final: 0.8218 (tp) REVERT: I 149 CYS cc_start: 0.8652 (OUTLIER) cc_final: 0.8312 (m) REVERT: I 154 LYS cc_start: 0.8359 (mttt) cc_final: 0.8070 (tppp) REVERT: I 165 VAL cc_start: 0.9043 (OUTLIER) cc_final: 0.8748 (m) REVERT: I 186 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8682 (tt) REVERT: I 188 GLU cc_start: 0.8147 (tp30) cc_final: 0.7465 (mm-30) REVERT: I 230 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.7203 (pm20) REVERT: I 240 THR cc_start: 0.7984 (m) cc_final: 0.7654 (p) REVERT: I 272 GLN cc_start: 0.8056 (tm-30) cc_final: 0.7568 (mm-40) REVERT: I 284 GLN cc_start: 0.8602 (tp-100) cc_final: 0.7595 (tp40) REVERT: I 290 LYS cc_start: 0.8808 (tppt) cc_final: 0.8423 (tppp) REVERT: I 297 GLU cc_start: 0.7491 (tm-30) cc_final: 0.6858 (pp20) REVERT: I 306 GLU cc_start: 0.7497 (tp30) cc_final: 0.6863 (tm-30) REVERT: I 312 ASP cc_start: 0.8866 (OUTLIER) cc_final: 0.8629 (m-30) REVERT: I 330 GLN cc_start: 0.7873 (pm20) cc_final: 0.7627 (pp30) REVERT: I 353 GLU cc_start: 0.8105 (tm-30) cc_final: 0.7588 (tm-30) REVERT: I 365 MET cc_start: 0.8430 (mmm) cc_final: 0.8174 (tmm) REVERT: I 367 VAL cc_start: 0.8660 (p) cc_final: 0.8376 (m) REVERT: I 372 ASP cc_start: 0.7978 (m-30) cc_final: 0.7757 (m-30) REVERT: I 460 ASP cc_start: 0.7936 (p0) cc_final: 0.6649 (p0) REVERT: I 461 VAL cc_start: 0.8322 (m) cc_final: 0.7960 (p) REVERT: I 463 GLN cc_start: 0.8191 (tm-30) cc_final: 0.7770 (tm-30) REVERT: I 464 LYS cc_start: 0.7912 (mmtm) cc_final: 0.7678 (mmtm) REVERT: I 472 LYS cc_start: 0.8691 (mttt) cc_final: 0.8375 (mmmm) REVERT: I 500 TYR cc_start: 0.8163 (t80) cc_final: 0.7892 (t80) REVERT: I 519 GLU cc_start: 0.7835 (tm-30) cc_final: 0.7568 (tp30) REVERT: I 522 LYS cc_start: 0.8530 (tttt) cc_final: 0.8230 (tmmt) REVERT: I 587 LYS cc_start: 0.8510 (pttm) cc_final: 0.8199 (pttt) REVERT: I 607 GLN cc_start: 0.8283 (mt0) cc_final: 0.8002 (mp10) REVERT: I 612 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8425 (tm) REVERT: I 636 LEU cc_start: 0.8642 (tm) cc_final: 0.8195 (pp) REVERT: J 45 CYS cc_start: 0.7513 (OUTLIER) cc_final: 0.7068 (m) REVERT: L 29 THR cc_start: 0.7956 (OUTLIER) cc_final: 0.7614 (p) REVERT: L 94 LYS cc_start: 0.8827 (mmmm) cc_final: 0.8323 (mmmm) REVERT: M 102 ASP cc_start: 0.7887 (p0) cc_final: 0.7652 (p0) REVERT: M 125 LYS cc_start: 0.8675 (mmtp) cc_final: 0.8299 (mmtp) REVERT: M 133 ASP cc_start: 0.8079 (p0) cc_final: 0.7576 (p0) REVERT: M 168 SER cc_start: 0.8975 (t) cc_final: 0.8662 (p) REVERT: M 276 VAL cc_start: 0.8140 (OUTLIER) cc_final: 0.7860 (m) REVERT: M 294 ARG cc_start: 0.8290 (OUTLIER) cc_final: 0.6881 (ptm160) REVERT: M 310 PRO cc_start: 0.8681 (Cg_endo) cc_final: 0.8232 (Cg_exo) REVERT: N 20 ARG cc_start: 0.8507 (OUTLIER) cc_final: 0.7839 (ttm170) REVERT: N 31 LEU cc_start: 0.8400 (mp) cc_final: 0.8092 (mp) REVERT: N 37 LEU cc_start: 0.9020 (mp) cc_final: 0.8797 (mt) REVERT: N 71 ARG cc_start: 0.8451 (ttt-90) cc_final: 0.8169 (ttt180) outliers start: 119 outliers final: 85 residues processed: 903 average time/residue: 0.7390 time to fit residues: 770.2291 Evaluate side-chains 944 residues out of total 3383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 835 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 151 ASN Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 262 LYS Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 74 GLN Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 327 GLU Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 222 GLU Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 114 TYR Chi-restraints excluded: chain D residue 117 GLU Chi-restraints excluded: chain D residue 155 TYR Chi-restraints excluded: chain D residue 160 ASP Chi-restraints excluded: chain D residue 170 ARG Chi-restraints excluded: chain D residue 177 GLU Chi-restraints excluded: chain D residue 179 THR Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 333 ILE Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 83 VAL Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 112 PHE Chi-restraints excluded: chain F residue 145 ILE Chi-restraints excluded: chain F residue 150 LEU Chi-restraints excluded: chain F residue 206 MET Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 246 GLU Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 103 SER Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 151 LEU Chi-restraints excluded: chain G residue 162 ILE Chi-restraints excluded: chain G residue 165 LYS Chi-restraints excluded: chain G residue 175 HIS Chi-restraints excluded: chain G residue 210 GLU Chi-restraints excluded: chain G residue 216 ILE Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 157 SER Chi-restraints excluded: chain I residue 20 ILE Chi-restraints excluded: chain I residue 47 THR Chi-restraints excluded: chain I residue 149 CYS Chi-restraints excluded: chain I residue 151 GLU Chi-restraints excluded: chain I residue 165 VAL Chi-restraints excluded: chain I residue 170 CYS Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain I residue 230 GLU Chi-restraints excluded: chain I residue 239 ASP Chi-restraints excluded: chain I residue 257 VAL Chi-restraints excluded: chain I residue 312 ASP Chi-restraints excluded: chain I residue 333 LEU Chi-restraints excluded: chain I residue 402 PHE Chi-restraints excluded: chain I residue 416 SER Chi-restraints excluded: chain I residue 451 VAL Chi-restraints excluded: chain I residue 501 THR Chi-restraints excluded: chain I residue 555 LEU Chi-restraints excluded: chain I residue 572 SER Chi-restraints excluded: chain I residue 591 VAL Chi-restraints excluded: chain I residue 612 LEU Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 45 CYS Chi-restraints excluded: chain J residue 104 GLN Chi-restraints excluded: chain L residue 29 THR Chi-restraints excluded: chain L residue 131 THR Chi-restraints excluded: chain L residue 146 THR Chi-restraints excluded: chain M residue 105 LEU Chi-restraints excluded: chain M residue 132 SER Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain M residue 256 SER Chi-restraints excluded: chain M residue 276 VAL Chi-restraints excluded: chain M residue 283 GLU Chi-restraints excluded: chain M residue 294 ARG Chi-restraints excluded: chain M residue 299 LYS Chi-restraints excluded: chain M residue 323 LEU Chi-restraints excluded: chain M residue 325 ASN Chi-restraints excluded: chain M residue 355 GLU Chi-restraints excluded: chain M residue 361 THR Chi-restraints excluded: chain M residue 394 THR Chi-restraints excluded: chain M residue 409 ILE Chi-restraints excluded: chain N residue 13 ASP Chi-restraints excluded: chain N residue 20 ARG Chi-restraints excluded: chain N residue 46 LEU Chi-restraints excluded: chain N residue 59 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 114 optimal weight: 0.0970 chunk 325 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 285 optimal weight: 0.2980 chunk 305 optimal weight: 2.9990 chunk 373 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 371 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 463 GLN B 208 GLN B 436 GLN D 349 ASN E 258 ASN F 141 GLN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 304 HIS I 308 GLN I 324 ASN I 346 ASN ** I 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 45 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.141024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.120074 restraints weight = 48666.754| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 2.32 r_work: 0.3475 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3316 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.166 31254 Z= 0.177 Angle : 0.794 59.158 42214 Z= 0.426 Chirality : 0.042 0.628 4761 Planarity : 0.004 0.070 5382 Dihedral : 5.410 60.060 4162 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.58 % Allowed : 28.19 % Favored : 68.23 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % 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: 0.47 (0.14), residues: 3745 helix: 1.39 (0.11), residues: 2343 sheet: 0.02 (0.36), residues: 212 loop : -1.85 (0.17), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG I 328 TYR 0.037 0.001 TYR B 132 PHE 0.020 0.001 PHE D 48 TRP 0.029 0.002 TRP J 33 HIS 0.010 0.001 HIS A 277 Details of bonding type rmsd covalent geometry : bond 0.00409 (31240) covalent geometry : angle 0.78449 (42204) SS BOND : bond 0.00621 ( 2) SS BOND : angle 10.91660 ( 4) hydrogen bonds : bond 0.04896 ( 1704) hydrogen bonds : angle 3.96701 ( 5004) metal coordination : bond 0.01390 ( 12) metal coordination : angle 5.67473 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15099.99 seconds wall clock time: 256 minutes 7.51 seconds (15367.51 seconds total)