Starting phenix.real_space_refine on Tue Jun 17 20:56:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tc7_25804/06_2025/7tc7_25804.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tc7_25804/06_2025/7tc7_25804.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tc7_25804/06_2025/7tc7_25804.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tc7_25804/06_2025/7tc7_25804.map" model { file = "/net/cci-nas-00/data/ceres_data/7tc7_25804/06_2025/7tc7_25804.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tc7_25804/06_2025/7tc7_25804.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.189 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 Fe 4 7.16 5 S 60 5.16 5 C 11119 2.51 5 N 3017 2.21 5 O 3167 1.98 5 H 3200 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 62 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 20567 Number of models: 1 Model: "" Number of chains: 8 Chain: "D" Number of atoms: 5106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 510, 5106 Classifications: {'peptide': 510} Link IDs: {'PTRANS': 21, 'TRANS': 488} Chain: "E" Number of atoms: 5112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 5112 Classifications: {'peptide': 511} Link IDs: {'PTRANS': 21, 'TRANS': 489} Chain: "B" Number of atoms: 3167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 3167 Classifications: {'peptide': 384} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 367} Chain: "C" Number of atoms: 3872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 3872 Classifications: {'peptide': 384} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 367} Chain: "G" Number of atoms: 1653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1653 Classifications: {'peptide': 162} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 156} Chain: "H" Number of atoms: 1653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1653 Classifications: {'peptide': 162} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 156} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 11.09, per 1000 atoms: 0.54 Number of scatterers: 20567 At special positions: 0 Unit cell: (108.915, 142.823, 113.025, 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) Fe 4 26.01 S 60 16.00 O 3167 8.00 N 3017 7.00 C 11119 6.00 H 3200 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.55 Conformation dependent library (CDL) restraints added in 2.2 seconds 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3958 Finding SS restraints... Secondary structure from input PDB file: 122 helices and 4 sheets defined 71.7% alpha, 1.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.78 Creating SS restraints... Processing helix chain 'D' and resid 24 through 30 removed outlier: 3.512A pdb=" N VAL D 28 " --> pdb=" O ASN D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 35 Processing helix chain 'D' and resid 63 through 84 removed outlier: 3.508A pdb=" N LYS D 74 " --> pdb=" O MET D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 89 Processing helix chain 'D' and resid 96 through 128 removed outlier: 3.641A pdb=" N LYS D 104 " --> pdb=" O ASN D 100 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL D 105 " --> pdb=" O GLU D 101 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA D 119 " --> pdb=" O TYR D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 162 Processing helix chain 'D' and resid 170 through 175 Processing helix chain 'D' and resid 179 through 189 removed outlier: 3.897A pdb=" N GLY D 183 " --> pdb=" O PRO D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 194 removed outlier: 3.744A pdb=" N ILE D 193 " --> pdb=" O SER D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 205 Processing helix chain 'D' and resid 207 through 212 Processing helix chain 'D' and resid 212 through 227 Processing helix chain 'D' and resid 230 through 241 removed outlier: 3.926A pdb=" N SER D 238 " --> pdb=" O THR D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 257 removed outlier: 3.935A pdb=" N HIS D 246 " --> pdb=" O ASP D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 283 removed outlier: 3.699A pdb=" N ALA D 264 " --> pdb=" O ASP D 260 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N ASN D 268 " --> pdb=" O ALA D 264 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N THR D 269 " --> pdb=" O LYS D 265 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N TYR D 281 " --> pdb=" O THR D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 293 removed outlier: 3.685A pdb=" N GLY D 287 " --> pdb=" O THR D 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 310 Processing helix chain 'D' and resid 316 through 321 removed outlier: 3.560A pdb=" N LEU D 321 " --> pdb=" O TRP D 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 325 Processing helix chain 'D' and resid 331 through 339 Processing helix chain 'D' and resid 341 through 353 Processing helix chain 'D' and resid 354 through 357 Processing helix chain 'D' and resid 365 through 376 Processing helix chain 'D' and resid 378 through 393 removed outlier: 4.120A pdb=" N HIS D 382 " --> pdb=" O GLY D 378 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N LYS D 385 " --> pdb=" O ASP D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 401 removed outlier: 3.651A pdb=" N GLY D 401 " --> pdb=" O PRO D 398 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 411 removed outlier: 3.889A pdb=" N TRP D 407 " --> pdb=" O ILE D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 460 Processing helix chain 'D' and resid 461 through 464 Processing helix chain 'D' and resid 468 through 473 Processing helix chain 'D' and resid 477 through 485 Processing helix chain 'D' and resid 508 through 516 removed outlier: 3.711A pdb=" N LEU D 515 " --> pdb=" O ASP D 511 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASN D 516 " --> pdb=" O ILE D 512 " (cutoff:3.500A) Processing helix chain 'D' and resid 521 through 526 removed outlier: 3.647A pdb=" N ALA D 525 " --> pdb=" O PRO D 522 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 30 Processing helix chain 'E' and resid 31 through 35 Processing helix chain 'E' and resid 63 through 84 removed outlier: 3.560A pdb=" N LYS E 74 " --> pdb=" O MET E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 84 through 89 Processing helix chain 'E' and resid 96 through 128 removed outlier: 3.698A pdb=" N VAL E 105 " --> pdb=" O GLU E 101 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA E 119 " --> pdb=" O TYR E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 162 Processing helix chain 'E' and resid 170 through 175 Processing helix chain 'E' and resid 176 through 178 No H-bonds generated for 'chain 'E' and resid 176 through 178' Processing helix chain 'E' and resid 179 through 189 removed outlier: 3.839A pdb=" N GLY E 183 " --> pdb=" O PRO E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 189 through 194 removed outlier: 3.681A pdb=" N ILE E 193 " --> pdb=" O SER E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 196 through 205 Processing helix chain 'E' and resid 207 through 212 Processing helix chain 'E' and resid 212 through 227 removed outlier: 3.830A pdb=" N VAL E 218 " --> pdb=" O ASN E 214 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 241 removed outlier: 3.906A pdb=" N SER E 238 " --> pdb=" O THR E 234 " (cutoff:3.500A) Processing helix chain 'E' and resid 242 through 257 removed outlier: 3.897A pdb=" N HIS E 246 " --> pdb=" O ASP E 242 " (cutoff:3.500A) Processing helix chain 'E' and resid 261 through 293 removed outlier: 3.854A pdb=" N LYS E 265 " --> pdb=" O PRO E 261 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N ASN E 268 " --> pdb=" O ALA E 264 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N THR E 269 " --> pdb=" O LYS E 265 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N TYR E 281 " --> pdb=" O THR E 277 " (cutoff:3.500A) Proline residue: E 284 - end of helix removed outlier: 3.683A pdb=" N GLY E 287 " --> pdb=" O THR E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 300 through 310 Processing helix chain 'E' and resid 315 through 322 Processing helix chain 'E' and resid 323 through 325 No H-bonds generated for 'chain 'E' and resid 323 through 325' Processing helix chain 'E' and resid 331 through 339 Processing helix chain 'E' and resid 341 through 353 Processing helix chain 'E' and resid 354 through 357 Processing helix chain 'E' and resid 365 through 376 Processing helix chain 'E' and resid 378 through 394 removed outlier: 3.989A pdb=" N HIS E 382 " --> pdb=" O GLY E 378 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N LYS E 385 " --> pdb=" O ASP E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 403 through 411 removed outlier: 3.799A pdb=" N TRP E 407 " --> pdb=" O ILE E 403 " (cutoff:3.500A) Processing helix chain 'E' and resid 450 through 460 Processing helix chain 'E' and resid 461 through 464 Processing helix chain 'E' and resid 468 through 473 Processing helix chain 'E' and resid 477 through 485 Processing helix chain 'E' and resid 508 through 516 removed outlier: 3.737A pdb=" N ASN E 516 " --> pdb=" O ILE E 512 " (cutoff:3.500A) Processing helix chain 'E' and resid 521 through 526 removed outlier: 3.561A pdb=" N ALA E 525 " --> pdb=" O PRO E 522 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE E 526 " --> pdb=" O VAL E 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 24 Processing helix chain 'B' and resid 47 through 54 Processing helix chain 'B' and resid 84 through 88 removed outlier: 3.594A pdb=" N THR B 87 " --> pdb=" O GLY B 84 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N THR B 88 " --> pdb=" O ASN B 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 84 through 88' Processing helix chain 'B' and resid 94 through 98 removed outlier: 3.626A pdb=" N LYS B 97 " --> pdb=" O ASP B 94 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N HIS B 98 " --> pdb=" O TRP B 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 94 through 98' Processing helix chain 'B' and resid 105 through 131 Processing helix chain 'B' and resid 132 through 136 Processing helix chain 'B' and resid 137 through 144 Processing helix chain 'B' and resid 147 through 162 removed outlier: 3.895A pdb=" N LEU B 153 " --> pdb=" O TRP B 149 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N PHE B 154 " --> pdb=" O GLY B 150 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ASN B 155 " --> pdb=" O ALA B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 170 Processing helix chain 'B' and resid 172 through 204 Processing helix chain 'B' and resid 211 through 221 Processing helix chain 'B' and resid 224 through 237 Processing helix chain 'B' and resid 240 through 251 Processing helix chain 'B' and resid 251 through 264 removed outlier: 4.090A pdb=" N GLN B 258 " --> pdb=" O ALA B 254 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE B 264 " --> pdb=" O VAL B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 269 Processing helix chain 'B' and resid 270 through 273 Processing helix chain 'B' and resid 276 through 300 removed outlier: 3.663A pdb=" N PHE B 280 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN B 283 " --> pdb=" O PHE B 279 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN B 293 " --> pdb=" O GLN B 289 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLY B 294 " --> pdb=" O ILE B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 336 removed outlier: 4.246A pdb=" N GLU B 326 " --> pdb=" O GLY B 322 " (cutoff:3.500A) Proline residue: B 327 - end of helix Processing helix chain 'B' and resid 337 through 341 Processing helix chain 'B' and resid 348 through 367 Processing helix chain 'B' and resid 368 through 372 removed outlier: 3.549A pdb=" N ILE B 371 " --> pdb=" O ALA B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 386 Processing helix chain 'C' and resid 13 through 24 Processing helix chain 'C' and resid 47 through 54 Processing helix chain 'C' and resid 84 through 88 removed outlier: 3.563A pdb=" N THR C 88 " --> pdb=" O ASN C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 131 Processing helix chain 'C' and resid 132 through 136 Processing helix chain 'C' and resid 137 through 144 Processing helix chain 'C' and resid 147 through 162 removed outlier: 3.754A pdb=" N LEU C 153 " --> pdb=" O TRP C 149 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N PHE C 154 " --> pdb=" O GLY C 150 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ASN C 155 " --> pdb=" O ALA C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 170 Processing helix chain 'C' and resid 172 through 204 Processing helix chain 'C' and resid 211 through 221 Processing helix chain 'C' and resid 224 through 237 Processing helix chain 'C' and resid 240 through 251 removed outlier: 3.511A pdb=" N VAL C 251 " --> pdb=" O SER C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 263 removed outlier: 4.228A pdb=" N GLN C 258 " --> pdb=" O ALA C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 269 Processing helix chain 'C' and resid 270 through 273 Processing helix chain 'C' and resid 276 through 300 removed outlier: 3.559A pdb=" N PHE C 280 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLN C 283 " --> pdb=" O PHE C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 336 removed outlier: 4.182A pdb=" N GLU C 326 " --> pdb=" O GLY C 322 " (cutoff:3.500A) Proline residue: C 327 - end of helix Processing helix chain 'C' and resid 337 through 342 removed outlier: 3.525A pdb=" N ALA C 340 " --> pdb=" O GLY C 337 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU C 342 " --> pdb=" O PHE C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 348 through 367 Processing helix chain 'C' and resid 368 through 372 removed outlier: 3.662A pdb=" N ILE C 371 " --> pdb=" O ALA C 368 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASP C 372 " --> pdb=" O SER C 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 368 through 372' Processing helix chain 'C' and resid 376 through 386 Processing helix chain 'G' and resid 9 through 20 Processing helix chain 'G' and resid 24 through 40 Processing helix chain 'G' and resid 52 through 72 Processing helix chain 'G' and resid 73 through 80 Processing helix chain 'G' and resid 86 through 100 Processing helix chain 'G' and resid 103 through 119 Processing helix chain 'G' and resid 124 through 144 Processing helix chain 'G' and resid 151 through 160 Processing helix chain 'H' and resid 9 through 20 Processing helix chain 'H' and resid 24 through 40 Processing helix chain 'H' and resid 52 through 72 Processing helix chain 'H' and resid 73 through 80 Processing helix chain 'H' and resid 86 through 101 Processing helix chain 'H' and resid 103 through 119 Processing helix chain 'H' and resid 124 through 144 Processing helix chain 'H' and resid 151 through 160 Processing sheet with id=AA1, first strand: chain 'D' and resid 416 through 417 Processing sheet with id=AA2, first strand: chain 'D' and resid 444 through 448 Processing sheet with id=AA3, first strand: chain 'E' and resid 416 through 417 Processing sheet with id=AA4, first strand: chain 'E' and resid 444 through 448 993 hydrogen bonds defined for protein. 2883 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: 5.96 Time building geometry restraints manager: 6.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 3200 1.03 - 1.23: 29 1.23 - 1.42: 7980 1.42 - 1.61: 9748 1.61 - 1.81: 104 Bond restraints: 21061 Sorted by residual: bond pdb=" C GLN E 444 " pdb=" O GLN E 444 " ideal model delta sigma weight residual 1.235 1.074 0.161 1.22e-02 6.72e+03 1.74e+02 bond pdb=" C TRP E 305 " pdb=" O TRP E 305 " ideal model delta sigma weight residual 1.237 1.093 0.144 1.16e-02 7.43e+03 1.53e+02 bond pdb=" C ARG E 307 " pdb=" O ARG E 307 " ideal model delta sigma weight residual 1.237 1.093 0.143 1.17e-02 7.31e+03 1.50e+02 bond pdb=" C GLN D 444 " pdb=" O GLN D 444 " ideal model delta sigma weight residual 1.234 1.087 0.147 1.26e-02 6.30e+03 1.37e+02 bond pdb=" C ASN E 306 " pdb=" O ASN E 306 " ideal model delta sigma weight residual 1.237 1.104 0.133 1.17e-02 7.31e+03 1.29e+02 ... (remaining 21056 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.11: 29913 3.11 - 6.22: 106 6.22 - 9.33: 6 9.33 - 12.44: 0 12.44 - 15.55: 1 Bond angle restraints: 30026 Sorted by residual: angle pdb=" N GLN G 21 " pdb=" CA GLN G 21 " pdb=" CB GLN G 21 " ideal model delta sigma weight residual 110.70 102.89 7.81 1.49e+00 4.50e-01 2.75e+01 angle pdb=" CB LEU H 22 " pdb=" CG LEU H 22 " pdb=" CD2 LEU H 22 " ideal model delta sigma weight residual 110.70 95.15 15.55 3.00e+00 1.11e-01 2.69e+01 angle pdb=" N GLN G 21 " pdb=" CA GLN G 21 " pdb=" C GLN G 21 " ideal model delta sigma weight residual 112.72 118.24 -5.52 1.14e+00 7.69e-01 2.34e+01 angle pdb=" CA ASN E 306 " pdb=" C ASN E 306 " pdb=" N ARG E 307 " ideal model delta sigma weight residual 117.30 122.87 -5.57 1.16e+00 7.43e-01 2.30e+01 angle pdb=" CA TRP E 305 " pdb=" C TRP E 305 " pdb=" N ASN E 306 " ideal model delta sigma weight residual 117.17 122.79 -5.62 1.18e+00 7.18e-01 2.27e+01 ... (remaining 30021 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 11804 17.74 - 35.47: 790 35.47 - 53.21: 138 53.21 - 70.95: 75 70.95 - 88.69: 25 Dihedral angle restraints: 12832 sinusoidal: 6526 harmonic: 6306 Sorted by residual: dihedral pdb=" CA THR H 40 " pdb=" C THR H 40 " pdb=" N THR H 41 " pdb=" CA THR H 41 " ideal model delta harmonic sigma weight residual 180.00 154.13 25.87 0 5.00e+00 4.00e-02 2.68e+01 dihedral pdb=" CA ASN E 17 " pdb=" C ASN E 17 " pdb=" N ARG E 18 " pdb=" CA ARG E 18 " ideal model delta harmonic sigma weight residual 180.00 156.18 23.82 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CA THR G 40 " pdb=" C THR G 40 " pdb=" N THR G 41 " pdb=" CA THR G 41 " ideal model delta harmonic sigma weight residual 180.00 157.70 22.30 0 5.00e+00 4.00e-02 1.99e+01 ... (remaining 12829 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 2409 0.107 - 0.214: 45 0.214 - 0.321: 3 0.321 - 0.428: 3 0.428 - 0.535: 1 Chirality restraints: 2461 Sorted by residual: chirality pdb=" CA ASN E 306 " pdb=" N ASN E 306 " pdb=" C ASN E 306 " pdb=" CB ASN E 306 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 7.16e+00 chirality pdb=" CA GLN G 21 " pdb=" N GLN G 21 " pdb=" C GLN G 21 " pdb=" CB GLN G 21 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.55e+00 chirality pdb=" CA TRP E 305 " pdb=" N TRP E 305 " pdb=" C TRP E 305 " pdb=" CB TRP E 305 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.42e+00 ... (remaining 2458 not shown) Planarity restraints: 4809 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP E 125 " 0.014 2.00e-02 2.50e+03 2.25e-02 1.39e+01 pdb=" CG TRP E 125 " -0.057 2.00e-02 2.50e+03 pdb=" CD1 TRP E 125 " 0.042 2.00e-02 2.50e+03 pdb=" CD2 TRP E 125 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP E 125 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP E 125 " -0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP E 125 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 125 " -0.008 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 125 " 0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP E 125 " 0.002 2.00e-02 2.50e+03 pdb=" HE1 TRP E 125 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN H 21 " 0.015 2.00e-02 2.50e+03 2.91e-02 8.46e+00 pdb=" C GLN H 21 " -0.050 2.00e-02 2.50e+03 pdb=" O GLN H 21 " 0.018 2.00e-02 2.50e+03 pdb=" N LEU H 22 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN D 444 " 0.014 2.00e-02 2.50e+03 2.86e-02 8.15e+00 pdb=" C GLN D 444 " -0.049 2.00e-02 2.50e+03 pdb=" O GLN D 444 " 0.019 2.00e-02 2.50e+03 pdb=" N MET D 445 " 0.016 2.00e-02 2.50e+03 ... (remaining 4806 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.14: 379 2.14 - 2.75: 11615 2.75 - 3.37: 37166 3.37 - 3.98: 52395 3.98 - 4.60: 79795 Nonbonded interactions: 181350 Sorted by model distance: nonbonded pdb=" OE2 GLU D 462 " pdb="HH12 ARG G 143 " model vdw 1.522 2.450 nonbonded pdb=" OE1 GLU C 116 " pdb=" HH TYR C 287 " model vdw 1.577 2.450 nonbonded pdb=" HH TYR E 137 " pdb=" OG1 THR E 253 " model vdw 1.587 2.450 nonbonded pdb=" HH TYR D 115 " pdb=" OE1 GLN B 57 " model vdw 1.603 2.450 nonbonded pdb="HH21 ARG H 36 " pdb=" OE2 GLU H 61 " model vdw 1.604 2.450 ... (remaining 181345 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'B' selection = (chain 'C' and ((resid 6 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD or name OE1 or name OE2)) or (resid 7 through 9 and (name N \ or name CA or name C or name O or name CB or name CG or name CD or name NE or n \ ame CZ or name NH1 or name NH2)) or (resid 10 and (name N or name CA or name C o \ r name O )) or (resid 11 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD1 or name CD2)) or (resid 12 and (name N or name CA or name \ C or name O or name CB or name OG1 or name CG2)) or (resid 13 and (name N or nam \ e CA or name C or name O or name CB or name CG or name OD1 or name OD2)) or resi \ d 14 or (resid 15 and (name N or name CA or name C or name O or name CB or name \ CG or name CD or name OE1 or name OE2)) or (resid 16 and (name N or name CA or n \ ame C or name O or name CB or name CG or name SD or name CE )) or (resid 17 thro \ ugh 18 and (name N or name CA or name C or name O or name CB )) or (resid 19 and \ (name N or name CA or name C or name O or name CB or name CG1 or name CG2)) or \ (resid 20 and (name N or name CA or name C or name O or name CB or name CG1 or n \ ame CG2 or name CD1)) or (resid 21 and (name N or name CA or name C or name O or \ name CB or name CG or name CD1 or name CD2)) or (resid 22 and (name N or name C \ A or name C or name O or name CB or name CG or name CD or name CE or name NZ )) \ or (resid 23 and (name N or name CA or name C or name O or name CB )) or (resid \ 24 and (name N or name CA or name C or name O or name CB or name CG or name CD1 \ or name CD2)) or resid 25 or (resid 26 and (name N or name CA or name C or name \ O or name CB or name CG or name CD or name OE1 or name OE2)) or (resid 27 and (n \ ame N or name CA or name C or name O or name CB )) or resid 28 or (resid 29 and \ (name N or name CA or name C or name O or name CB or name CG or name CD1 or name \ CD2)) or (resid 30 and (name N or name CA or name C or name O or name CB or nam \ e CG or name OD1 or name OD2)) or (resid 31 and (name N or name CA or name C or \ name O )) or (resid 32 through 33 and (name N or name CA or name C or name O or \ name CB or name CG or name OD1 or name ND2)) or (resid 34 and (name N or name CA \ or name C or name O or name CB or name CG or name CD or name CE or name NZ )) o \ r (resid 35 and (name N or name CA or name C or name O or name CB or name CG or \ name SD or name CE )) or (resid 36 and (name N or name CA or name C or name O )) \ or (resid 37 and (name N or name CA or name C or name O or name CB or name CG o \ r name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name OH )) or (resi \ d 38 and (name N or name CA or name C or name O or name CB or name CG or name CD \ 1 or name CD2 or name CE1 or name CE2 or name CZ )) or (resid 39 and (name N or \ name CA or name C or name O or name CB or name CG1 or name CG2)) or (resid 40 an \ d (name N or name CA or name C or name O or name CB or name OG1 or name CG2)) or \ resid 41 or (resid 42 and (name N or name CA or name C or name O or name CB or \ name CG or name CD or name NE or name CZ or name NH1 or name NH2)) or (resid 43 \ and (name N or name CA or name C or name O or name CB or name CG or name CD1 or \ name CD2 or name NE1 or name CE2 or name CE3 or name CZ2 or name CZ3 or name CH2 \ )) or (resid 44 and (name N or name CA or name C or name O or name CB or name CG \ or name CD or name CE or name NZ )) or (resid 45 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 \ or name NH2)) or (resid 46 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2)) or (resid 47 and (name N or name CA or nam \ e C or name O or name CB or name OG1 or name CG2)) or (resid 48 and (name N or n \ ame CA or name C or name O or name CB or name CG or name CD or name OE1 or name \ OE2)) or (resid 49 and (name N or name CA or name C or name O or name CB or name \ CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name OH )) or \ (resid 50 and (name N or name CA or name C or name O or name CB or name CG or na \ me CD or name OE1 or name OE2)) or (resid 51 and (name N or name CA or name C or \ name O or name CB )) or (resid 52 and (name N or name CA or name C or name O or \ name CB or name CG or name CD1 or name CD2)) or (resid 53 and (name N or name C \ A or name C or name O or name CB or name OG1 or name CG2)) or (resid 54 and (nam \ e N or name CA or name C or name O or name CB or name CG1 or name CG2)) or (resi \ d 55 and (name N or name CA or name C or name O or name CB or name CG or name CD \ 1 or name CD2 or name CE1 or name CE2 or name CZ or name OH )) or (resid 56 and \ (name N or name CA or name C or name O or name CB )) or (resid 57 and (name N or \ name CA or name C or name O or name CB or name CG or name CD or name OE1 or nam \ e NE2)) or resid 58 or (resid 59 and (name N or name CA or name C or name O or n \ ame CB or name CG or name OD1 or name ND2)) or (resid 60 and (name N or name CA \ or name C or name O or name CB )) or (resid 61 and (name N or name CA or name C \ or name O or name CB or name CG or name OD1 or name OD2)) or (resid 62 and (name \ N or name CA or name C or name O or name CB or name CG or name CD1 or name CD2 \ or name NE1 or name CE2 or name CE3 or name CZ2 or name CZ3 or name CH2)) or (re \ sid 63 and (name N or name CA or name C or name O or name CB or name CG1 or name \ CG2 or name CD1)) or (resid 64 and (name N or name CA or name C or name O or na \ me CB )) or (resid 65 through 66 and (name N or name CA or name C or name O )) o \ r (resid 67 and (name N or name CA or name C or name O or name CB or name CG or \ name CD1 or name CD2)) or (resid 68 and (name N or name CA or name C or name O o \ r name CB or name CG or name OD1 or name OD2)) or (resid 69 and (name N or name \ CA or name C or name O or name CB or name CG or name CD1 or name CD2 or name NE1 \ or name CE2 or name CE3 or name CZ2 or name CZ3 or name CH2)) or (resid 70 and \ (name N or name CA or name C or name O )) or (resid 71 and (name N or name CA or \ name C or name O or name CB or name CG or name OD1 or name OD2)) or (resid 72 a \ nd (name N or name CA or name C or name O or name CB or name CG or name CD1 or n \ ame CD2 or name NE1 or name CE2 or name CE3 or name CZ2 or name CZ3 or name CH2) \ ) or (resid 73 and (name N or name CA or name C or name O or name CB or name OG1 \ or name CG2)) or (resid 74 and (name N or name CA or name C or name O or name C \ B or name CG or name CD or name OE1 or name NE2)) or (resid 75 and (name N or na \ me CA or name C or name O or name CB or name CG or name CD or name CE or name NZ \ )) or (resid 76 and (name N or name CA or name C or name O or name CB or name C \ G or name CD1 or name CD2 or name CE1 or name CE2 or name CZ )) or (resid 77 and \ (name N or name CA or name C or name O or name CB or name CG or name ND1 or nam \ e CD2 or name CE1 or name NE2)) or (resid 78 through 79 and (name N or name CA o \ r name C or name O )) or (resid 80 and (name N or name CA or name C or name O or \ name CB or name CG or name CD or name NE or name CZ or name NH1 or name NH2)) o \ r resid 81 or (resid 82 and (name N or name CA or name C or name O or name CB or \ name OG )) or (resid 83 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD1 or name CD2 or name NE1 or name CE2 or name CE3 or name CZ \ 2 or name CZ3 or name CH2)) or (resid 84 and (name N or name CA or name C or nam \ e O )) or (resid 85 and (name N or name CA or name C or name O or name CB or nam \ e CG or name OD1 or name ND2)) or (resid 86 and (name N or name CA or name C or \ name O or name CB or name CG or name CD or name OE1 or name OE2)) or (resid 87 t \ hrough 88 and (name N or name CA or name C or name O or name CB or name OG1 or n \ ame CG2)) or (resid 89 and (name N or name CA or name C or name O or name CB or \ name CG or name CD or name OE1 or name OE2)) or (resid 90 and (name N or name CA \ or name C or name O or name CB or name CG or name CD1 or name CD2)) or (resid 9 \ 1 and (name N or name CA or name C or name O or name CB or name CG or name CD or \ name NE or name CZ or name NH1 or name NH2)) or (resid 92 and (name N or name C \ A or name C or name O or name CB or name OG1 or name CG2)) or (resid 93 and (nam \ e N or name CA or name C or name O or name CB or name CG1 or name CG2)) or (resi \ d 94 and (name N or name CA or name C or name O or name CB or name CG or name OD \ 1 or name OD2)) or (resid 95 and (name N or name CA or name C or name O or name \ CB or name CG or name CD1 or name CD2 or name NE1 or name CE2 or name CE3 or nam \ e CZ2 or name CZ3 or name CH2)) or (resid 96 and (name N or name CA or name C or \ name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or \ name CZ )) or (resid 97 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD or name CE or name NZ )) or (resid 98 and (name N or name C \ A or name C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 \ or name NE2)) or (resid 99 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name NE or name CZ or name NH1 or name NH2)) or (resid \ 100 and (name N or name CA or name C or name O or name CB or name CG or name OD \ 1 or name OD2)) or resid 101 or (resid 102 and (name N or name CA or name C or n \ ame O or name CB or name CG or name CD1 or name CD2)) or (resid 103 through 104 \ and (name N or name CA or name C or name O or name CB or name CG or name CD or n \ ame NE or name CZ or name NH1 or name NH2)) or (resid 105 and (name N or name CA \ or name C or name O or name CB or name CG or name CD1 or name CD2 or name NE1 o \ r name CE2 or name CE3 or name CZ2 or name CZ3 or name CH2)) or (resid 106 and ( \ name N or name CA or name C or name O or name CB or name CG or name ND1 or name \ CD2 or name CE1 or name NE2)) or (resid 107 and (name N or name CA or name C or \ name O or name CB )) or resid 108 or (resid 109 and (name N or name CA or name C \ or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 \ or name CZ or name OH )) or (resid 110 and (name N or name CA or name C or name \ O or name CB or name CG1 or name CG2)) or (resid 111 and (name N or name CA or \ name C or name O or name CB or name CG or name CD or name CE or name NZ )) or (r \ esid 112 and (name N or name CA or name C or name O or name CB or name CG or nam \ e OD1 or name OD2)) or (resid 113 and (name N or name CA or name C or name O or \ name CB or name CG or name CD or name CE or name NZ )) or (resid 114 and (name N \ or name CA or name C or name O or name CB )) or (resid 115 through 116 and (nam \ e N or name CA or name C or name O or name CB or name CG or name CD or name OE1 \ or name OE2)) or (resid 117 and (name N or name CA or name C or name O or name C \ B or name CG or name CD1 or name CD2 or name NE1 or name CE2 or name CE3 or name \ CZ2 or name CZ3 or name CH2)) or (resid 118 and (name N or name CA or name C or \ name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or na \ me NH2)) or (resid 119 and (name N or name CA or name C or name O or name CB or \ name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name OH )) \ or (resid 120 and (name N or name CA or name C or name O or name CB or name OG1 \ or name CG2)) or (resid 121 and (name N or name CA or name C or name O or name \ CB or name CG or name OD1 or name OD2)) or (resid 122 and (name N or name CA or \ name C or name O or name CB or name CG or name CD or name NE or name CZ or name \ NH1 or name NH2)) or (resid 123 and (name N or name CA or name C or name O or na \ me CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ )) o \ r (resid 124 and (name N or name CA or name C or name O or name CB or name CG or \ name CD1 or name CD2)) or (resid 125 and (name N or name CA or name C or name O \ or name CB or name CG or name CD or name OE1 or name NE2)) or (resid 126 and (n \ ame N or name CA or name C or name O )) or (resid 127 and (name N or name CA or \ name C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or na \ me CE2 or name CZ or name OH )) or (resid 128 and (name N or name CA or name C o \ r name O or name CB or name OG )) or (resid 129 and (name N or name CA or name C \ or name O or name CB )) or (resid 130 and (name N or name CA or name C or name \ O or name CB or name CG or name OD1 or name OD2)) or (resid 131 and (name N or n \ ame CA or name C or name O )) or (resid 132 and (name N or name CA or name C or \ name O or name CB or name CG or name CD or name OE1 or name NE2)) or (resid 133 \ and (name N or name CA or name C or name O or name CB or name CG1 or name CG2 or \ name CD1)) or (resid 134 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name NE or name CZ or name NH1 or name NH2)) or (resid \ 135 and (name N or name CA or name C or name O or name CB )) or (resid 136 and ( \ name N or name CA or name C or name O or name CB or name CG or name SD or name C \ E )) or (resid 137 and (name N or name CA or name C or name O or name CB or name \ CG or name OD1 or name ND2)) or resid 138 or (resid 139 and (name N or name CA \ or name C or name O or name CB or name OG1 or name CG2)) or (resid 140 and (name \ N or name CA or name C or name O or name CB or name CG or name CD1 or name CD2 \ or name NE1 or name CE2 or name CE3 or name CZ2 or name CZ3 or name CH2)) or (re \ sid 141 and (name N or name CA or name C or name O or name CB or name CG or name \ CD or name NE or name CZ or name NH1 or name NH2)) or (resid 142 and (name N or \ name CA or name C or name O or name CB or name CG or name OD1 or name OD2)) or \ (resid 143 and (name N or name CA or name C or name O or name CB or name CG or n \ ame CD or name OE1 or name OE2)) or (resid 144 and (name N or name CA or name C \ or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 \ or name CZ )) or (resid 145 and (name N or name CA or name C or name O or name C \ B or name CG1 or name CG2 or name CD1)) or (resid 146 and (name N or name CA or \ name C or name O or name CB or name CG or name OD1 or name ND2)) or (resid 147 a \ nd (name N or name CA or name C or name O or name CB or name CG or name CD or na \ me NE or name CZ or name NH1 or name NH2)) or (resid 148 and (name N or name CA \ or name C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or \ name CE2 or name CZ or name OH )) or (resid 149 and (name N or name CA or name \ C or name O or name CB or name CG or name CD1 or name CD2 or name NE1 or name CE \ 2 or name CE3 or name CZ2 or name CZ3 or name CH2)) or (resid 150 and (name N or \ name CA or name C or name O )) or (resid 151 and (name N or name CA or name C o \ r name O or name CB )) or (resid 152 and (name N or name CA or name C or name O \ or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ \ )) or (resid 153 and (name N or name CA or name C or name O or name CB or name \ CG or name CD1 or name CD2)) or (resid 154 and (name N or name CA or name C or n \ ame O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or n \ ame CZ )) or (resid 155 and (name N or name CA or name C or name O or name CB or \ name CG or name OD1 or name ND2)) or (resid 156 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name OE1 or name OE2)) or (resid \ 157 and (name N or name CA or name C or name O or name CB or name CG or name CD \ 1 or name CD2 or name CE1 or name CE2 or name CZ or name OH )) or (resid 158 and \ (name N or name CA or name C or name O )) or (resid 159 and (name N or name CA \ or name C or name O or name CB or name CG or name CD1 or name CD2)) or (resid 16 \ 0 and (name N or name CA or name C or name O or name CB or name CG or name CD1 o \ r name CD2 or name CE1 or name CE2 or name CZ )) or (resid 161 and (name N or na \ me CA or name C or name O or name CB or name CG or name OD1 or name ND2)) or (re \ sid 162 and (name N or name CA or name C or name O or name CB )) or (resid 163 a \ nd (name N or name CA or name C or name O or name CB or name CG or name ND1 or n \ ame CD2 or name CE1 or name NE2)) or (resid 164 and (name N or name CA or name C \ or name O or name CB or name OG )) or (resid 165 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name OE1 or name NE2)) or (resi \ d 166 and (name N or name CA or name C or name O )) or (resid 167 and (name N or \ name CA or name C or name O or name CB )) or (resid 168 and (name N or name CA \ or name C or name O or name CB or name CG or name CD or name NE or name CZ or na \ me NH1 or name NH2)) or (resid 169 and (name N or name CA or name C or name O or \ name CB or name CG or name CD or name OE1 or name OE2)) or (resid 170 and (name \ N or name CA or name C or name O or name CB )) or (resid 171 and (name N or nam \ e CA or name C or name O or name CB or name CG or name CD1 or name CD2)) or (res \ id 172 and (name N or name CA or name C or name O or name CB or name OG )) or (r \ esid 173 and (name N or name CA or name C or name O or name CB or name CG or nam \ e OD1 or name OD2)) or (resid 174 and (name N or name CA or name C or name O or \ name CB or name CG1 or name CG2)) or (resid 175 and (name N or name CA or name C \ or name O or name CB or name OG1 or name CG2)) or (resid 176 and (name N or nam \ e CA or name C or name O or name CB or name CG or name CD or name NE or name CZ \ or name NH1 or name NH2)) or (resid 177 and (name N or name CA or name C or name \ O or name CB or name CG1 or name CG2)) or (resid 178 and (name N or name CA or \ name C or name O or name CB or name OG )) or (resid 179 and (name N or name CA o \ r name C or name O or name CB or name CG or name CD1 or name CD2)) or (resid 180 \ and (name N or name CA or name C or name O or name CB )) or (resid 181 and (nam \ e N or name CA or name C or name O or name CB or name CG or name CD1 or name CD2 \ or name CE1 or name CE2 or name CZ )) or (resid 182 and (name N or name CA or n \ ame C or name O or name CB or name CG or name CD1 or name CD2 or name NE1 or nam \ e CE2 or name CE3 or name CZ2 or name CZ3 or name CH2)) or (resid 183 and (name \ N or name CA or name C or name O )) or (resid 184 and (name N or name CA or name \ C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name C \ E2 or name CZ )) or (resid 185 and (name N or name CA or name C or name O or nam \ e CB or name CG or name OD1 or name OD2)) or (resid 186 and (name N or name CA o \ r name C or name O or name CB or name CG or name CD or name CE or name NZ )) or \ (resid 187 and (name N or name CA or name C or name O or name CB or name CG1 or \ name CG2 or name CD1)) or (resid 188 and (name N or name CA or name C or name O \ or name CB or name CG or name OD1 or name OD2)) or (resid 189 and (name N or nam \ e CA or name C or name O or name CB or name CG1 or name CG2 or name CD1)) or (re \ sid 190 and (name N or name CA or name C or name O or name CB )) or (resid 191 a \ nd (name N or name CA or name C or name O or name CB or name CG or name CD or na \ me OE1 or name NE2)) or (resid 192 and (name N or name CA or name C or name O or \ name CB or name CG or name SD or name CE )) or (resid 193 and (name N or name C \ A or name C or name O or name CB or name CG1 or name CG2 or name CD1)) or (resid \ 194 and (name N or name CA or name C or name O or name CB or name CG or name CD \ or name OE1 or name NE2)) or (resid 195 and (name N or name CA or name C or nam \ e O or name CB or name CG or name CD1 or name CD2)) or (resid 196 and (name N or \ name CA or name C or name O or name CB or name CG or name CD or name OE1 or nam \ e OE2)) or (resid 197 and (name N or name CA or name C or name O or name CB or n \ ame CG or name CD or name NE or name CZ or name NH1 or name NH2)) or (resid 198 \ and (name N or name CA or name C or name O )) or (resid 199 and (name N or name \ CA or name C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 \ or name CE2 or name CZ )) or (resid 200 and (name N or name CA or name C or nam \ e O or name CB or name CG or name CD1 or name CD2)) or (resid 201 and (name N or \ name CA or name C or name O or name CB )) or (resid 202 and (name N or name CA \ or name C or name O or name CB or name CG or name CD or name CE or name NZ )) or \ (resid 203 and (name N or name CA or name C or name O or name CB or name CG1 or \ name CG2 or name CD1)) or (resid 204 and (name N or name CA or name C or name O \ or name CB or name CG1 or name CG2)) or resid 205 or (resid 206 and (name N or \ name CA or name C or name O )) or (resid 207 and (name N or name CA or name C or \ name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or \ name CZ )) or (resid 208 and (name N or name CA or name C or name O or name CB \ or name CG or name OD1 or name OD2)) or (resid 209 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name OE1 or name OE2)) or (res \ id 210 and (name N or name CA or name C or name O or name CB or name OG )) or (r \ esid 211 and (name N or name CA or name C or name O or name CB or name OG1 or na \ me CG2)) or (resid 212 and (name N or name CA or name C or name O or name CB )) \ or (resid 213 and (name N or name CA or name C or name O or name CB or name CG1 \ or name CG2)) or resid 214 or (resid 215 and (name N or name CA or name C or nam \ e O or name CB or name CG or name CD or name CE or name NZ )) or (resid 216 and \ (name N or name CA or name C or name O or name CB )) or (resid 217 and (name N o \ r name CA or name C or name O or name CB or name CG or name CD or name OE1 or na \ me OE2)) or (resid 218 and (name N or name CA or name C or name O or name CB or \ name CG or name CD1 or name CD2 or name NE1 or name CE2 or name CE3 or name CZ2 \ or name CZ3 or name CH2)) or (resid 219 and (name N or name CA or name C or name \ O or name CB or name OG1 or name CG2)) or (resid 220 and (name N or name CA or \ name C or name O or name CB or name CG or name OD1 or name ND2)) or (resid 221 a \ nd (name N or name CA or name C or name O )) or (resid 222 and (name N or name C \ A or name C or name O or name CB or name CG or name CD or name OE1 or name OE2)) \ or (resid 223 and (name N or name CA or name C or name O or name CB or name CG1 \ or name CG2)) or (resid 224 and (name N or name CA or name C or name O or name \ CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name \ OH )) or (resid 225 and (name N or name CA or name C or name O or name CB or na \ me CG or name CD or name CE or name NZ )) or (resid 226 and (name N or name CA o \ r name C or name O or name CB or name OG )) or (resid 227 and (name N or name CA \ or name C or name O or name CB )) or (resid 228 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 o \ r name NH2)) or (resid 229 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2)) or (resid 230 and (name N or name CA or na \ me C or name O or name CB )) or (resid 231 and (name N or name CA or name C or n \ ame O or name CB or name CG1 or name CG2)) or (resid 232 and (name N or name CA \ or name C or name O or name CB or name CG or name CD or name OE1 or name OE2)) o \ r (resid 233 and (name N or name CA or name C or name O )) or (resid 234 and (na \ me N or name CA or name C or name O or name CB or name CG or name CD1 or name CD \ 2)) or (resid 235 and (name N or name CA or name C or name O or name CB or name \ CG or name CD1 or name CD2 or name NE1 or name CE2 or name CE3 or name CZ2 or na \ me CZ3 or name CH2)) or (resid 236 and (name N or name CA or name C or name O or \ name CB or name CG or name CD or name OE1 or name NE2)) or (resid 237 and (name \ N or name CA or name C or name O or name CB or name CG or name CD or name OE1 o \ r name OE2)) or (resid 238 and (name N or name CA or name C or name O or name CB \ or name CG1 or name CG2)) or (resid 239 and (name N or name CA or name C or nam \ e O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or nam \ e CZ )) or (resid 240 and (name N or name CA or name C or name O or name CB or n \ ame CG or name OD1 or name OD2)) or (resid 241 and (name N or name CA or name C \ or name O or name CB or name CG or name CD1 or name CD2 or name NE1 or name CE2 \ or name CE3 or name CZ2 or name CZ3 or name CH2)) or (resid 242 and (name N or n \ ame CA or name C or name O or name CB or name CG or name OD1 or name ND2)) or (r \ esid 243 and (name N or name CA or name C or name O or name CB or name CG or nam \ e CD or name OE1 or name OE2)) or (resid 244 and (name N or name CA or name C or \ name O or name CB or name OG )) or (resid 245 and (name N or name CA or name C \ or name O or name CB )) or (resid 246 and (name N or name CA or name C or name O \ or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name C \ Z )) or (resid 247 and (name N or name CA or name C or name O or name CB or name \ OG )) or (resid 248 and (name N or name CA or name C or name O or name CB or na \ me CG1 or name CG2)) or (resid 249 and (name N or name CA or name C or name O or \ name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2)) or (resid \ 250 and (name N or name CA or name C or name O or name CB )) or (resid 251 and ( \ name N or name CA or name C or name O or name CB or name CG1 or name CG2)) or (r \ esid 252 and (name N or name CA or name C or name O or name CB or name CG or nam \ e CD1 or name CD2 or name CE1 or name CE2 or name CZ or name OH )) or (resid 253 \ and (name N or name CA or name C or name O or name CB or name CG or name OD1 or \ name OD2)) or (resid 254 and (name N or name CA or name C or name O or name CB \ )) or (resid 255 and (name N or name CA or name C or name O or name CB or name C \ G or name CD1 or name CD2)) or (resid 256 and (name N or name CA or name C or na \ me O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or na \ me CZ )) or (resid 257 and (name N or name CA or name C or name O )) or (resid 2 \ 58 and (name N or name CA or name C or name O or name CB or name CG or name CD o \ r name OE1 or name NE2)) or (resid 259 and (name N or name CA or name C or name \ O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name \ CZ )) or (resid 260 and (name N or name CA or name C or name O or name CB or nam \ e CG1 or name CG2)) or (resid 261 through 262 and (name N or name CA or name C o \ r name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or n \ ame NH2)) or (resid 263 and (name N or name CA or name C or name O or name CB or \ name CG or name CD or name OE1 or name OE2)) or (resid 264 through 265 and (nam \ e N or name CA or name C or name O or name CB or name CG or name CD1 or name CD2 \ or name CE1 or name CE2 or name CZ )) or (resid 266 and (name N or name CA or n \ ame C or name O or name CB or name CG or name CD or name OE1 or name NE2)) or (r \ esid 267 and (name N or name CA or name C or name O or name CB or name CG or nam \ e CD or name NE or name CZ or name NH1 or name NH2)) or (resid 268 and (name N o \ r name CA or name C or name O or name CB or name CG or name CD1 or name CD2)) or \ (resid 269 and (name N or name CA or name C or name O or name CB )) or resid 27 \ 0 or (resid 271 and (name N or name CA or name C or name O or name CB or name CG \ or name CD or name NE or name CZ or name NH1 or name NH2)) or (resid 272 and (n \ ame N or name CA or name C or name O or name CB or name CG or name CD1 or name C \ D2 or name CE1 or name CE2 or name CZ )) or (resid 273 and (name N or name CA or \ name C or name O )) or (resid 274 and (name N or name CA or name C or name O or \ name CB or name CG or name OD1 or name OD2)) or (resid 275 and (name N or name \ CA or name C or name O or name CB or name CG or name OD1 or name ND2)) or (resid \ 276 and (name N or name CA or name C or name O or name CB or name CG or name CD \ 1 or name CD2)) or (resid 277 and (name N or name CA or name C or name O or name \ CB or name OG1 or name CG2)) or resid 278 or (resid 279 through 280 and (name N \ or name CA or name C or name O or name CB or name CG or name CD1 or name CD2 or \ name CE1 or name CE2 or name CZ )) or (resid 281 and (name N or name CA or name \ C or name O or name CB or name CG1 or name CG2 or name CD1)) or (resid 282 and \ (name N or name CA or name C or name O or name CB or name CG or name OD1 or name \ ND2)) or (resid 283 and (name N or name CA or name C or name O or name CB or na \ me CG or name CD or name OE1 or name NE2)) or (resid 284 and (name N or name CA \ or name C or name O or name CB )) or (resid 285 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name OE1 or name NE2)) or (resid \ 286 and (name N or name CA or name C or name O or name CB or name OG1 or name CG \ 2)) or (resid 287 and (name N or name CA or name C or name O or name CB or name \ CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name OH )) or ( \ resid 288 and (name N or name CA or name C or name O or name CB or name CG or na \ me CD1 or name CD2 or name CE1 or name CE2 or name CZ )) or (resid 289 and (name \ N or name CA or name C or name O or name CB or name CG or name CD or name OE1 o \ r name NE2)) or (resid 290 and (name N or name CA or name C or name O or name CB \ or name CG1 or name CG2 or name CD1)) or (resid 291 and (name N or name CA or n \ ame C or name O or name CB )) or (resid 292 and (name N or name CA or name C or \ name O or name CB or name CG or name CD or name CE or name NZ )) or (resid 293 a \ nd (name N or name CA or name C or name O or name CB or name CG or name CD or na \ me OE1 or name NE2)) or (resid 294 and (name N or name CA or name C or name O )) \ or (resid 295 and (name N or name CA or name C or name O or name CB or name CG1 \ or name CG2)) or (resid 296 and (name N or name CA or name C or name O or name \ CB or name CG or name CD or name OE1 or name NE2)) or (resid 297 and (name N or \ name CA or name C or name O or name CB or name CG or name OD1 or name OD2)) or ( \ resid 298 and (name N or name CA or name C or name O or name CB or name CG or na \ me CD1 or name CD2)) or (resid 299 through 300 and (name N or name CA or name C \ or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 \ or name CZ or name OH )) or (resid 301 and (name N or name CA or name C or name \ O or name CB or name CG or name OD1 or name ND2)) or (resid 302 and (name N or n \ ame CA or name C or name O or name CB or name SG )) or (resid 303 and (name N or \ name CA or name C or name O or name CB or name CG or name CD1 or name CD2)) or \ (resid 304 and (name N or name CA or name C or name O )) or (resid 305 through 3 \ 06 and (name N or name CA or name C or name O or name CB or name CG or name OD1 \ or name OD2)) or resid 307 or (resid 308 and (name N or name CA or name C or nam \ e O or name CB or name CG or name CD or name OE1 or name OE2)) or (resid 309 and \ (name N or name CA or name C or name O or name CB or name CG or name CD1 or nam \ e CD2 or name CE1 or name CE2 or name CZ )) or (resid 310 and (name N or name CA \ or name C or name O or name CB or name OG )) or (resid 311 and (name N or name \ CA or name C or name O or name CB or name CG or name OD1 or name OD2)) or (resid \ 312 and (name N or name CA or name C or name O or name CB or name CG or name CD \ 1 or name CD2 or name CE1 or name CE2 or name CZ or name OH )) or (resid 313 and \ (name N or name CA or name C or name O or name CB or name CG or name OD1 or nam \ e ND2)) or (resid 314 and (name N or name CA or name C or name O or name CB or n \ ame CG or name CD or name NE or name CZ or name NH1 or name NH2)) or (resid 315 \ and (name N or name CA or name C or name O or name CB or name OG1 or name CG2)) \ or (resid 316 and (name N or name CA or name C or name O or name CB or name CG1 \ or name CG2)) or (resid 317 and (name N or name CA or name C or name O or name C \ B or name CG or name SD or name CE )) or (resid 318 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name NE or name CZ or name NH \ 1 or name NH2)) or (resid 319 and (name N or name CA or name C or name O or name \ CB or name CG or name OD1 or name ND2)) or (resid 320 and (name N or name CA or \ name C or name O or name CB or name CG or name CD1 or name CD2 or name NE1 or n \ ame CE2 or name CE3 or name CZ2 or name CZ3 or name CH2)) or (resid 321 and (nam \ e N or name CA or name C or name O or name CB or name OG1 or name CG2)) or (resi \ d 322 and (name N or name CA or name C or name O )) or (resid 323 and (name N or \ name CA or name C or name O or name CB or name CG or name CD or name CE or name \ NZ )) or (resid 324 and (name N or name CA or name C or name O or name CB or na \ me CG or name CD1 or name CD2 or name NE1 or name CE2 or name CE3 or name CZ2 or \ name CZ3 or name CH2)) or (resid 325 and (name N or name CA or name C or name O \ or name CB or name CG or name CD1 or name CD2)) or (resid 326 and (name N or na \ me CA or name C or name O or name CB or name CG or name CD or name OE1 or name O \ E2)) or resid 327 or (resid 328 and (name N or name CA or name C or name O or na \ me CB or name OG1 or name CG2)) or (resid 329 and (name N or name CA or name C o \ r name O or name CB or name CG1 or name CG2 or name CD1)) or (resid 330 through \ 331 and (name N or name CA or name C or name O or name CB )) or (resid 332 and ( \ name N or name CA or name C or name O or name CB or name CG or name CD1 or name \ CD2)) or (resid 333 and (name N or name CA or name C or name O or name CB or nam \ e CG or name CD or name NE or name CZ or name NH1 or name NH2)) or (resid 334 an \ d (name N or name CA or name C or name O or name CB or name CG or name OD1 or na \ me OD2)) or (resid 335 and (name N or name CA or name C or name O or name CB or \ name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ )) or (resid \ 336 and (name N or name CA or name C or name O or name CB or name CG or name SD \ or name CE )) or (resid 337 and (name N or name CA or name C or name O )) or (re \ sid 338 and (name N or name CA or name C or name O or name CB or name CG or name \ CD1 or name CD2)) or (resid 339 and (name N or name CA or name C or name O or n \ ame CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ )) \ or (resid 340 and (name N or name CA or name C or name O or name CB )) or (resid \ 341 and (name N or name CA or name C or name O or name CB or name CG or name CD \ or name CE or name NZ )) or (resid 342 and (name N or name CA or name C or name \ O or name CB or name CG or name CD1 or name CD2)) or resid 343 or (resid 344 an \ d (name N or name CA or name C or name O or name CB )) or (resid 345 and (name N \ or name CA or name C or name O )) or (resid 346 through 347 and (name N or name \ CA or name C or name O or name CB or name OG1 or name CG2)) or (resid 348 and ( \ name N or name CA or name C or name O or name CB or name CG or name OD1 or name \ OD2)) or (resid 349 and (name N or name CA or name C or name O or name CB or nam \ e CG or name CD or name CE or name NZ )) or (resid 350 through 351 and (name N o \ r name CA or name C or name O or name CB or name CG or name CD or name OE1 or na \ me OE2)) or (resid 352 and (name N or name CA or name C or name O or name CB or \ name CG1 or name CG2 or name CD1)) or (resid 353 and (name N or name CA or name \ C or name O or name CB or name OG1 or name CG2)) or (resid 354 and (name N or na \ me CA or name C or name O or name CB )) or (resid 355 and (name N or name CA or \ name C or name O or name CB or name OG )) or (resid 356 and (name N or name CA o \ r name C or name O or name CB or name CG or name CD1 or name CD2)) or (resid 357 \ and (name N or name CA or name C or name O or name CB or name CG or name CD1 or \ name CD2 or name CE1 or name CE2 or name CZ or name OH )) or (resid 358 and (na \ me N or name CA or name C or name O or name CB or name CG or name CD or name NE \ or name CZ or name NH1 or name NH2)) or (resid 359 through 360 and (name N or na \ me CA or name C or name O or name CB or name CG1 or name CG2)) or (resid 361 thr \ ough 362 and (name N or name CA or name C or name O or name CB or name CG or nam \ e OD1 or name OD2)) or (resid 363 and (name N or name CA or name C or name O or \ name CB or name CG or name CD1 or name CD2 or name NE1 or name CE2 or name CE3 o \ r name CZ2 or name CZ3 or name CH2)) or (resid 364 and (name N or name CA or nam \ e C or name O or name CB or name CG1 or name CG2 or name CD1)) or (resid 365 and \ (name N or name CA or name C or name O or name CB or name CG or name CD or name \ OE1 or name OE2)) or (resid 366 and (name N or name CA or name C or name O or n \ ame CB or name CG or name OD1 or name OD2)) or (resid 367 and (name N or name CA \ or name C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 o \ r name CE2 or name CZ or name OH )) or (resid 368 and (name N or name CA or name \ C or name O or name CB )) or (resid 369 and (name N or name CA or name C or nam \ e O or name CB or name OG )) or (resid 370 and (name N or name CA or name C or n \ ame O or name CB or name CG or name CD or name NE or name CZ or name NH1 or name \ NH2)) or (resid 371 and (name N or name CA or name C or name O or name CB or na \ me CG1 or name CG2 or name CD1)) or (resid 372 and (name N or name CA or name C \ or name O or name CB or name CG or name OD1 or name OD2)) or (resid 373 and (nam \ e N or name CA or name C or name O or name CB or name CG or name CD1 or name CD2 \ or name CE1 or name CE2 or name CZ )) or (resid 374 and (name N or name CA or n \ ame C or name O or name CB or name CG or name CD or name CE or name NZ )) or (re \ sid 375 and (name N or name CA or name C or name O or name CB )) or (resid 376 a \ nd (name N or name CA or name C or name O or name CB or name CG or name OD1 or n \ ame OD2)) or (resid 377 and (name N or name CA or name C or name O or name CB or \ name CG or name CD or name NE or name CZ or name NH1 or name NH2)) or (resid 37 \ 8 and (name N or name CA or name C or name O or name CB or name CG or name OD1 o \ r name OD2)) or (resid 379 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name OE1 or name NE2)) or (resid 380 and (name N or na \ me CA or name C or name O or name CB or name CG1 or name CG2 or name CD1)) or (r \ esid 381 and (name N or name CA or name C or name O or name CB or name CG1 or na \ me CG2)) or (resid 382 and (name N or name CA or name C or name O or name CB or \ name CG or name CD or name CE or name NZ )) or (resid 383 and (name N or name CA \ or name C or name O or name CB )) or (resid 384 and (name N or name CA or name \ C or name O or name CB or name CG1 or name CG2)) or (resid 385 and (name N or na \ me CA or name C or name O or name CB or name CG or name CD1 or name CD2)) or (re \ sid 386 and (name N or name CA or name C or name O or name CB )) or (resid 387 a \ nd (name N or name CA or name C or name O )) or (resid 388 and (name N or name C \ A or name C or name O or name CB or name CG or name CD1 or name CD2)) or (resid \ 389 and (name N or name CA or name C or name O or name CB or name CG or name CD \ or name CE or name NZ or name OXT)))) } ncs_group { reference = chain 'D' selection = (chain 'E' and (resid 17 through 526 or resid 601 through 602)) } ncs_group { reference = chain 'G' selection = chain 'H' } 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: 1.170 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: 0.470 Extract box with map and model: 0.790 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 44.280 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.080 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:13.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.172 17861 Z= 0.396 Angle : 0.582 15.550 24231 Z= 0.339 Chirality : 0.045 0.535 2461 Planarity : 0.005 0.058 3153 Dihedral : 13.888 88.687 6469 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.17 % Allowed : 0.17 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.19), residues: 2101 helix: 1.07 (0.14), residues: 1337 sheet: 1.86 (0.87), residues: 44 loop : -0.00 (0.24), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP E 125 HIS 0.008 0.001 HIS G 111 PHE 0.040 0.002 PHE E 188 TYR 0.037 0.002 TYR E 310 ARG 0.019 0.001 ARG E 307 Details of bonding type rmsd hydrogen bonds : bond 0.13061 ( 993) hydrogen bonds : angle 6.32667 ( 2883) covalent geometry : bond 0.00711 (17861) covalent geometry : angle 0.58219 (24231) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 19 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue VAL 23 is missing expected H atoms. Skipping. Residue ALA 25 is missing expected H atoms. Skipping. Residue VAL 28 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue THR 44 is missing expected H atoms. Skipping. Residue ALA 47 is missing expected H atoms. Skipping. Residue THR 48 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ALA 53 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue ALA 64 is missing expected H atoms. Skipping. Residue ALA 68 is missing expected H atoms. Skipping. Residue MET 70 is missing expected H atoms. Skipping. Residue ALA 72 is missing expected H atoms. Skipping. Residue VAL 73 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue ALA 85 is missing expected H atoms. Skipping. Residue LEU 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue ALA 91 is missing expected H atoms. Skipping. Residue VAL 93 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue THR 102 is missing expected H atoms. Skipping. Residue MET 103 is missing expected H atoms. Skipping. Residue VAL 105 is missing expected H atoms. Skipping. Residue VAL 106 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue VAL 112 is missing expected H atoms. Skipping. Residue ALA 117 is missing expected H atoms. Skipping. Residue ILE 118 is missing expected H atoms. Skipping. Residue ALA 119 is missing expected H atoms. Skipping. Residue ALA 120 is missing expected H atoms. Skipping. Residue THR 121 is missing expected H atoms. Skipping. Residue MET 123 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Residue ALA 128 is missing expected H atoms. Skipping. Residue ALA 130 is missing expected H atoms. Skipping. Residue ALA 131 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue ALA 139 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue THR 148 is missing expected H atoms. Skipping. Residue ALA 152 is missing expected H atoms. Skipping. Residue VAL 154 is missing expected H atoms. Skipping. Residue ALA 159 is missing expected H atoms. Skipping. Residue ALA 166 is missing expected H atoms. Skipping. Residue ALA 171 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue ILE 177 is missing expected H atoms. Skipping. Residue LEU 180 is missing expected H atoms. Skipping. Residue MET 184 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue ILE 193 is missing expected H atoms. Skipping. Residue ALA 197 is missing expected H atoms. Skipping. Residue VAL 198 is missing expected H atoms. Skipping. Residue LEU 202 is missing expected H atoms. Skipping. Residue LEU 204 is missing expected H atoms. Skipping. Residue LEU 206 is missing expected H atoms. Skipping. Residue VAL 207 is missing expected H atoms. Skipping. Residue ALA 210 is missing expected H atoms. Skipping. Residue THR 213 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue ILE 217 is missing expected H atoms. Skipping. Residue VAL 218 is missing expected H atoms. Skipping. Residue ALA 219 is missing expected H atoms. Skipping. Residue VAL 220 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue ALA 224 is missing expected H atoms. Skipping. Residue ALA 225 is missing expected H atoms. Skipping. Residue ALA 226 is missing expected H atoms. Skipping. Residue ILE 231 is missing expected H atoms. Skipping. Residue THR 232 is missing expected H atoms. Skipping. Residue THR 234 is missing expected H atoms. Skipping. Residue VAL 235 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue ILE 239 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LEU 244 is missing expected H atoms. Skipping. Residue MET 247 is missing expected H atoms. Skipping. Residue ALA 248 is missing expected H atoms. Skipping. Residue THR 253 is missing expected H atoms. Skipping. Residue VAL 254 is missing expected H atoms. Skipping. Residue VAL 255 is missing expected H atoms. Skipping. Residue ILE 257 is missing expected H atoms. Skipping. Residue ALA 258 is missing expected H atoms. Skipping. Residue ALA 262 is missing expected H atoms. Skipping. Residue ALA 264 is missing expected H atoms. Skipping. Residue LEU 267 is missing expected H atoms. Skipping. Residue THR 269 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue ALA 274 is missing expected H atoms. Skipping. Residue THR 277 is missing expected H atoms. Skipping. Residue THR 283 is missing expected H atoms. Skipping. Residue VAL 285 is missing expected H atoms. Skipping. Residue LEU 286 is missing expected H atoms. Skipping. Residue MET 288 is missing expected H atoms. Skipping. Residue LEU 289 is missing expected H atoms. Skipping. Residue VAL 298 is missing expected H atoms. Skipping. Residue VAL 302 is missing expected H atoms. Skipping. Residue THR 304 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Residue ILE 316 is missing expected H atoms. Skipping. Residue ILE 318 is missing expected H atoms. Skipping. Residue LEU 321 is missing expected H atoms. Skipping. Residue VAL 326 is missing expected H atoms. Skipping. Residue LEU 332 is missing expected H atoms. Skipping. Residue ALA 335 is missing expected H atoms. Skipping. Residue ALA 339 is missing expected H atoms. Skipping. Residue ALA 342 is missing expected H atoms. Skipping. Residue LEU 346 is missing expected H atoms. Skipping. Residue LEU 348 is missing expected H atoms. Skipping. Residue LEU 349 is missing expected H atoms. Skipping. Residue ALA 350 is missing expected H atoms. Skipping. Residue ALA 352 is missing expected H atoms. Skipping. Residue LEU 353 is missing expected H atoms. Skipping. Residue THR 356 is missing expected H atoms. Skipping. Residue LEU 361 is missing expected H atoms. Skipping. Residue ALA 362 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue MET 369 is missing expected H atoms. Skipping. Residue ALA 374 is missing expected H atoms. Skipping. Residue ILE 386 is missing expected H atoms. Skipping. Residue ALA 392 is missing expected H atoms. Skipping. Residue ILE 403 is missing expected H atoms. Skipping. Residue LEU 405 is missing expected H atoms. Skipping. Residue MET 406 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 415 is missing expected H atoms. Skipping. Residue ILE 417 is missing expected H atoms. Skipping. Residue VAL 420 is missing expected H atoms. Skipping. Residue VAL 423 is missing expected H atoms. Skipping. Residue LEU 429 is missing expected H atoms. Skipping. Residue ALA 430 is missing expected H atoms. Skipping. Residue ALA 433 is missing expected H atoms. Skipping. Residue THR 435 is missing expected H atoms. Skipping. Residue LEU 436 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue MET 445 is missing expected H atoms. Skipping. Residue THR 447 is missing expected H atoms. Skipping. Residue MET 456 is missing expected H atoms. Skipping. Residue LEU 458 is missing expected H atoms. Skipping. Residue ALA 459 is missing expected H atoms. Skipping. Residue ILE 469 is missing expected H atoms. Skipping. Residue LEU 478 is missing expected H atoms. Skipping. Residue VAL 481 is missing expected H atoms. Skipping. Residue ILE 482 is missing expected H atoms. Skipping. Residue ALA 483 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue LEU 488 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue LEU 495 is missing expected H atoms. Skipping. Residue ILE 496 is missing expected H atoms. Skipping. Residue ALA 497 is missing expected H atoms. Skipping. Residue VAL 501 is missing expected H atoms. Skipping. Residue LEU 506 is missing expected H atoms. Skipping. Residue THR 508 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue LEU 515 is missing expected H atoms. Skipping. Residue VAL 518 is missing expected H atoms. Skipping. Residue VAL 523 is missing expected H atoms. Skipping. Residue ALA 525 is missing expected H atoms. Skipping. Residue ALA 16 is missing expected H atoms. Skipping. Residue ALA 19 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue VAL 23 is missing expected H atoms. Skipping. Residue ALA 25 is missing expected H atoms. Skipping. Residue VAL 28 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue THR 44 is missing expected H atoms. Skipping. Residue ALA 47 is missing expected H atoms. Skipping. Residue THR 48 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ALA 53 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue ALA 64 is missing expected H atoms. Skipping. Residue ALA 68 is missing expected H atoms. Skipping. Residue MET 70 is missing expected H atoms. Skipping. Residue ALA 72 is missing expected H atoms. Skipping. Residue VAL 73 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue ALA 85 is missing expected H atoms. Skipping. Residue LEU 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue ALA 91 is missing expected H atoms. Skipping. Residue VAL 93 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue THR 102 is missing expected H atoms. Skipping. Residue MET 103 is missing expected H atoms. Skipping. Residue VAL 105 is missing expected H atoms. Skipping. Residue VAL 106 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue VAL 112 is missing expected H atoms. Skipping. Residue ALA 117 is missing expected H atoms. Skipping. Residue ILE 118 is missing expected H atoms. Skipping. Residue ALA 119 is missing expected H atoms. Skipping. Residue ALA 120 is missing expected H atoms. Skipping. Residue THR 121 is missing expected H atoms. Skipping. Residue MET 123 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Residue ALA 128 is missing expected H atoms. Skipping. Residue ALA 130 is missing expected H atoms. Skipping. Residue ALA 131 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue ALA 139 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue THR 148 is missing expected H atoms. Skipping. Residue ALA 152 is missing expected H atoms. Skipping. Residue VAL 154 is missing expected H atoms. Skipping. Residue ALA 159 is missing expected H atoms. Skipping. Residue ALA 166 is missing expected H atoms. Skipping. Residue ALA 171 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue ILE 177 is missing expected H atoms. Skipping. Residue LEU 180 is missing expected H atoms. Skipping. Residue MET 184 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue ILE 193 is missing expected H atoms. Skipping. Residue ALA 197 is missing expected H atoms. Skipping. Residue VAL 198 is missing expected H atoms. Skipping. Residue LEU 202 is missing expected H atoms. Skipping. Residue LEU 204 is missing expected H atoms. Skipping. Residue LEU 206 is missing expected H atoms. Skipping. Residue VAL 207 is missing expected H atoms. Skipping. Residue ALA 210 is missing expected H atoms. Skipping. Residue THR 213 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue ILE 217 is missing expected H atoms. Skipping. Residue VAL 218 is missing expected H atoms. Skipping. Residue ALA 219 is missing expected H atoms. Skipping. Residue VAL 220 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue ALA 224 is missing expected H atoms. Skipping. Residue ALA 225 is missing expected H atoms. Skipping. Residue ALA 226 is missing expected H atoms. Skipping. Residue ILE 231 is missing expected H atoms. Skipping. Residue THR 232 is missing expected H atoms. Skipping. Residue THR 234 is missing expected H atoms. Skipping. Residue VAL 235 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue ILE 239 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LEU 244 is missing expected H atoms. Skipping. Residue MET 247 is missing expected H atoms. Skipping. Residue ALA 248 is missing expected H atoms. Skipping. Residue THR 253 is missing expected H atoms. Skipping. Residue VAL 254 is missing expected H atoms. Skipping. Residue VAL 255 is missing expected H atoms. Skipping. Residue ILE 257 is missing expected H atoms. Skipping. Residue ALA 258 is missing expected H atoms. Skipping. Residue ALA 262 is missing expected H atoms. Skipping. Residue ALA 264 is missing expected H atoms. Skipping. Residue LEU 267 is missing expected H atoms. Skipping. Residue THR 269 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue ALA 274 is missing expected H atoms. Skipping. Residue THR 277 is missing expected H atoms. Skipping. Residue THR 283 is missing expected H atoms. Skipping. Residue VAL 285 is missing expected H atoms. Skipping. Residue LEU 286 is missing expected H atoms. Skipping. Residue MET 288 is missing expected H atoms. Skipping. Residue LEU 289 is missing expected H atoms. Skipping. Residue VAL 298 is missing expected H atoms. Skipping. Residue VAL 302 is missing expected H atoms. Skipping. Residue THR 304 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Residue ILE 316 is missing expected H atoms. Skipping. Residue ILE 318 is missing expected H atoms. Skipping. Residue LEU 321 is missing expected H atoms. Skipping. Residue VAL 326 is missing expected H atoms. Skipping. Residue LEU 332 is missing expected H atoms. Skipping. Residue ALA 335 is missing expected H atoms. Skipping. Residue ALA 339 is missing expected H atoms. Skipping. Residue ALA 342 is missing expected H atoms. Skipping. Residue LEU 346 is missing expected H atoms. Skipping. Residue LEU 348 is missing expected H atoms. Skipping. Residue LEU 349 is missing expected H atoms. Skipping. Residue ALA 350 is missing expected H atoms. Skipping. Residue ALA 352 is missing expected H atoms. Skipping. Residue LEU 353 is missing expected H atoms. Skipping. Residue THR 356 is missing expected H atoms. Skipping. Residue LEU 361 is missing expected H atoms. Skipping. Residue ALA 362 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue MET 369 is missing expected H atoms. Skipping. Residue ALA 374 is missing expected H atoms. Skipping. Residue ILE 386 is missing expected H atoms. Skipping. Residue ALA 392 is missing expected H atoms. Skipping. Residue ILE 403 is missing expected H atoms. Skipping. Residue LEU 405 is missing expected H atoms. Skipping. Residue MET 406 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 415 is missing expected H atoms. Skipping. Residue ILE 417 is missing expected H atoms. Skipping. Residue VAL 420 is missing expected H atoms. Skipping. Residue VAL 423 is missing expected H atoms. Skipping. Residue LEU 429 is missing expected H atoms. Skipping. Residue ALA 430 is missing expected H atoms. Skipping. Residue ALA 433 is missing expected H atoms. Skipping. Residue THR 435 is missing expected H atoms. Skipping. Residue LEU 436 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue MET 445 is missing expected H atoms. Skipping. Residue THR 447 is missing expected H atoms. Skipping. Residue MET 456 is missing expected H atoms. Skipping. Residue LEU 458 is missing expected H atoms. Skipping. Residue ALA 459 is missing expected H atoms. Skipping. Residue ILE 469 is missing expected H atoms. Skipping. Residue LEU 478 is missing expected H atoms. Skipping. Residue VAL 481 is missing expected H atoms. Skipping. Residue ILE 482 is missing expected H atoms. Skipping. Residue ALA 483 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue LEU 488 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue LEU 495 is missing expected H atoms. Skipping. Residue ILE 496 is missing expected H atoms. Skipping. Residue ALA 497 is missing expected H atoms. Skipping. Residue VAL 501 is missing expected H atoms. Skipping. Residue LEU 506 is missing expected H atoms. Skipping. Residue THR 508 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue LEU 515 is missing expected H atoms. Skipping. Residue VAL 518 is missing expected H atoms. Skipping. Residue VAL 523 is missing expected H atoms. Skipping. Residue ALA 525 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue MET 16 is missing expected H atoms. Skipping. Residue ALA 17 is missing expected H atoms. Skipping. Residue ALA 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 20 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue ALA 23 is missing expected H atoms. Skipping. Residue LEU 24 is missing expected H atoms. Skipping. Residue ALA 27 is missing expected H atoms. Skipping. Residue LEU 29 is missing expected H atoms. Skipping. Residue MET 35 is missing expected H atoms. Skipping. Residue VAL 39 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue THR 47 is missing expected H atoms. Skipping. Residue ALA 51 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue THR 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ALA 56 is missing expected H atoms. Skipping. Residue ALA 60 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue ALA 64 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue THR 92 is missing expected H atoms. Skipping. Residue VAL 93 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue ALA 107 is missing expected H atoms. Skipping. Residue VAL 110 is missing expected H atoms. Skipping. Residue ALA 114 is missing expected H atoms. Skipping. Residue THR 120 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Residue ALA 129 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue ALA 135 is missing expected H atoms. Skipping. Residue MET 136 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue ALA 151 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue ALA 162 is missing expected H atoms. Skipping. Residue ALA 167 is missing expected H atoms. Skipping. Residue ALA 170 is missing expected H atoms. Skipping. Residue LEU 171 is missing expected H atoms. Skipping. Residue VAL 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue ALA 180 is missing expected H atoms. Skipping. Residue ILE 187 is missing expected H atoms. Skipping. Residue ILE 189 is missing expected H atoms. Skipping. Residue ALA 190 is missing expected H atoms. Skipping. Residue MET 192 is missing expected H atoms. Skipping. Residue ILE 193 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue LEU 200 is missing expected H atoms. Skipping. Residue ALA 201 is missing expected H atoms. Skipping. Residue ILE 203 is missing expected H atoms. Skipping. Residue VAL 204 is missing expected H atoms. Skipping. Residue THR 211 is missing expected H atoms. Skipping. Residue ALA 212 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue ALA 216 is missing expected H atoms. Skipping. Residue THR 219 is missing expected H atoms. Skipping. Residue VAL 223 is missing expected H atoms. Skipping. Residue ALA 227 is missing expected H atoms. Skipping. Residue LEU 229 is missing expected H atoms. Skipping. Residue ALA 230 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue VAL 238 is missing expected H atoms. Skipping. Residue ALA 245 is missing expected H atoms. Skipping. Residue VAL 248 is missing expected H atoms. Skipping. Residue ALA 250 is missing expected H atoms. Skipping. Residue VAL 251 is missing expected H atoms. Skipping. Residue ALA 254 is missing expected H atoms. Skipping. Residue LEU 255 is missing expected H atoms. Skipping. Residue VAL 260 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue ALA 269 is missing expected H atoms. Skipping. Residue LEU 276 is missing expected H atoms. Skipping. Residue THR 277 is missing expected H atoms. Skipping. Residue ILE 281 is missing expected H atoms. Skipping. Residue ALA 284 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue ILE 290 is missing expected H atoms. Skipping. Residue ALA 291 is missing expected H atoms. Skipping. Residue VAL 295 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LEU 303 is missing expected H atoms. Skipping. Residue THR 315 is missing expected H atoms. Skipping. Residue VAL 316 is missing expected H atoms. Skipping. Residue MET 317 is missing expected H atoms. Skipping. Residue THR 321 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue THR 328 is missing expected H atoms. Skipping. Residue ILE 329 is missing expected H atoms. Skipping. Residue ALA 330 is missing expected H atoms. Skipping. Residue ALA 331 is missing expected H atoms. Skipping. Residue LEU 332 is missing expected H atoms. Skipping. Residue MET 336 is missing expected H atoms. Skipping. Residue LEU 338 is missing expected H atoms. Skipping. Residue ALA 340 is missing expected H atoms. Skipping. Residue LEU 342 is missing expected H atoms. Skipping. Residue ALA 344 is missing expected H atoms. Skipping. Residue THR 346 is missing expected H atoms. Skipping. Residue THR 347 is missing expected H atoms. Skipping. Residue ILE 352 is missing expected H atoms. Skipping. Residue THR 353 is missing expected H atoms. Skipping. Residue ALA 354 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue VAL 360 is missing expected H atoms. Skipping. Residue ILE 364 is missing expected H atoms. Skipping. Residue ALA 368 is missing expected H atoms. Skipping. Residue ILE 371 is missing expected H atoms. Skipping. Residue ALA 375 is missing expected H atoms. Skipping. Residue ILE 380 is missing expected H atoms. Skipping. Residue VAL 381 is missing expected H atoms. Skipping. Residue ALA 383 is missing expected H atoms. Skipping. Residue VAL 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue ALA 386 is missing expected H atoms. Skipping. Residue LEU 388 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue ILE 6 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue ILE 19 is missing expected H atoms. Skipping. Residue ALA 20 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue THR 24 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue ALA 28 is missing expected H atoms. Skipping. Residue ALA 29 is missing expected H atoms. Skipping. Residue MET 31 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue MET 37 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue THR 41 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue ILE 56 is missing expected H atoms. Skipping. Residue ALA 58 is missing expected H atoms. Skipping. Residue LEU 60 is missing expected H atoms. Skipping. Residue VAL 64 is missing expected H atoms. Skipping. Residue ALA 65 is missing expected H atoms. Skipping. Residue VAL 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue ALA 69 is missing expected H atoms. Skipping. Residue ALA 71 is missing expected H atoms. Skipping. Residue VAL 75 is missing expected H atoms. Skipping. Residue THR 81 is missing expected H atoms. Skipping. Residue ALA 82 is missing expected H atoms. Skipping. Residue ALA 87 is missing expected H atoms. Skipping. Residue VAL 90 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue THR 94 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue MET 98 is missing expected H atoms. Skipping. Residue ALA 100 is missing expected H atoms. Skipping. Residue ALA 101 is missing expected H atoms. Skipping. Residue ALA 107 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 112 is missing expected H atoms. Skipping. Residue ALA 117 is missing expected H atoms. Skipping. Residue ILE 122 is missing expected H atoms. Skipping. Residue MET 123 is missing expected H atoms. Skipping. Residue VAL 125 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue THR 137 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue MET 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue THR 150 is missing expected H atoms. Skipping. Residue LEU 152 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue VAL 161 is missing expected H atoms. Skipping. Residue VAL 163 is missing expected H atoms. Skipping. Residue VAL 164 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue ILE 6 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue ILE 19 is missing expected H atoms. Skipping. Residue ALA 20 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue THR 24 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue ALA 28 is missing expected H atoms. Skipping. Residue ALA 29 is missing expected H atoms. Skipping. Residue MET 31 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue MET 37 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue THR 41 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue ILE 56 is missing expected H atoms. Skipping. Residue ALA 58 is missing expected H atoms. Skipping. Residue LEU 60 is missing expected H atoms. Skipping. Residue VAL 64 is missing expected H atoms. Skipping. Residue ALA 65 is missing expected H atoms. Skipping. Residue VAL 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue ALA 69 is missing expected H atoms. Skipping. Residue ALA 71 is missing expected H atoms. Skipping. Residue VAL 75 is missing expected H atoms. Skipping. Residue THR 81 is missing expected H atoms. Skipping. Residue ALA 82 is missing expected H atoms. Skipping. Residue ALA 87 is missing expected H atoms. Skipping. Residue VAL 90 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue THR 94 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue MET 98 is missing expected H atoms. Skipping. Residue ALA 100 is missing expected H atoms. Skipping. Residue ALA 101 is missing expected H atoms. Skipping. Residue ALA 107 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 112 is missing expected H atoms. Skipping. Residue ALA 117 is missing expected H atoms. Skipping. Residue ILE 122 is missing expected H atoms. Skipping. Residue MET 123 is missing expected H atoms. Skipping. Residue VAL 125 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue THR 137 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue MET 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue THR 150 is missing expected H atoms. Skipping. Residue LEU 152 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue VAL 161 is missing expected H atoms. Skipping. Residue VAL 163 is missing expected H atoms. Skipping. Residue VAL 164 is missing expected H atoms. Skipping. Evaluate side-chains 205 residues out of total 1782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 202 time to evaluate : 2.045 Fit side-chains revert: symmetry clash REVERT: D 209 GLU cc_start: 0.8161 (mt-10) cc_final: 0.7809 (mt-10) REVERT: E 30 ARG cc_start: 0.8362 (tmt-80) cc_final: 0.7587 (ttm110) REVERT: E 70 MET cc_start: 0.8462 (ptt) cc_final: 0.8226 (ptm) REVERT: E 184 MET cc_start: 0.8629 (tpt) cc_final: 0.8404 (tpt) REVERT: E 520 LYS cc_start: 0.8059 (mttm) cc_final: 0.7730 (mtmt) REVERT: B 308 GLU cc_start: 0.7382 (tt0) cc_final: 0.7181 (tp30) REVERT: G 31 MET cc_start: 0.8419 (ttm) cc_final: 0.8206 (ttm) outliers start: 3 outliers final: 3 residues processed: 205 average time/residue: 2.2281 time to fit residues: 495.1693 Evaluate side-chains 152 residues out of total 1782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 149 time to evaluate : 2.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 444 GLN Chi-restraints excluded: chain E residue 307 ARG Chi-restraints excluded: chain E residue 474 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 5.9990 chunk 159 optimal weight: 3.9990 chunk 88 optimal weight: 6.9990 chunk 54 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 chunk 164 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 190 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 59 GLN ** D 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 306 ASN B 165 GLN G 9 ASN G 17 ASN ** G 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 9 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.091422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.081329 restraints weight = 33146.023| |-----------------------------------------------------------------------------| r_work (start): 0.2781 rms_B_bonded: 1.12 r_work: 0.2687 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.2583 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.2583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.0826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 17861 Z= 0.223 Angle : 0.519 6.236 24231 Z= 0.290 Chirality : 0.042 0.163 2461 Planarity : 0.005 0.046 3153 Dihedral : 5.301 67.640 2349 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.29 % Allowed : 5.27 % Favored : 93.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.19), residues: 2101 helix: 1.11 (0.14), residues: 1354 sheet: 2.14 (0.83), residues: 44 loop : -0.12 (0.24), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 125 HIS 0.008 0.001 HIS D 382 PHE 0.022 0.002 PHE E 188 TYR 0.025 0.002 TYR E 310 ARG 0.005 0.001 ARG C 104 Details of bonding type rmsd hydrogen bonds : bond 0.05964 ( 993) hydrogen bonds : angle 5.44571 ( 2883) covalent geometry : bond 0.00515 (17861) covalent geometry : angle 0.51862 (24231) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 19 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue VAL 23 is missing expected H atoms. Skipping. Residue ALA 25 is missing expected H atoms. Skipping. Residue VAL 28 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue THR 44 is missing expected H atoms. Skipping. Residue ALA 47 is missing expected H atoms. Skipping. Residue THR 48 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ALA 53 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue ALA 64 is missing expected H atoms. Skipping. Residue ALA 68 is missing expected H atoms. Skipping. Residue MET 70 is missing expected H atoms. Skipping. Residue ALA 72 is missing expected H atoms. Skipping. Residue VAL 73 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue ALA 85 is missing expected H atoms. Skipping. Residue LEU 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue ALA 91 is missing expected H atoms. Skipping. Residue VAL 93 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue THR 102 is missing expected H atoms. Skipping. Residue MET 103 is missing expected H atoms. Skipping. Residue VAL 105 is missing expected H atoms. Skipping. Residue VAL 106 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue VAL 112 is missing expected H atoms. Skipping. Residue ALA 117 is missing expected H atoms. Skipping. Residue ILE 118 is missing expected H atoms. Skipping. Residue ALA 119 is missing expected H atoms. Skipping. Residue ALA 120 is missing expected H atoms. Skipping. Residue THR 121 is missing expected H atoms. Skipping. Residue MET 123 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Residue ALA 128 is missing expected H atoms. Skipping. Residue ALA 130 is missing expected H atoms. Skipping. Residue ALA 131 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue ALA 139 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue THR 148 is missing expected H atoms. Skipping. Residue ALA 152 is missing expected H atoms. Skipping. Residue VAL 154 is missing expected H atoms. Skipping. Residue ALA 159 is missing expected H atoms. Skipping. Residue ALA 166 is missing expected H atoms. Skipping. Residue ALA 171 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue ILE 177 is missing expected H atoms. Skipping. Residue LEU 180 is missing expected H atoms. Skipping. Residue MET 184 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue ILE 193 is missing expected H atoms. Skipping. Residue ALA 197 is missing expected H atoms. Skipping. Residue VAL 198 is missing expected H atoms. Skipping. Residue LEU 202 is missing expected H atoms. Skipping. Residue LEU 204 is missing expected H atoms. Skipping. Residue LEU 206 is missing expected H atoms. Skipping. Residue VAL 207 is missing expected H atoms. Skipping. Residue ALA 210 is missing expected H atoms. Skipping. Residue THR 213 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue ILE 217 is missing expected H atoms. Skipping. Residue VAL 218 is missing expected H atoms. Skipping. Residue ALA 219 is missing expected H atoms. Skipping. Residue VAL 220 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue ALA 224 is missing expected H atoms. Skipping. Residue ALA 225 is missing expected H atoms. Skipping. Residue ALA 226 is missing expected H atoms. Skipping. Residue ILE 231 is missing expected H atoms. Skipping. Residue THR 232 is missing expected H atoms. Skipping. Residue THR 234 is missing expected H atoms. Skipping. Residue VAL 235 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue ILE 239 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LEU 244 is missing expected H atoms. Skipping. Residue MET 247 is missing expected H atoms. Skipping. Residue ALA 248 is missing expected H atoms. Skipping. Residue THR 253 is missing expected H atoms. Skipping. Residue VAL 254 is missing expected H atoms. Skipping. Residue VAL 255 is missing expected H atoms. Skipping. Residue ILE 257 is missing expected H atoms. Skipping. Residue ALA 258 is missing expected H atoms. Skipping. Residue ALA 262 is missing expected H atoms. Skipping. Residue ALA 264 is missing expected H atoms. Skipping. Residue LEU 267 is missing expected H atoms. Skipping. Residue THR 269 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue ALA 274 is missing expected H atoms. Skipping. Residue THR 277 is missing expected H atoms. Skipping. Residue THR 283 is missing expected H atoms. Skipping. Residue VAL 285 is missing expected H atoms. Skipping. Residue LEU 286 is missing expected H atoms. Skipping. Residue MET 288 is missing expected H atoms. Skipping. Residue LEU 289 is missing expected H atoms. Skipping. Residue VAL 298 is missing expected H atoms. Skipping. Residue VAL 302 is missing expected H atoms. Skipping. Residue THR 304 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Residue ILE 316 is missing expected H atoms. Skipping. Residue ILE 318 is missing expected H atoms. Skipping. Residue LEU 321 is missing expected H atoms. Skipping. Residue VAL 326 is missing expected H atoms. Skipping. Residue LEU 332 is missing expected H atoms. Skipping. Residue ALA 335 is missing expected H atoms. Skipping. Residue ALA 339 is missing expected H atoms. Skipping. Residue ALA 342 is missing expected H atoms. Skipping. Residue LEU 346 is missing expected H atoms. Skipping. Residue LEU 348 is missing expected H atoms. Skipping. Residue LEU 349 is missing expected H atoms. Skipping. Residue ALA 350 is missing expected H atoms. Skipping. Residue ALA 352 is missing expected H atoms. Skipping. Residue LEU 353 is missing expected H atoms. Skipping. Residue THR 356 is missing expected H atoms. Skipping. Residue LEU 361 is missing expected H atoms. Skipping. Residue ALA 362 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue MET 369 is missing expected H atoms. Skipping. Residue ALA 374 is missing expected H atoms. Skipping. Residue ILE 386 is missing expected H atoms. Skipping. Residue ALA 392 is missing expected H atoms. Skipping. Residue ILE 403 is missing expected H atoms. Skipping. Residue LEU 405 is missing expected H atoms. Skipping. Residue MET 406 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 415 is missing expected H atoms. Skipping. Residue ILE 417 is missing expected H atoms. Skipping. Residue VAL 420 is missing expected H atoms. Skipping. Residue VAL 423 is missing expected H atoms. Skipping. Residue LEU 429 is missing expected H atoms. Skipping. Residue ALA 430 is missing expected H atoms. Skipping. Residue ALA 433 is missing expected H atoms. Skipping. Residue THR 435 is missing expected H atoms. Skipping. Residue LEU 436 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue MET 445 is missing expected H atoms. Skipping. Residue THR 447 is missing expected H atoms. Skipping. Residue MET 456 is missing expected H atoms. Skipping. Residue LEU 458 is missing expected H atoms. Skipping. Residue ALA 459 is missing expected H atoms. Skipping. Residue ILE 469 is missing expected H atoms. Skipping. Residue LEU 478 is missing expected H atoms. Skipping. Residue VAL 481 is missing expected H atoms. Skipping. Residue ILE 482 is missing expected H atoms. Skipping. Residue ALA 483 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue LEU 488 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue LEU 495 is missing expected H atoms. Skipping. Residue ILE 496 is missing expected H atoms. Skipping. Residue ALA 497 is missing expected H atoms. Skipping. Residue VAL 501 is missing expected H atoms. Skipping. Residue LEU 506 is missing expected H atoms. Skipping. Residue THR 508 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue LEU 515 is missing expected H atoms. Skipping. Residue VAL 518 is missing expected H atoms. Skipping. Residue VAL 523 is missing expected H atoms. Skipping. Residue ALA 525 is missing expected H atoms. Skipping. Residue ALA 16 is missing expected H atoms. Skipping. Residue ALA 19 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue VAL 23 is missing expected H atoms. Skipping. Residue ALA 25 is missing expected H atoms. Skipping. Residue VAL 28 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue THR 44 is missing expected H atoms. Skipping. Residue ALA 47 is missing expected H atoms. Skipping. Residue THR 48 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ALA 53 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue ALA 64 is missing expected H atoms. Skipping. Residue ALA 68 is missing expected H atoms. Skipping. Residue MET 70 is missing expected H atoms. Skipping. Residue ALA 72 is missing expected H atoms. Skipping. Residue VAL 73 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue ALA 85 is missing expected H atoms. Skipping. Residue LEU 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue ALA 91 is missing expected H atoms. Skipping. Residue VAL 93 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue THR 102 is missing expected H atoms. Skipping. Residue MET 103 is missing expected H atoms. Skipping. Residue VAL 105 is missing expected H atoms. Skipping. Residue VAL 106 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue VAL 112 is missing expected H atoms. Skipping. Residue ALA 117 is missing expected H atoms. Skipping. Residue ILE 118 is missing expected H atoms. Skipping. Residue ALA 119 is missing expected H atoms. Skipping. Residue ALA 120 is missing expected H atoms. Skipping. Residue THR 121 is missing expected H atoms. Skipping. Residue MET 123 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Residue ALA 128 is missing expected H atoms. Skipping. Residue ALA 130 is missing expected H atoms. Skipping. Residue ALA 131 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue ALA 139 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue THR 148 is missing expected H atoms. Skipping. Residue ALA 152 is missing expected H atoms. Skipping. Residue VAL 154 is missing expected H atoms. Skipping. Residue ALA 159 is missing expected H atoms. Skipping. Residue ALA 166 is missing expected H atoms. Skipping. Residue ALA 171 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue ILE 177 is missing expected H atoms. Skipping. Residue LEU 180 is missing expected H atoms. Skipping. Residue MET 184 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue ILE 193 is missing expected H atoms. Skipping. Residue ALA 197 is missing expected H atoms. Skipping. Residue VAL 198 is missing expected H atoms. Skipping. Residue LEU 202 is missing expected H atoms. Skipping. Residue LEU 204 is missing expected H atoms. Skipping. Residue LEU 206 is missing expected H atoms. Skipping. Residue VAL 207 is missing expected H atoms. Skipping. Residue ALA 210 is missing expected H atoms. Skipping. Residue THR 213 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue ILE 217 is missing expected H atoms. Skipping. Residue VAL 218 is missing expected H atoms. Skipping. Residue ALA 219 is missing expected H atoms. Skipping. Residue VAL 220 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue ALA 224 is missing expected H atoms. Skipping. Residue ALA 225 is missing expected H atoms. Skipping. Residue ALA 226 is missing expected H atoms. Skipping. Residue ILE 231 is missing expected H atoms. Skipping. Residue THR 232 is missing expected H atoms. Skipping. Residue THR 234 is missing expected H atoms. Skipping. Residue VAL 235 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue ILE 239 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LEU 244 is missing expected H atoms. Skipping. Residue MET 247 is missing expected H atoms. Skipping. Residue ALA 248 is missing expected H atoms. Skipping. Residue THR 253 is missing expected H atoms. Skipping. Residue VAL 254 is missing expected H atoms. Skipping. Residue VAL 255 is missing expected H atoms. Skipping. Residue ILE 257 is missing expected H atoms. Skipping. Residue ALA 258 is missing expected H atoms. Skipping. Residue ALA 262 is missing expected H atoms. Skipping. Residue ALA 264 is missing expected H atoms. Skipping. Residue LEU 267 is missing expected H atoms. Skipping. Residue THR 269 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue ALA 274 is missing expected H atoms. Skipping. Residue THR 277 is missing expected H atoms. Skipping. Residue THR 283 is missing expected H atoms. Skipping. Residue VAL 285 is missing expected H atoms. Skipping. Residue LEU 286 is missing expected H atoms. Skipping. Residue MET 288 is missing expected H atoms. Skipping. Residue LEU 289 is missing expected H atoms. Skipping. Residue VAL 298 is missing expected H atoms. Skipping. Residue VAL 302 is missing expected H atoms. Skipping. Residue THR 304 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Residue ILE 316 is missing expected H atoms. Skipping. Residue ILE 318 is missing expected H atoms. Skipping. Residue LEU 321 is missing expected H atoms. Skipping. Residue VAL 326 is missing expected H atoms. Skipping. Residue LEU 332 is missing expected H atoms. Skipping. Residue ALA 335 is missing expected H atoms. Skipping. Residue ALA 339 is missing expected H atoms. Skipping. Residue ALA 342 is missing expected H atoms. Skipping. Residue LEU 346 is missing expected H atoms. Skipping. Residue LEU 348 is missing expected H atoms. Skipping. Residue LEU 349 is missing expected H atoms. Skipping. Residue ALA 350 is missing expected H atoms. Skipping. Residue ALA 352 is missing expected H atoms. Skipping. Residue LEU 353 is missing expected H atoms. Skipping. Residue THR 356 is missing expected H atoms. Skipping. Residue LEU 361 is missing expected H atoms. Skipping. Residue ALA 362 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue MET 369 is missing expected H atoms. Skipping. Residue ALA 374 is missing expected H atoms. Skipping. Residue ILE 386 is missing expected H atoms. Skipping. Residue ALA 392 is missing expected H atoms. Skipping. Residue ILE 403 is missing expected H atoms. Skipping. Residue LEU 405 is missing expected H atoms. Skipping. Residue MET 406 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 415 is missing expected H atoms. Skipping. Residue ILE 417 is missing expected H atoms. Skipping. Residue VAL 420 is missing expected H atoms. Skipping. Residue VAL 423 is missing expected H atoms. Skipping. Residue LEU 429 is missing expected H atoms. Skipping. Residue ALA 430 is missing expected H atoms. Skipping. Residue ALA 433 is missing expected H atoms. Skipping. Residue THR 435 is missing expected H atoms. Skipping. Residue LEU 436 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue MET 445 is missing expected H atoms. Skipping. Residue THR 447 is missing expected H atoms. Skipping. Residue MET 456 is missing expected H atoms. Skipping. Residue LEU 458 is missing expected H atoms. Skipping. Residue ALA 459 is missing expected H atoms. Skipping. Residue ILE 469 is missing expected H atoms. Skipping. Residue LEU 478 is missing expected H atoms. Skipping. Residue VAL 481 is missing expected H atoms. Skipping. Residue ILE 482 is missing expected H atoms. Skipping. Residue ALA 483 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue LEU 488 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue LEU 495 is missing expected H atoms. Skipping. Residue ILE 496 is missing expected H atoms. Skipping. Residue ALA 497 is missing expected H atoms. Skipping. Residue VAL 501 is missing expected H atoms. Skipping. Residue LEU 506 is missing expected H atoms. Skipping. Residue THR 508 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue LEU 515 is missing expected H atoms. Skipping. Residue VAL 518 is missing expected H atoms. Skipping. Residue VAL 523 is missing expected H atoms. Skipping. Residue ALA 525 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue MET 16 is missing expected H atoms. Skipping. Residue ALA 17 is missing expected H atoms. Skipping. Residue ALA 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 20 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue ALA 23 is missing expected H atoms. Skipping. Residue LEU 24 is missing expected H atoms. Skipping. Residue ALA 27 is missing expected H atoms. Skipping. Residue LEU 29 is missing expected H atoms. Skipping. Residue MET 35 is missing expected H atoms. Skipping. Residue VAL 39 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue THR 47 is missing expected H atoms. Skipping. Residue ALA 51 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue THR 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ALA 56 is missing expected H atoms. Skipping. Residue ALA 60 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue ALA 64 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue THR 92 is missing expected H atoms. Skipping. Residue VAL 93 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue ALA 107 is missing expected H atoms. Skipping. Residue VAL 110 is missing expected H atoms. Skipping. Residue ALA 114 is missing expected H atoms. Skipping. Residue THR 120 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Residue ALA 129 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue ALA 135 is missing expected H atoms. Skipping. Residue MET 136 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue ALA 151 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue ALA 162 is missing expected H atoms. Skipping. Residue ALA 167 is missing expected H atoms. Skipping. Residue ALA 170 is missing expected H atoms. Skipping. Residue LEU 171 is missing expected H atoms. Skipping. Residue VAL 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue ALA 180 is missing expected H atoms. Skipping. Residue ILE 187 is missing expected H atoms. Skipping. Residue ILE 189 is missing expected H atoms. Skipping. Residue ALA 190 is missing expected H atoms. Skipping. Residue MET 192 is missing expected H atoms. Skipping. Residue ILE 193 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue LEU 200 is missing expected H atoms. Skipping. Residue ALA 201 is missing expected H atoms. Skipping. Residue ILE 203 is missing expected H atoms. Skipping. Residue VAL 204 is missing expected H atoms. Skipping. Residue THR 211 is missing expected H atoms. Skipping. Residue ALA 212 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue ALA 216 is missing expected H atoms. Skipping. Residue THR 219 is missing expected H atoms. Skipping. Residue VAL 223 is missing expected H atoms. Skipping. Residue ALA 227 is missing expected H atoms. Skipping. Residue LEU 229 is missing expected H atoms. Skipping. Residue ALA 230 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue VAL 238 is missing expected H atoms. Skipping. Residue ALA 245 is missing expected H atoms. Skipping. Residue VAL 248 is missing expected H atoms. Skipping. Residue ALA 250 is missing expected H atoms. Skipping. Residue VAL 251 is missing expected H atoms. Skipping. Residue ALA 254 is missing expected H atoms. Skipping. Residue LEU 255 is missing expected H atoms. Skipping. Residue VAL 260 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue ALA 269 is missing expected H atoms. Skipping. Residue LEU 276 is missing expected H atoms. Skipping. Residue THR 277 is missing expected H atoms. Skipping. Residue ILE 281 is missing expected H atoms. Skipping. Residue ALA 284 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue ILE 290 is missing expected H atoms. Skipping. Residue ALA 291 is missing expected H atoms. Skipping. Residue VAL 295 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LEU 303 is missing expected H atoms. Skipping. Residue THR 315 is missing expected H atoms. Skipping. Residue VAL 316 is missing expected H atoms. Skipping. Residue MET 317 is missing expected H atoms. Skipping. Residue THR 321 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue THR 328 is missing expected H atoms. Skipping. Residue ILE 329 is missing expected H atoms. Skipping. Residue ALA 330 is missing expected H atoms. Skipping. Residue ALA 331 is missing expected H atoms. Skipping. Residue LEU 332 is missing expected H atoms. Skipping. Residue MET 336 is missing expected H atoms. Skipping. Residue LEU 338 is missing expected H atoms. Skipping. Residue ALA 340 is missing expected H atoms. Skipping. Residue LEU 342 is missing expected H atoms. Skipping. Residue ALA 344 is missing expected H atoms. Skipping. Residue THR 346 is missing expected H atoms. Skipping. Residue THR 347 is missing expected H atoms. Skipping. Residue ILE 352 is missing expected H atoms. Skipping. Residue THR 353 is missing expected H atoms. Skipping. Residue ALA 354 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue VAL 360 is missing expected H atoms. Skipping. Residue ILE 364 is missing expected H atoms. Skipping. Residue ALA 368 is missing expected H atoms. Skipping. Residue ILE 371 is missing expected H atoms. Skipping. Residue ALA 375 is missing expected H atoms. Skipping. Residue ILE 380 is missing expected H atoms. Skipping. Residue VAL 381 is missing expected H atoms. Skipping. Residue ALA 383 is missing expected H atoms. Skipping. Residue VAL 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue ALA 386 is missing expected H atoms. Skipping. Residue LEU 388 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue ILE 6 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue ILE 19 is missing expected H atoms. Skipping. Residue ALA 20 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue THR 24 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue ALA 28 is missing expected H atoms. Skipping. Residue ALA 29 is missing expected H atoms. Skipping. Residue MET 31 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue MET 37 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue THR 41 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue ILE 56 is missing expected H atoms. Skipping. Residue ALA 58 is missing expected H atoms. Skipping. Residue LEU 60 is missing expected H atoms. Skipping. Residue VAL 64 is missing expected H atoms. Skipping. Residue ALA 65 is missing expected H atoms. Skipping. Residue VAL 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue ALA 69 is missing expected H atoms. Skipping. Residue ALA 71 is missing expected H atoms. Skipping. Residue VAL 75 is missing expected H atoms. Skipping. Residue THR 81 is missing expected H atoms. Skipping. Residue ALA 82 is missing expected H atoms. Skipping. Residue ALA 87 is missing expected H atoms. Skipping. Residue VAL 90 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue THR 94 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue MET 98 is missing expected H atoms. Skipping. Residue ALA 100 is missing expected H atoms. Skipping. Residue ALA 101 is missing expected H atoms. Skipping. Residue ALA 107 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 112 is missing expected H atoms. Skipping. Residue ALA 117 is missing expected H atoms. Skipping. Residue ILE 122 is missing expected H atoms. Skipping. Residue MET 123 is missing expected H atoms. Skipping. Residue VAL 125 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue THR 137 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue MET 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue THR 150 is missing expected H atoms. Skipping. Residue LEU 152 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue VAL 161 is missing expected H atoms. Skipping. Residue VAL 163 is missing expected H atoms. Skipping. Residue VAL 164 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue ILE 6 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue ILE 19 is missing expected H atoms. Skipping. Residue ALA 20 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue THR 24 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue ALA 28 is missing expected H atoms. Skipping. Residue ALA 29 is missing expected H atoms. Skipping. Residue MET 31 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue MET 37 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue THR 41 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue ILE 56 is missing expected H atoms. Skipping. Residue ALA 58 is missing expected H atoms. Skipping. Residue LEU 60 is missing expected H atoms. Skipping. Residue VAL 64 is missing expected H atoms. Skipping. Residue ALA 65 is missing expected H atoms. Skipping. Residue VAL 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue ALA 69 is missing expected H atoms. Skipping. Residue ALA 71 is missing expected H atoms. Skipping. Residue VAL 75 is missing expected H atoms. Skipping. Residue THR 81 is missing expected H atoms. Skipping. Residue ALA 82 is missing expected H atoms. Skipping. Residue ALA 87 is missing expected H atoms. Skipping. Residue VAL 90 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue THR 94 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue MET 98 is missing expected H atoms. Skipping. Residue ALA 100 is missing expected H atoms. Skipping. Residue ALA 101 is missing expected H atoms. Skipping. Residue ALA 107 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 112 is missing expected H atoms. Skipping. Residue ALA 117 is missing expected H atoms. Skipping. Residue ILE 122 is missing expected H atoms. Skipping. Residue MET 123 is missing expected H atoms. Skipping. Residue VAL 125 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue THR 137 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue MET 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue THR 150 is missing expected H atoms. Skipping. Residue LEU 152 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue VAL 161 is missing expected H atoms. Skipping. Residue VAL 163 is missing expected H atoms. Skipping. Residue VAL 164 is missing expected H atoms. Skipping. Evaluate side-chains 178 residues out of total 1782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 155 time to evaluate : 2.202 Fit side-chains revert: symmetry clash REVERT: D 311 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.6784 (mm-30) REVERT: D 333 LYS cc_start: 0.8374 (OUTLIER) cc_final: 0.7807 (mtpp) REVERT: D 336 LYS cc_start: 0.8514 (tttp) cc_final: 0.8293 (tmtm) REVERT: E 30 ARG cc_start: 0.8573 (tmt-80) cc_final: 0.7602 (ttm110) REVERT: E 70 MET cc_start: 0.8909 (ptt) cc_final: 0.8560 (ptm) REVERT: E 184 MET cc_start: 0.8927 (tpt) cc_final: 0.8716 (tpt) REVERT: E 307 ARG cc_start: 0.8619 (OUTLIER) cc_final: 0.7211 (ttm-80) REVERT: E 520 LYS cc_start: 0.8293 (mttm) cc_final: 0.7947 (mtmt) REVERT: B 7 ARG cc_start: 0.7610 (OUTLIER) cc_final: 0.6464 (mmm-85) REVERT: B 86 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.8511 (pt0) REVERT: B 308 GLU cc_start: 0.7918 (tt0) cc_final: 0.7472 (tp30) REVERT: C 165 GLN cc_start: 0.8809 (OUTLIER) cc_final: 0.7906 (tm-30) REVERT: C 225 LYS cc_start: 0.8760 (OUTLIER) cc_final: 0.8530 (tttm) REVERT: G 74 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7647 (mt-10) REVERT: H 21 GLN cc_start: 0.8358 (OUTLIER) cc_final: 0.7945 (mp10) outliers start: 23 outliers final: 8 residues processed: 173 average time/residue: 2.1994 time to fit residues: 413.8119 Evaluate side-chains 166 residues out of total 1782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 149 time to evaluate : 2.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 76 GLU Chi-restraints excluded: chain D residue 125 TRP Chi-restraints excluded: chain D residue 311 GLU Chi-restraints excluded: chain D residue 333 LYS Chi-restraints excluded: chain D residue 409 ILE Chi-restraints excluded: chain D residue 444 GLN Chi-restraints excluded: chain D residue 517 CYS Chi-restraints excluded: chain E residue 307 ARG Chi-restraints excluded: chain E residue 381 ASP Chi-restraints excluded: chain B residue 7 ARG Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain C residue 165 GLN Chi-restraints excluded: chain C residue 173 ASP Chi-restraints excluded: chain C residue 225 LYS Chi-restraints excluded: chain G residue 74 GLU Chi-restraints excluded: chain H residue 21 GLN Chi-restraints excluded: chain H residue 37 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 70 optimal weight: 0.2980 chunk 49 optimal weight: 6.9990 chunk 120 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 101 optimal weight: 6.9990 chunk 150 optimal weight: 4.9990 chunk 179 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 91 optimal weight: 3.9990 overall best weight: 2.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 59 GLN D 100 ASN ** D 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 214 ASN G 45 ASN ** G 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.091628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.081546 restraints weight = 32958.986| |-----------------------------------------------------------------------------| r_work (start): 0.2786 rms_B_bonded: 1.11 r_work: 0.2693 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.2588 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.2588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.1006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 17861 Z= 0.198 Angle : 0.488 5.548 24231 Z= 0.273 Chirality : 0.041 0.157 2461 Planarity : 0.004 0.045 3153 Dihedral : 5.139 68.622 2346 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.63 % Allowed : 6.62 % Favored : 91.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.19), residues: 2101 helix: 1.16 (0.14), residues: 1358 sheet: 1.92 (0.81), residues: 44 loop : -0.16 (0.24), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 43 HIS 0.007 0.001 HIS D 382 PHE 0.016 0.002 PHE E 39 TYR 0.021 0.002 TYR E 310 ARG 0.004 0.000 ARG C 104 Details of bonding type rmsd hydrogen bonds : bond 0.05625 ( 993) hydrogen bonds : angle 5.25822 ( 2883) covalent geometry : bond 0.00456 (17861) covalent geometry : angle 0.48773 (24231) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 19 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue VAL 23 is missing expected H atoms. Skipping. Residue ALA 25 is missing expected H atoms. Skipping. Residue VAL 28 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue THR 44 is missing expected H atoms. Skipping. Residue ALA 47 is missing expected H atoms. Skipping. Residue THR 48 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ALA 53 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue ALA 64 is missing expected H atoms. Skipping. Residue ALA 68 is missing expected H atoms. Skipping. Residue MET 70 is missing expected H atoms. Skipping. Residue ALA 72 is missing expected H atoms. Skipping. Residue VAL 73 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue ALA 85 is missing expected H atoms. Skipping. Residue LEU 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue ALA 91 is missing expected H atoms. Skipping. Residue VAL 93 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue THR 102 is missing expected H atoms. Skipping. Residue MET 103 is missing expected H atoms. Skipping. Residue VAL 105 is missing expected H atoms. Skipping. Residue VAL 106 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue VAL 112 is missing expected H atoms. Skipping. Residue ALA 117 is missing expected H atoms. Skipping. Residue ILE 118 is missing expected H atoms. Skipping. Residue ALA 119 is missing expected H atoms. Skipping. Residue ALA 120 is missing expected H atoms. Skipping. Residue THR 121 is missing expected H atoms. Skipping. Residue MET 123 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Residue ALA 128 is missing expected H atoms. Skipping. Residue ALA 130 is missing expected H atoms. Skipping. Residue ALA 131 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue ALA 139 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue THR 148 is missing expected H atoms. Skipping. Residue ALA 152 is missing expected H atoms. Skipping. Residue VAL 154 is missing expected H atoms. Skipping. Residue ALA 159 is missing expected H atoms. Skipping. Residue ALA 166 is missing expected H atoms. Skipping. Residue ALA 171 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue ILE 177 is missing expected H atoms. Skipping. Residue LEU 180 is missing expected H atoms. Skipping. Residue MET 184 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue ILE 193 is missing expected H atoms. Skipping. Residue ALA 197 is missing expected H atoms. Skipping. Residue VAL 198 is missing expected H atoms. Skipping. Residue LEU 202 is missing expected H atoms. Skipping. Residue LEU 204 is missing expected H atoms. Skipping. Residue LEU 206 is missing expected H atoms. Skipping. Residue VAL 207 is missing expected H atoms. Skipping. Residue ALA 210 is missing expected H atoms. Skipping. Residue THR 213 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue ILE 217 is missing expected H atoms. Skipping. Residue VAL 218 is missing expected H atoms. Skipping. Residue ALA 219 is missing expected H atoms. Skipping. Residue VAL 220 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue ALA 224 is missing expected H atoms. Skipping. Residue ALA 225 is missing expected H atoms. Skipping. Residue ALA 226 is missing expected H atoms. Skipping. Residue ILE 231 is missing expected H atoms. Skipping. Residue THR 232 is missing expected H atoms. Skipping. Residue THR 234 is missing expected H atoms. Skipping. Residue VAL 235 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue ILE 239 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LEU 244 is missing expected H atoms. Skipping. Residue MET 247 is missing expected H atoms. Skipping. Residue ALA 248 is missing expected H atoms. Skipping. Residue THR 253 is missing expected H atoms. Skipping. Residue VAL 254 is missing expected H atoms. Skipping. Residue VAL 255 is missing expected H atoms. Skipping. Residue ILE 257 is missing expected H atoms. Skipping. Residue ALA 258 is missing expected H atoms. Skipping. Residue ALA 262 is missing expected H atoms. Skipping. Residue ALA 264 is missing expected H atoms. Skipping. Residue LEU 267 is missing expected H atoms. Skipping. Residue THR 269 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue ALA 274 is missing expected H atoms. Skipping. Residue THR 277 is missing expected H atoms. Skipping. Residue THR 283 is missing expected H atoms. Skipping. Residue VAL 285 is missing expected H atoms. Skipping. Residue LEU 286 is missing expected H atoms. Skipping. Residue MET 288 is missing expected H atoms. Skipping. Residue LEU 289 is missing expected H atoms. Skipping. Residue VAL 298 is missing expected H atoms. Skipping. Residue VAL 302 is missing expected H atoms. Skipping. Residue THR 304 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Residue ILE 316 is missing expected H atoms. Skipping. Residue ILE 318 is missing expected H atoms. Skipping. Residue LEU 321 is missing expected H atoms. Skipping. Residue VAL 326 is missing expected H atoms. Skipping. Residue LEU 332 is missing expected H atoms. Skipping. Residue ALA 335 is missing expected H atoms. Skipping. Residue ALA 339 is missing expected H atoms. Skipping. Residue ALA 342 is missing expected H atoms. Skipping. Residue LEU 346 is missing expected H atoms. Skipping. Residue LEU 348 is missing expected H atoms. Skipping. Residue LEU 349 is missing expected H atoms. Skipping. Residue ALA 350 is missing expected H atoms. Skipping. Residue ALA 352 is missing expected H atoms. Skipping. Residue LEU 353 is missing expected H atoms. Skipping. Residue THR 356 is missing expected H atoms. Skipping. Residue LEU 361 is missing expected H atoms. Skipping. Residue ALA 362 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue MET 369 is missing expected H atoms. Skipping. Residue ALA 374 is missing expected H atoms. Skipping. Residue ILE 386 is missing expected H atoms. Skipping. Residue ALA 392 is missing expected H atoms. Skipping. Residue ILE 403 is missing expected H atoms. Skipping. Residue LEU 405 is missing expected H atoms. Skipping. Residue MET 406 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 415 is missing expected H atoms. Skipping. Residue ILE 417 is missing expected H atoms. Skipping. Residue VAL 420 is missing expected H atoms. Skipping. Residue VAL 423 is missing expected H atoms. Skipping. Residue LEU 429 is missing expected H atoms. Skipping. Residue ALA 430 is missing expected H atoms. Skipping. Residue ALA 433 is missing expected H atoms. Skipping. Residue THR 435 is missing expected H atoms. Skipping. Residue LEU 436 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue MET 445 is missing expected H atoms. Skipping. Residue THR 447 is missing expected H atoms. Skipping. Residue MET 456 is missing expected H atoms. Skipping. Residue LEU 458 is missing expected H atoms. Skipping. Residue ALA 459 is missing expected H atoms. Skipping. Residue ILE 469 is missing expected H atoms. Skipping. Residue LEU 478 is missing expected H atoms. Skipping. Residue VAL 481 is missing expected H atoms. Skipping. Residue ILE 482 is missing expected H atoms. Skipping. Residue ALA 483 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue LEU 488 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue LEU 495 is missing expected H atoms. Skipping. Residue ILE 496 is missing expected H atoms. Skipping. Residue ALA 497 is missing expected H atoms. Skipping. Residue VAL 501 is missing expected H atoms. Skipping. Residue LEU 506 is missing expected H atoms. Skipping. Residue THR 508 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue LEU 515 is missing expected H atoms. Skipping. Residue VAL 518 is missing expected H atoms. Skipping. Residue VAL 523 is missing expected H atoms. Skipping. Residue ALA 525 is missing expected H atoms. Skipping. Residue ALA 16 is missing expected H atoms. Skipping. Residue ALA 19 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue VAL 23 is missing expected H atoms. Skipping. Residue ALA 25 is missing expected H atoms. Skipping. Residue VAL 28 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue THR 44 is missing expected H atoms. Skipping. Residue ALA 47 is missing expected H atoms. Skipping. Residue THR 48 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ALA 53 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue ALA 64 is missing expected H atoms. Skipping. Residue ALA 68 is missing expected H atoms. Skipping. Residue MET 70 is missing expected H atoms. Skipping. Residue ALA 72 is missing expected H atoms. Skipping. Residue VAL 73 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue ALA 85 is missing expected H atoms. Skipping. Residue LEU 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue ALA 91 is missing expected H atoms. Skipping. Residue VAL 93 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue THR 102 is missing expected H atoms. Skipping. Residue MET 103 is missing expected H atoms. Skipping. Residue VAL 105 is missing expected H atoms. Skipping. Residue VAL 106 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue VAL 112 is missing expected H atoms. Skipping. Residue ALA 117 is missing expected H atoms. Skipping. Residue ILE 118 is missing expected H atoms. Skipping. Residue ALA 119 is missing expected H atoms. Skipping. Residue ALA 120 is missing expected H atoms. Skipping. Residue THR 121 is missing expected H atoms. Skipping. Residue MET 123 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Residue ALA 128 is missing expected H atoms. Skipping. Residue ALA 130 is missing expected H atoms. Skipping. Residue ALA 131 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue ALA 139 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue THR 148 is missing expected H atoms. Skipping. Residue ALA 152 is missing expected H atoms. Skipping. Residue VAL 154 is missing expected H atoms. Skipping. Residue ALA 159 is missing expected H atoms. Skipping. Residue ALA 166 is missing expected H atoms. Skipping. Residue ALA 171 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue ILE 177 is missing expected H atoms. Skipping. Residue LEU 180 is missing expected H atoms. Skipping. Residue MET 184 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue ILE 193 is missing expected H atoms. Skipping. Residue ALA 197 is missing expected H atoms. Skipping. Residue VAL 198 is missing expected H atoms. Skipping. Residue LEU 202 is missing expected H atoms. Skipping. Residue LEU 204 is missing expected H atoms. Skipping. Residue LEU 206 is missing expected H atoms. Skipping. Residue VAL 207 is missing expected H atoms. Skipping. Residue ALA 210 is missing expected H atoms. Skipping. Residue THR 213 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue ILE 217 is missing expected H atoms. Skipping. Residue VAL 218 is missing expected H atoms. Skipping. Residue ALA 219 is missing expected H atoms. Skipping. Residue VAL 220 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue ALA 224 is missing expected H atoms. Skipping. Residue ALA 225 is missing expected H atoms. Skipping. Residue ALA 226 is missing expected H atoms. Skipping. Residue ILE 231 is missing expected H atoms. Skipping. Residue THR 232 is missing expected H atoms. Skipping. Residue THR 234 is missing expected H atoms. Skipping. Residue VAL 235 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue ILE 239 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LEU 244 is missing expected H atoms. Skipping. Residue MET 247 is missing expected H atoms. Skipping. Residue ALA 248 is missing expected H atoms. Skipping. Residue THR 253 is missing expected H atoms. Skipping. Residue VAL 254 is missing expected H atoms. Skipping. Residue VAL 255 is missing expected H atoms. Skipping. Residue ILE 257 is missing expected H atoms. Skipping. Residue ALA 258 is missing expected H atoms. Skipping. Residue ALA 262 is missing expected H atoms. Skipping. Residue ALA 264 is missing expected H atoms. Skipping. Residue LEU 267 is missing expected H atoms. Skipping. Residue THR 269 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue ALA 274 is missing expected H atoms. Skipping. Residue THR 277 is missing expected H atoms. Skipping. Residue THR 283 is missing expected H atoms. Skipping. Residue VAL 285 is missing expected H atoms. Skipping. Residue LEU 286 is missing expected H atoms. Skipping. Residue MET 288 is missing expected H atoms. Skipping. Residue LEU 289 is missing expected H atoms. Skipping. Residue VAL 298 is missing expected H atoms. Skipping. Residue VAL 302 is missing expected H atoms. Skipping. Residue THR 304 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Residue ILE 316 is missing expected H atoms. Skipping. Residue ILE 318 is missing expected H atoms. Skipping. Residue LEU 321 is missing expected H atoms. Skipping. Residue VAL 326 is missing expected H atoms. Skipping. Residue LEU 332 is missing expected H atoms. Skipping. Residue ALA 335 is missing expected H atoms. Skipping. Residue ALA 339 is missing expected H atoms. Skipping. Residue ALA 342 is missing expected H atoms. Skipping. Residue LEU 346 is missing expected H atoms. Skipping. Residue LEU 348 is missing expected H atoms. Skipping. Residue LEU 349 is missing expected H atoms. Skipping. Residue ALA 350 is missing expected H atoms. Skipping. Residue ALA 352 is missing expected H atoms. Skipping. Residue LEU 353 is missing expected H atoms. Skipping. Residue THR 356 is missing expected H atoms. Skipping. Residue LEU 361 is missing expected H atoms. Skipping. Residue ALA 362 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue MET 369 is missing expected H atoms. Skipping. Residue ALA 374 is missing expected H atoms. Skipping. Residue ILE 386 is missing expected H atoms. Skipping. Residue ALA 392 is missing expected H atoms. Skipping. Residue ILE 403 is missing expected H atoms. Skipping. Residue LEU 405 is missing expected H atoms. Skipping. Residue MET 406 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 415 is missing expected H atoms. Skipping. Residue ILE 417 is missing expected H atoms. Skipping. Residue VAL 420 is missing expected H atoms. Skipping. Residue VAL 423 is missing expected H atoms. Skipping. Residue LEU 429 is missing expected H atoms. Skipping. Residue ALA 430 is missing expected H atoms. Skipping. Residue ALA 433 is missing expected H atoms. Skipping. Residue THR 435 is missing expected H atoms. Skipping. Residue LEU 436 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue MET 445 is missing expected H atoms. Skipping. Residue THR 447 is missing expected H atoms. Skipping. Residue MET 456 is missing expected H atoms. Skipping. Residue LEU 458 is missing expected H atoms. Skipping. Residue ALA 459 is missing expected H atoms. Skipping. Residue ILE 469 is missing expected H atoms. Skipping. Residue LEU 478 is missing expected H atoms. Skipping. Residue VAL 481 is missing expected H atoms. Skipping. Residue ILE 482 is missing expected H atoms. Skipping. Residue ALA 483 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue LEU 488 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue LEU 495 is missing expected H atoms. Skipping. Residue ILE 496 is missing expected H atoms. Skipping. Residue ALA 497 is missing expected H atoms. Skipping. Residue VAL 501 is missing expected H atoms. Skipping. Residue LEU 506 is missing expected H atoms. Skipping. Residue THR 508 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue LEU 515 is missing expected H atoms. Skipping. Residue VAL 518 is missing expected H atoms. Skipping. Residue VAL 523 is missing expected H atoms. Skipping. Residue ALA 525 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue MET 16 is missing expected H atoms. Skipping. Residue ALA 17 is missing expected H atoms. Skipping. Residue ALA 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 20 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue ALA 23 is missing expected H atoms. Skipping. Residue LEU 24 is missing expected H atoms. Skipping. Residue ALA 27 is missing expected H atoms. Skipping. Residue LEU 29 is missing expected H atoms. Skipping. Residue MET 35 is missing expected H atoms. Skipping. Residue VAL 39 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue THR 47 is missing expected H atoms. Skipping. Residue ALA 51 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue THR 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ALA 56 is missing expected H atoms. Skipping. Residue ALA 60 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue ALA 64 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue THR 92 is missing expected H atoms. Skipping. Residue VAL 93 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue ALA 107 is missing expected H atoms. Skipping. Residue VAL 110 is missing expected H atoms. Skipping. Residue ALA 114 is missing expected H atoms. Skipping. Residue THR 120 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Residue ALA 129 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue ALA 135 is missing expected H atoms. Skipping. Residue MET 136 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue ALA 151 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue ALA 162 is missing expected H atoms. Skipping. Residue ALA 167 is missing expected H atoms. Skipping. Residue ALA 170 is missing expected H atoms. Skipping. Residue LEU 171 is missing expected H atoms. Skipping. Residue VAL 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue ALA 180 is missing expected H atoms. Skipping. Residue ILE 187 is missing expected H atoms. Skipping. Residue ILE 189 is missing expected H atoms. Skipping. Residue ALA 190 is missing expected H atoms. Skipping. Residue MET 192 is missing expected H atoms. Skipping. Residue ILE 193 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue LEU 200 is missing expected H atoms. Skipping. Residue ALA 201 is missing expected H atoms. Skipping. Residue ILE 203 is missing expected H atoms. Skipping. Residue VAL 204 is missing expected H atoms. Skipping. Residue THR 211 is missing expected H atoms. Skipping. Residue ALA 212 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue ALA 216 is missing expected H atoms. Skipping. Residue THR 219 is missing expected H atoms. Skipping. Residue VAL 223 is missing expected H atoms. Skipping. Residue ALA 227 is missing expected H atoms. Skipping. Residue LEU 229 is missing expected H atoms. Skipping. Residue ALA 230 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue VAL 238 is missing expected H atoms. Skipping. Residue ALA 245 is missing expected H atoms. Skipping. Residue VAL 248 is missing expected H atoms. Skipping. Residue ALA 250 is missing expected H atoms. Skipping. Residue VAL 251 is missing expected H atoms. Skipping. Residue ALA 254 is missing expected H atoms. Skipping. Residue LEU 255 is missing expected H atoms. Skipping. Residue VAL 260 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue ALA 269 is missing expected H atoms. Skipping. Residue LEU 276 is missing expected H atoms. Skipping. Residue THR 277 is missing expected H atoms. Skipping. Residue ILE 281 is missing expected H atoms. Skipping. Residue ALA 284 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue ILE 290 is missing expected H atoms. Skipping. Residue ALA 291 is missing expected H atoms. Skipping. Residue VAL 295 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LEU 303 is missing expected H atoms. Skipping. Residue THR 315 is missing expected H atoms. Skipping. Residue VAL 316 is missing expected H atoms. Skipping. Residue MET 317 is missing expected H atoms. Skipping. Residue THR 321 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue THR 328 is missing expected H atoms. Skipping. Residue ILE 329 is missing expected H atoms. Skipping. Residue ALA 330 is missing expected H atoms. Skipping. Residue ALA 331 is missing expected H atoms. Skipping. Residue LEU 332 is missing expected H atoms. Skipping. Residue MET 336 is missing expected H atoms. Skipping. Residue LEU 338 is missing expected H atoms. Skipping. Residue ALA 340 is missing expected H atoms. Skipping. Residue LEU 342 is missing expected H atoms. Skipping. Residue ALA 344 is missing expected H atoms. Skipping. Residue THR 346 is missing expected H atoms. Skipping. Residue THR 347 is missing expected H atoms. Skipping. Residue ILE 352 is missing expected H atoms. Skipping. Residue THR 353 is missing expected H atoms. Skipping. Residue ALA 354 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue VAL 360 is missing expected H atoms. Skipping. Residue ILE 364 is missing expected H atoms. Skipping. Residue ALA 368 is missing expected H atoms. Skipping. Residue ILE 371 is missing expected H atoms. Skipping. Residue ALA 375 is missing expected H atoms. Skipping. Residue ILE 380 is missing expected H atoms. Skipping. Residue VAL 381 is missing expected H atoms. Skipping. Residue ALA 383 is missing expected H atoms. Skipping. Residue VAL 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue ALA 386 is missing expected H atoms. Skipping. Residue LEU 388 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue ILE 6 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue ILE 19 is missing expected H atoms. Skipping. Residue ALA 20 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue THR 24 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue ALA 28 is missing expected H atoms. Skipping. Residue ALA 29 is missing expected H atoms. Skipping. Residue MET 31 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue MET 37 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue THR 41 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue ILE 56 is missing expected H atoms. Skipping. Residue ALA 58 is missing expected H atoms. Skipping. Residue LEU 60 is missing expected H atoms. Skipping. Residue VAL 64 is missing expected H atoms. Skipping. Residue ALA 65 is missing expected H atoms. Skipping. Residue VAL 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue ALA 69 is missing expected H atoms. Skipping. Residue ALA 71 is missing expected H atoms. Skipping. Residue VAL 75 is missing expected H atoms. Skipping. Residue THR 81 is missing expected H atoms. Skipping. Residue ALA 82 is missing expected H atoms. Skipping. Residue ALA 87 is missing expected H atoms. Skipping. Residue VAL 90 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue THR 94 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue MET 98 is missing expected H atoms. Skipping. Residue ALA 100 is missing expected H atoms. Skipping. Residue ALA 101 is missing expected H atoms. Skipping. Residue ALA 107 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 112 is missing expected H atoms. Skipping. Residue ALA 117 is missing expected H atoms. Skipping. Residue ILE 122 is missing expected H atoms. Skipping. Residue MET 123 is missing expected H atoms. Skipping. Residue VAL 125 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue THR 137 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue MET 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue THR 150 is missing expected H atoms. Skipping. Residue LEU 152 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue VAL 161 is missing expected H atoms. Skipping. Residue VAL 163 is missing expected H atoms. Skipping. Residue VAL 164 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue ILE 6 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue ILE 19 is missing expected H atoms. Skipping. Residue ALA 20 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue THR 24 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue ALA 28 is missing expected H atoms. Skipping. Residue ALA 29 is missing expected H atoms. Skipping. Residue MET 31 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue MET 37 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue THR 41 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue ILE 56 is missing expected H atoms. Skipping. Residue ALA 58 is missing expected H atoms. Skipping. Residue LEU 60 is missing expected H atoms. Skipping. Residue VAL 64 is missing expected H atoms. Skipping. Residue ALA 65 is missing expected H atoms. Skipping. Residue VAL 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue ALA 69 is missing expected H atoms. Skipping. Residue ALA 71 is missing expected H atoms. Skipping. Residue VAL 75 is missing expected H atoms. Skipping. Residue THR 81 is missing expected H atoms. Skipping. Residue ALA 82 is missing expected H atoms. Skipping. Residue ALA 87 is missing expected H atoms. Skipping. Residue VAL 90 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue THR 94 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue MET 98 is missing expected H atoms. Skipping. Residue ALA 100 is missing expected H atoms. Skipping. Residue ALA 101 is missing expected H atoms. Skipping. Residue ALA 107 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 112 is missing expected H atoms. Skipping. Residue ALA 117 is missing expected H atoms. Skipping. Residue ILE 122 is missing expected H atoms. Skipping. Residue MET 123 is missing expected H atoms. Skipping. Residue VAL 125 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue THR 137 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue MET 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue THR 150 is missing expected H atoms. Skipping. Residue LEU 152 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue VAL 161 is missing expected H atoms. Skipping. Residue VAL 163 is missing expected H atoms. Skipping. Residue VAL 164 is missing expected H atoms. Skipping. Evaluate side-chains 179 residues out of total 1782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 150 time to evaluate : 2.209 Fit side-chains revert: symmetry clash REVERT: D 55 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7737 (pm20) REVERT: D 311 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.6890 (mm-30) REVERT: D 445 MET cc_start: 0.9107 (OUTLIER) cc_final: 0.8792 (mtm) REVERT: E 30 ARG cc_start: 0.8592 (tmt-80) cc_final: 0.7613 (ttm110) REVERT: E 70 MET cc_start: 0.8851 (ptt) cc_final: 0.8366 (ptm) REVERT: E 307 ARG cc_start: 0.8601 (OUTLIER) cc_final: 0.7214 (ttm-80) REVERT: E 520 LYS cc_start: 0.8298 (mttm) cc_final: 0.7950 (mtmt) REVERT: B 7 ARG cc_start: 0.7616 (OUTLIER) cc_final: 0.6451 (mmm-85) REVERT: B 86 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.8470 (pt0) REVERT: B 103 ARG cc_start: 0.8826 (OUTLIER) cc_final: 0.7344 (mtp180) REVERT: B 308 GLU cc_start: 0.7958 (tt0) cc_final: 0.7515 (tp30) REVERT: C 130 ASP cc_start: 0.8700 (OUTLIER) cc_final: 0.8396 (t70) REVERT: C 165 GLN cc_start: 0.8798 (OUTLIER) cc_final: 0.7822 (tm-30) REVERT: C 225 LYS cc_start: 0.8766 (OUTLIER) cc_final: 0.8535 (tttm) REVERT: G 74 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7643 (mt-10) REVERT: H 21 GLN cc_start: 0.8418 (OUTLIER) cc_final: 0.8041 (mp10) REVERT: H 70 ARG cc_start: 0.8362 (ttp-110) cc_final: 0.8083 (mtp180) outliers start: 29 outliers final: 12 residues processed: 170 average time/residue: 2.1539 time to fit residues: 399.3911 Evaluate side-chains 170 residues out of total 1782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 146 time to evaluate : 2.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 40 LYS Chi-restraints excluded: chain D residue 55 GLU Chi-restraints excluded: chain D residue 76 GLU Chi-restraints excluded: chain D residue 125 TRP Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain D residue 311 GLU Chi-restraints excluded: chain D residue 444 GLN Chi-restraints excluded: chain D residue 445 MET Chi-restraints excluded: chain D residue 460 GLU Chi-restraints excluded: chain E residue 125 TRP Chi-restraints excluded: chain E residue 307 ARG Chi-restraints excluded: chain E residue 474 GLU Chi-restraints excluded: chain B residue 7 ARG Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 103 ARG Chi-restraints excluded: chain B residue 173 ASP Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 165 GLN Chi-restraints excluded: chain C residue 173 ASP Chi-restraints excluded: chain C residue 225 LYS Chi-restraints excluded: chain G residue 41 THR Chi-restraints excluded: chain G residue 74 GLU Chi-restraints excluded: chain H residue 21 GLN Chi-restraints excluded: chain H residue 37 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 54 optimal weight: 5.9990 chunk 186 optimal weight: 6.9990 chunk 180 optimal weight: 5.9990 chunk 146 optimal weight: 7.9990 chunk 7 optimal weight: 0.6980 chunk 102 optimal weight: 2.9990 chunk 140 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 189 optimal weight: 7.9990 chunk 48 optimal weight: 0.9980 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 59 GLN ** D 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 17 ASN ** G 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.091230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.081196 restraints weight = 33450.876| |-----------------------------------------------------------------------------| r_work (start): 0.2785 rms_B_bonded: 1.11 r_work: 0.2691 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.2585 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.2585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.1099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 17861 Z= 0.215 Angle : 0.497 5.774 24231 Z= 0.278 Chirality : 0.041 0.163 2461 Planarity : 0.005 0.046 3153 Dihedral : 5.149 70.463 2346 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.74 % Allowed : 7.69 % Favored : 90.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.19), residues: 2101 helix: 1.11 (0.14), residues: 1359 sheet: 1.86 (0.80), residues: 44 loop : -0.21 (0.24), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 125 HIS 0.008 0.001 HIS D 382 PHE 0.017 0.002 PHE E 39 TYR 0.015 0.002 TYR D 156 ARG 0.004 0.001 ARG C 104 Details of bonding type rmsd hydrogen bonds : bond 0.05714 ( 993) hydrogen bonds : angle 5.22333 ( 2883) covalent geometry : bond 0.00501 (17861) covalent geometry : angle 0.49686 (24231) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 19 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue VAL 23 is missing expected H atoms. Skipping. Residue ALA 25 is missing expected H atoms. Skipping. Residue VAL 28 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue THR 44 is missing expected H atoms. Skipping. Residue ALA 47 is missing expected H atoms. Skipping. Residue THR 48 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ALA 53 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue ALA 64 is missing expected H atoms. Skipping. Residue ALA 68 is missing expected H atoms. Skipping. Residue MET 70 is missing expected H atoms. Skipping. Residue ALA 72 is missing expected H atoms. Skipping. Residue VAL 73 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue ALA 85 is missing expected H atoms. Skipping. Residue LEU 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue ALA 91 is missing expected H atoms. Skipping. Residue VAL 93 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue THR 102 is missing expected H atoms. Skipping. Residue MET 103 is missing expected H atoms. Skipping. Residue VAL 105 is missing expected H atoms. Skipping. Residue VAL 106 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue VAL 112 is missing expected H atoms. Skipping. Residue ALA 117 is missing expected H atoms. Skipping. Residue ILE 118 is missing expected H atoms. Skipping. Residue ALA 119 is missing expected H atoms. Skipping. Residue ALA 120 is missing expected H atoms. Skipping. Residue THR 121 is missing expected H atoms. Skipping. Residue MET 123 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Residue ALA 128 is missing expected H atoms. Skipping. Residue ALA 130 is missing expected H atoms. Skipping. Residue ALA 131 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue ALA 139 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue THR 148 is missing expected H atoms. Skipping. Residue ALA 152 is missing expected H atoms. Skipping. Residue VAL 154 is missing expected H atoms. Skipping. Residue ALA 159 is missing expected H atoms. Skipping. Residue ALA 166 is missing expected H atoms. Skipping. Residue ALA 171 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue ILE 177 is missing expected H atoms. Skipping. Residue LEU 180 is missing expected H atoms. Skipping. Residue MET 184 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue ILE 193 is missing expected H atoms. Skipping. Residue ALA 197 is missing expected H atoms. Skipping. Residue VAL 198 is missing expected H atoms. Skipping. Residue LEU 202 is missing expected H atoms. Skipping. Residue LEU 204 is missing expected H atoms. Skipping. Residue LEU 206 is missing expected H atoms. Skipping. Residue VAL 207 is missing expected H atoms. Skipping. Residue ALA 210 is missing expected H atoms. Skipping. Residue THR 213 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue ILE 217 is missing expected H atoms. Skipping. Residue VAL 218 is missing expected H atoms. Skipping. Residue ALA 219 is missing expected H atoms. Skipping. Residue VAL 220 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue ALA 224 is missing expected H atoms. Skipping. Residue ALA 225 is missing expected H atoms. Skipping. Residue ALA 226 is missing expected H atoms. Skipping. Residue ILE 231 is missing expected H atoms. Skipping. Residue THR 232 is missing expected H atoms. Skipping. Residue THR 234 is missing expected H atoms. Skipping. Residue VAL 235 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue ILE 239 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LEU 244 is missing expected H atoms. Skipping. Residue MET 247 is missing expected H atoms. Skipping. Residue ALA 248 is missing expected H atoms. Skipping. Residue THR 253 is missing expected H atoms. Skipping. Residue VAL 254 is missing expected H atoms. Skipping. Residue VAL 255 is missing expected H atoms. Skipping. Residue ILE 257 is missing expected H atoms. Skipping. Residue ALA 258 is missing expected H atoms. Skipping. Residue ALA 262 is missing expected H atoms. Skipping. Residue ALA 264 is missing expected H atoms. Skipping. Residue LEU 267 is missing expected H atoms. Skipping. Residue THR 269 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue ALA 274 is missing expected H atoms. Skipping. Residue THR 277 is missing expected H atoms. Skipping. Residue THR 283 is missing expected H atoms. Skipping. Residue VAL 285 is missing expected H atoms. Skipping. Residue LEU 286 is missing expected H atoms. Skipping. Residue MET 288 is missing expected H atoms. Skipping. Residue LEU 289 is missing expected H atoms. Skipping. Residue VAL 298 is missing expected H atoms. Skipping. Residue VAL 302 is missing expected H atoms. Skipping. Residue THR 304 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Residue ILE 316 is missing expected H atoms. Skipping. Residue ILE 318 is missing expected H atoms. Skipping. Residue LEU 321 is missing expected H atoms. Skipping. Residue VAL 326 is missing expected H atoms. Skipping. Residue LEU 332 is missing expected H atoms. Skipping. Residue ALA 335 is missing expected H atoms. Skipping. Residue ALA 339 is missing expected H atoms. Skipping. Residue ALA 342 is missing expected H atoms. Skipping. Residue LEU 346 is missing expected H atoms. Skipping. Residue LEU 348 is missing expected H atoms. Skipping. Residue LEU 349 is missing expected H atoms. Skipping. Residue ALA 350 is missing expected H atoms. Skipping. Residue ALA 352 is missing expected H atoms. Skipping. Residue LEU 353 is missing expected H atoms. Skipping. Residue THR 356 is missing expected H atoms. Skipping. Residue LEU 361 is missing expected H atoms. Skipping. Residue ALA 362 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue MET 369 is missing expected H atoms. Skipping. Residue ALA 374 is missing expected H atoms. Skipping. Residue ILE 386 is missing expected H atoms. Skipping. Residue ALA 392 is missing expected H atoms. Skipping. Residue ILE 403 is missing expected H atoms. Skipping. Residue LEU 405 is missing expected H atoms. Skipping. Residue MET 406 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 415 is missing expected H atoms. Skipping. Residue ILE 417 is missing expected H atoms. Skipping. Residue VAL 420 is missing expected H atoms. Skipping. Residue VAL 423 is missing expected H atoms. Skipping. Residue LEU 429 is missing expected H atoms. Skipping. Residue ALA 430 is missing expected H atoms. Skipping. Residue ALA 433 is missing expected H atoms. Skipping. Residue THR 435 is missing expected H atoms. Skipping. Residue LEU 436 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue MET 445 is missing expected H atoms. Skipping. Residue THR 447 is missing expected H atoms. Skipping. Residue MET 456 is missing expected H atoms. Skipping. Residue LEU 458 is missing expected H atoms. Skipping. Residue ALA 459 is missing expected H atoms. Skipping. Residue ILE 469 is missing expected H atoms. Skipping. Residue LEU 478 is missing expected H atoms. Skipping. Residue VAL 481 is missing expected H atoms. Skipping. Residue ILE 482 is missing expected H atoms. Skipping. Residue ALA 483 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue LEU 488 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue LEU 495 is missing expected H atoms. Skipping. Residue ILE 496 is missing expected H atoms. Skipping. Residue ALA 497 is missing expected H atoms. Skipping. Residue VAL 501 is missing expected H atoms. Skipping. Residue LEU 506 is missing expected H atoms. Skipping. Residue THR 508 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue LEU 515 is missing expected H atoms. Skipping. Residue VAL 518 is missing expected H atoms. Skipping. Residue VAL 523 is missing expected H atoms. Skipping. Residue ALA 525 is missing expected H atoms. Skipping. Residue ALA 16 is missing expected H atoms. Skipping. Residue ALA 19 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue VAL 23 is missing expected H atoms. Skipping. Residue ALA 25 is missing expected H atoms. Skipping. Residue VAL 28 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue THR 44 is missing expected H atoms. Skipping. Residue ALA 47 is missing expected H atoms. Skipping. Residue THR 48 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ALA 53 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue ALA 64 is missing expected H atoms. Skipping. Residue ALA 68 is missing expected H atoms. Skipping. Residue MET 70 is missing expected H atoms. Skipping. Residue ALA 72 is missing expected H atoms. Skipping. Residue VAL 73 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue ALA 85 is missing expected H atoms. Skipping. Residue LEU 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue ALA 91 is missing expected H atoms. Skipping. Residue VAL 93 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue THR 102 is missing expected H atoms. Skipping. Residue MET 103 is missing expected H atoms. Skipping. Residue VAL 105 is missing expected H atoms. Skipping. Residue VAL 106 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue VAL 112 is missing expected H atoms. Skipping. Residue ALA 117 is missing expected H atoms. Skipping. Residue ILE 118 is missing expected H atoms. Skipping. Residue ALA 119 is missing expected H atoms. Skipping. Residue ALA 120 is missing expected H atoms. Skipping. Residue THR 121 is missing expected H atoms. Skipping. Residue MET 123 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Residue ALA 128 is missing expected H atoms. Skipping. Residue ALA 130 is missing expected H atoms. Skipping. Residue ALA 131 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue ALA 139 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue THR 148 is missing expected H atoms. Skipping. Residue ALA 152 is missing expected H atoms. Skipping. Residue VAL 154 is missing expected H atoms. Skipping. Residue ALA 159 is missing expected H atoms. Skipping. Residue ALA 166 is missing expected H atoms. Skipping. Residue ALA 171 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue ILE 177 is missing expected H atoms. Skipping. Residue LEU 180 is missing expected H atoms. Skipping. Residue MET 184 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue ILE 193 is missing expected H atoms. Skipping. Residue ALA 197 is missing expected H atoms. Skipping. Residue VAL 198 is missing expected H atoms. Skipping. Residue LEU 202 is missing expected H atoms. Skipping. Residue LEU 204 is missing expected H atoms. Skipping. Residue LEU 206 is missing expected H atoms. Skipping. Residue VAL 207 is missing expected H atoms. Skipping. Residue ALA 210 is missing expected H atoms. Skipping. Residue THR 213 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue ILE 217 is missing expected H atoms. Skipping. Residue VAL 218 is missing expected H atoms. Skipping. Residue ALA 219 is missing expected H atoms. Skipping. Residue VAL 220 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue ALA 224 is missing expected H atoms. Skipping. Residue ALA 225 is missing expected H atoms. Skipping. Residue ALA 226 is missing expected H atoms. Skipping. Residue ILE 231 is missing expected H atoms. Skipping. Residue THR 232 is missing expected H atoms. Skipping. Residue THR 234 is missing expected H atoms. Skipping. Residue VAL 235 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue ILE 239 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LEU 244 is missing expected H atoms. Skipping. Residue MET 247 is missing expected H atoms. Skipping. Residue ALA 248 is missing expected H atoms. Skipping. Residue THR 253 is missing expected H atoms. Skipping. Residue VAL 254 is missing expected H atoms. Skipping. Residue VAL 255 is missing expected H atoms. Skipping. Residue ILE 257 is missing expected H atoms. Skipping. Residue ALA 258 is missing expected H atoms. Skipping. Residue ALA 262 is missing expected H atoms. Skipping. Residue ALA 264 is missing expected H atoms. Skipping. Residue LEU 267 is missing expected H atoms. Skipping. Residue THR 269 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue ALA 274 is missing expected H atoms. Skipping. Residue THR 277 is missing expected H atoms. Skipping. Residue THR 283 is missing expected H atoms. Skipping. Residue VAL 285 is missing expected H atoms. Skipping. Residue LEU 286 is missing expected H atoms. Skipping. Residue MET 288 is missing expected H atoms. Skipping. Residue LEU 289 is missing expected H atoms. Skipping. Residue VAL 298 is missing expected H atoms. Skipping. Residue VAL 302 is missing expected H atoms. Skipping. Residue THR 304 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Residue ILE 316 is missing expected H atoms. Skipping. Residue ILE 318 is missing expected H atoms. Skipping. Residue LEU 321 is missing expected H atoms. Skipping. Residue VAL 326 is missing expected H atoms. Skipping. Residue LEU 332 is missing expected H atoms. Skipping. Residue ALA 335 is missing expected H atoms. Skipping. Residue ALA 339 is missing expected H atoms. Skipping. Residue ALA 342 is missing expected H atoms. Skipping. Residue LEU 346 is missing expected H atoms. Skipping. Residue LEU 348 is missing expected H atoms. Skipping. Residue LEU 349 is missing expected H atoms. Skipping. Residue ALA 350 is missing expected H atoms. Skipping. Residue ALA 352 is missing expected H atoms. Skipping. Residue LEU 353 is missing expected H atoms. Skipping. Residue THR 356 is missing expected H atoms. Skipping. Residue LEU 361 is missing expected H atoms. Skipping. Residue ALA 362 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue MET 369 is missing expected H atoms. Skipping. Residue ALA 374 is missing expected H atoms. Skipping. Residue ILE 386 is missing expected H atoms. Skipping. Residue ALA 392 is missing expected H atoms. Skipping. Residue ILE 403 is missing expected H atoms. Skipping. Residue LEU 405 is missing expected H atoms. Skipping. Residue MET 406 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 415 is missing expected H atoms. Skipping. Residue ILE 417 is missing expected H atoms. Skipping. Residue VAL 420 is missing expected H atoms. Skipping. Residue VAL 423 is missing expected H atoms. Skipping. Residue LEU 429 is missing expected H atoms. Skipping. Residue ALA 430 is missing expected H atoms. Skipping. Residue ALA 433 is missing expected H atoms. Skipping. Residue THR 435 is missing expected H atoms. Skipping. Residue LEU 436 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue MET 445 is missing expected H atoms. Skipping. Residue THR 447 is missing expected H atoms. Skipping. Residue MET 456 is missing expected H atoms. Skipping. Residue LEU 458 is missing expected H atoms. Skipping. Residue ALA 459 is missing expected H atoms. Skipping. Residue ILE 469 is missing expected H atoms. Skipping. Residue LEU 478 is missing expected H atoms. Skipping. Residue VAL 481 is missing expected H atoms. Skipping. Residue ILE 482 is missing expected H atoms. Skipping. Residue ALA 483 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue LEU 488 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue LEU 495 is missing expected H atoms. Skipping. Residue ILE 496 is missing expected H atoms. Skipping. Residue ALA 497 is missing expected H atoms. Skipping. Residue VAL 501 is missing expected H atoms. Skipping. Residue LEU 506 is missing expected H atoms. Skipping. Residue THR 508 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue LEU 515 is missing expected H atoms. Skipping. Residue VAL 518 is missing expected H atoms. Skipping. Residue VAL 523 is missing expected H atoms. Skipping. Residue ALA 525 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue MET 16 is missing expected H atoms. Skipping. Residue ALA 17 is missing expected H atoms. Skipping. Residue ALA 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 20 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue ALA 23 is missing expected H atoms. Skipping. Residue LEU 24 is missing expected H atoms. Skipping. Residue ALA 27 is missing expected H atoms. Skipping. Residue LEU 29 is missing expected H atoms. Skipping. Residue MET 35 is missing expected H atoms. Skipping. Residue VAL 39 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue THR 47 is missing expected H atoms. Skipping. Residue ALA 51 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue THR 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ALA 56 is missing expected H atoms. Skipping. Residue ALA 60 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue ALA 64 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue THR 92 is missing expected H atoms. Skipping. Residue VAL 93 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue ALA 107 is missing expected H atoms. Skipping. Residue VAL 110 is missing expected H atoms. Skipping. Residue ALA 114 is missing expected H atoms. Skipping. Residue THR 120 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Residue ALA 129 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue ALA 135 is missing expected H atoms. Skipping. Residue MET 136 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue ALA 151 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue ALA 162 is missing expected H atoms. Skipping. Residue ALA 167 is missing expected H atoms. Skipping. Residue ALA 170 is missing expected H atoms. Skipping. Residue LEU 171 is missing expected H atoms. Skipping. Residue VAL 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue ALA 180 is missing expected H atoms. Skipping. Residue ILE 187 is missing expected H atoms. Skipping. Residue ILE 189 is missing expected H atoms. Skipping. Residue ALA 190 is missing expected H atoms. Skipping. Residue MET 192 is missing expected H atoms. Skipping. Residue ILE 193 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue LEU 200 is missing expected H atoms. Skipping. Residue ALA 201 is missing expected H atoms. Skipping. Residue ILE 203 is missing expected H atoms. Skipping. Residue VAL 204 is missing expected H atoms. Skipping. Residue THR 211 is missing expected H atoms. Skipping. Residue ALA 212 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue ALA 216 is missing expected H atoms. Skipping. Residue THR 219 is missing expected H atoms. Skipping. Residue VAL 223 is missing expected H atoms. Skipping. Residue ALA 227 is missing expected H atoms. Skipping. Residue LEU 229 is missing expected H atoms. Skipping. Residue ALA 230 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue VAL 238 is missing expected H atoms. Skipping. Residue ALA 245 is missing expected H atoms. Skipping. Residue VAL 248 is missing expected H atoms. Skipping. Residue ALA 250 is missing expected H atoms. Skipping. Residue VAL 251 is missing expected H atoms. Skipping. Residue ALA 254 is missing expected H atoms. Skipping. Residue LEU 255 is missing expected H atoms. Skipping. Residue VAL 260 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue ALA 269 is missing expected H atoms. Skipping. Residue LEU 276 is missing expected H atoms. Skipping. Residue THR 277 is missing expected H atoms. Skipping. Residue ILE 281 is missing expected H atoms. Skipping. Residue ALA 284 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue ILE 290 is missing expected H atoms. Skipping. Residue ALA 291 is missing expected H atoms. Skipping. Residue VAL 295 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LEU 303 is missing expected H atoms. Skipping. Residue THR 315 is missing expected H atoms. Skipping. Residue VAL 316 is missing expected H atoms. Skipping. Residue MET 317 is missing expected H atoms. Skipping. Residue THR 321 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue THR 328 is missing expected H atoms. Skipping. Residue ILE 329 is missing expected H atoms. Skipping. Residue ALA 330 is missing expected H atoms. Skipping. Residue ALA 331 is missing expected H atoms. Skipping. Residue LEU 332 is missing expected H atoms. Skipping. Residue MET 336 is missing expected H atoms. Skipping. Residue LEU 338 is missing expected H atoms. Skipping. Residue ALA 340 is missing expected H atoms. Skipping. Residue LEU 342 is missing expected H atoms. Skipping. Residue ALA 344 is missing expected H atoms. Skipping. Residue THR 346 is missing expected H atoms. Skipping. Residue THR 347 is missing expected H atoms. Skipping. Residue ILE 352 is missing expected H atoms. Skipping. Residue THR 353 is missing expected H atoms. Skipping. Residue ALA 354 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue VAL 360 is missing expected H atoms. Skipping. Residue ILE 364 is missing expected H atoms. Skipping. Residue ALA 368 is missing expected H atoms. Skipping. Residue ILE 371 is missing expected H atoms. Skipping. Residue ALA 375 is missing expected H atoms. Skipping. Residue ILE 380 is missing expected H atoms. Skipping. Residue VAL 381 is missing expected H atoms. Skipping. Residue ALA 383 is missing expected H atoms. Skipping. Residue VAL 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue ALA 386 is missing expected H atoms. Skipping. Residue LEU 388 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue ILE 6 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue ILE 19 is missing expected H atoms. Skipping. Residue ALA 20 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue THR 24 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue ALA 28 is missing expected H atoms. Skipping. Residue ALA 29 is missing expected H atoms. Skipping. Residue MET 31 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue MET 37 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue THR 41 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue ILE 56 is missing expected H atoms. Skipping. Residue ALA 58 is missing expected H atoms. Skipping. Residue LEU 60 is missing expected H atoms. Skipping. Residue VAL 64 is missing expected H atoms. Skipping. Residue ALA 65 is missing expected H atoms. Skipping. Residue VAL 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue ALA 69 is missing expected H atoms. Skipping. Residue ALA 71 is missing expected H atoms. Skipping. Residue VAL 75 is missing expected H atoms. Skipping. Residue THR 81 is missing expected H atoms. Skipping. Residue ALA 82 is missing expected H atoms. Skipping. Residue ALA 87 is missing expected H atoms. Skipping. Residue VAL 90 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue THR 94 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue MET 98 is missing expected H atoms. Skipping. Residue ALA 100 is missing expected H atoms. Skipping. Residue ALA 101 is missing expected H atoms. Skipping. Residue ALA 107 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 112 is missing expected H atoms. Skipping. Residue ALA 117 is missing expected H atoms. Skipping. Residue ILE 122 is missing expected H atoms. Skipping. Residue MET 123 is missing expected H atoms. Skipping. Residue VAL 125 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue THR 137 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue MET 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue THR 150 is missing expected H atoms. Skipping. Residue LEU 152 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue VAL 161 is missing expected H atoms. Skipping. Residue VAL 163 is missing expected H atoms. Skipping. Residue VAL 164 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue ILE 6 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue ILE 19 is missing expected H atoms. Skipping. Residue ALA 20 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue THR 24 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue ALA 28 is missing expected H atoms. Skipping. Residue ALA 29 is missing expected H atoms. Skipping. Residue MET 31 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue MET 37 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue THR 41 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue ILE 56 is missing expected H atoms. Skipping. Residue ALA 58 is missing expected H atoms. Skipping. Residue LEU 60 is missing expected H atoms. Skipping. Residue VAL 64 is missing expected H atoms. Skipping. Residue ALA 65 is missing expected H atoms. Skipping. Residue VAL 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue ALA 69 is missing expected H atoms. Skipping. Residue ALA 71 is missing expected H atoms. Skipping. Residue VAL 75 is missing expected H atoms. Skipping. Residue THR 81 is missing expected H atoms. Skipping. Residue ALA 82 is missing expected H atoms. Skipping. Residue ALA 87 is missing expected H atoms. Skipping. Residue VAL 90 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue THR 94 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue MET 98 is missing expected H atoms. Skipping. Residue ALA 100 is missing expected H atoms. Skipping. Residue ALA 101 is missing expected H atoms. Skipping. Residue ALA 107 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 112 is missing expected H atoms. Skipping. Residue ALA 117 is missing expected H atoms. Skipping. Residue ILE 122 is missing expected H atoms. Skipping. Residue MET 123 is missing expected H atoms. Skipping. Residue VAL 125 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue THR 137 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue MET 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue THR 150 is missing expected H atoms. Skipping. Residue LEU 152 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue VAL 161 is missing expected H atoms. Skipping. Residue VAL 163 is missing expected H atoms. Skipping. Residue VAL 164 is missing expected H atoms. Skipping. Evaluate side-chains 179 residues out of total 1782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 148 time to evaluate : 2.782 Fit side-chains revert: symmetry clash REVERT: D 55 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7755 (pm20) REVERT: D 405 LEU cc_start: 0.8300 (tp) cc_final: 0.8098 (tp) REVERT: E 30 ARG cc_start: 0.8608 (tmt-80) cc_final: 0.7621 (ttm110) REVERT: E 70 MET cc_start: 0.8899 (ptt) cc_final: 0.8462 (ptm) REVERT: E 307 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.7216 (ttm-80) REVERT: E 520 LYS cc_start: 0.8319 (mttm) cc_final: 0.7970 (mtmt) REVERT: B 7 ARG cc_start: 0.7523 (OUTLIER) cc_final: 0.6512 (mmm-85) REVERT: B 86 GLU cc_start: 0.8785 (OUTLIER) cc_final: 0.8476 (pt0) REVERT: B 103 ARG cc_start: 0.8839 (OUTLIER) cc_final: 0.7322 (mtp180) REVERT: B 308 GLU cc_start: 0.7894 (tt0) cc_final: 0.7474 (tp30) REVERT: C 130 ASP cc_start: 0.8711 (OUTLIER) cc_final: 0.8409 (t70) REVERT: C 165 GLN cc_start: 0.8837 (OUTLIER) cc_final: 0.7532 (tm-30) REVERT: C 271 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.7548 (mtt-85) REVERT: G 26 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7448 (tt0) REVERT: G 74 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7653 (mt-10) REVERT: H 21 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.8106 (mp10) outliers start: 31 outliers final: 12 residues processed: 171 average time/residue: 2.1574 time to fit residues: 403.2469 Evaluate side-chains 166 residues out of total 1782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 143 time to evaluate : 2.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 40 LYS Chi-restraints excluded: chain D residue 55 GLU Chi-restraints excluded: chain D residue 76 GLU Chi-restraints excluded: chain D residue 125 TRP Chi-restraints excluded: chain D residue 409 ILE Chi-restraints excluded: chain D residue 444 GLN Chi-restraints excluded: chain D residue 460 GLU Chi-restraints excluded: chain D residue 517 CYS Chi-restraints excluded: chain E residue 125 TRP Chi-restraints excluded: chain E residue 307 ARG Chi-restraints excluded: chain B residue 7 ARG Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 103 ARG Chi-restraints excluded: chain B residue 173 ASP Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 165 GLN Chi-restraints excluded: chain C residue 173 ASP Chi-restraints excluded: chain C residue 271 ARG Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain G residue 41 THR Chi-restraints excluded: chain G residue 74 GLU Chi-restraints excluded: chain H residue 21 GLN Chi-restraints excluded: chain H residue 37 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 121 optimal weight: 3.9990 chunk 21 optimal weight: 7.9990 chunk 11 optimal weight: 4.9990 chunk 173 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 155 optimal weight: 0.6980 chunk 99 optimal weight: 0.2980 chunk 50 optimal weight: 0.9990 chunk 93 optimal weight: 4.9990 chunk 139 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 59 GLN ** D 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 203 ASN ** G 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.095052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.085200 restraints weight = 32868.407| |-----------------------------------------------------------------------------| r_work (start): 0.2821 rms_B_bonded: 1.02 r_work: 0.2738 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.2639 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.1321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 17861 Z= 0.108 Angle : 0.403 4.765 24231 Z= 0.228 Chirality : 0.036 0.135 2461 Planarity : 0.004 0.043 3153 Dihedral : 4.823 67.616 2346 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.18 % Allowed : 8.42 % Favored : 90.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.19), residues: 2101 helix: 1.47 (0.15), residues: 1359 sheet: 1.89 (0.79), residues: 44 loop : 0.00 (0.24), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 105 HIS 0.006 0.001 HIS D 343 PHE 0.010 0.001 PHE D 188 TYR 0.015 0.001 TYR D 156 ARG 0.002 0.000 ARG B 99 Details of bonding type rmsd hydrogen bonds : bond 0.04464 ( 993) hydrogen bonds : angle 4.86274 ( 2883) covalent geometry : bond 0.00223 (17861) covalent geometry : angle 0.40273 (24231) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 19 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue VAL 23 is missing expected H atoms. Skipping. Residue ALA 25 is missing expected H atoms. Skipping. Residue VAL 28 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue THR 44 is missing expected H atoms. Skipping. Residue ALA 47 is missing expected H atoms. Skipping. Residue THR 48 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ALA 53 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue ALA 64 is missing expected H atoms. Skipping. Residue ALA 68 is missing expected H atoms. Skipping. Residue MET 70 is missing expected H atoms. Skipping. Residue ALA 72 is missing expected H atoms. Skipping. Residue VAL 73 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue ALA 85 is missing expected H atoms. Skipping. Residue LEU 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue ALA 91 is missing expected H atoms. Skipping. Residue VAL 93 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue THR 102 is missing expected H atoms. Skipping. Residue MET 103 is missing expected H atoms. Skipping. Residue VAL 105 is missing expected H atoms. Skipping. Residue VAL 106 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue VAL 112 is missing expected H atoms. Skipping. Residue ALA 117 is missing expected H atoms. Skipping. Residue ILE 118 is missing expected H atoms. Skipping. Residue ALA 119 is missing expected H atoms. Skipping. Residue ALA 120 is missing expected H atoms. Skipping. Residue THR 121 is missing expected H atoms. Skipping. Residue MET 123 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Residue ALA 128 is missing expected H atoms. Skipping. Residue ALA 130 is missing expected H atoms. Skipping. Residue ALA 131 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue ALA 139 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue THR 148 is missing expected H atoms. Skipping. Residue ALA 152 is missing expected H atoms. Skipping. Residue VAL 154 is missing expected H atoms. Skipping. Residue ALA 159 is missing expected H atoms. Skipping. Residue ALA 166 is missing expected H atoms. Skipping. Residue ALA 171 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue ILE 177 is missing expected H atoms. Skipping. Residue LEU 180 is missing expected H atoms. Skipping. Residue MET 184 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue ILE 193 is missing expected H atoms. Skipping. Residue ALA 197 is missing expected H atoms. Skipping. Residue VAL 198 is missing expected H atoms. Skipping. Residue LEU 202 is missing expected H atoms. Skipping. Residue LEU 204 is missing expected H atoms. Skipping. Residue LEU 206 is missing expected H atoms. Skipping. Residue VAL 207 is missing expected H atoms. Skipping. Residue ALA 210 is missing expected H atoms. Skipping. Residue THR 213 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue ILE 217 is missing expected H atoms. Skipping. Residue VAL 218 is missing expected H atoms. Skipping. Residue ALA 219 is missing expected H atoms. Skipping. Residue VAL 220 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue ALA 224 is missing expected H atoms. Skipping. Residue ALA 225 is missing expected H atoms. Skipping. Residue ALA 226 is missing expected H atoms. Skipping. Residue ILE 231 is missing expected H atoms. Skipping. Residue THR 232 is missing expected H atoms. Skipping. Residue THR 234 is missing expected H atoms. Skipping. Residue VAL 235 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue ILE 239 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LEU 244 is missing expected H atoms. Skipping. Residue MET 247 is missing expected H atoms. Skipping. Residue ALA 248 is missing expected H atoms. Skipping. Residue THR 253 is missing expected H atoms. Skipping. Residue VAL 254 is missing expected H atoms. Skipping. Residue VAL 255 is missing expected H atoms. Skipping. Residue ILE 257 is missing expected H atoms. Skipping. Residue ALA 258 is missing expected H atoms. Skipping. Residue ALA 262 is missing expected H atoms. Skipping. Residue ALA 264 is missing expected H atoms. Skipping. Residue LEU 267 is missing expected H atoms. Skipping. Residue THR 269 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue ALA 274 is missing expected H atoms. Skipping. Residue THR 277 is missing expected H atoms. Skipping. Residue THR 283 is missing expected H atoms. Skipping. Residue VAL 285 is missing expected H atoms. Skipping. Residue LEU 286 is missing expected H atoms. Skipping. Residue MET 288 is missing expected H atoms. Skipping. Residue LEU 289 is missing expected H atoms. Skipping. Residue VAL 298 is missing expected H atoms. Skipping. Residue VAL 302 is missing expected H atoms. Skipping. Residue THR 304 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Residue ILE 316 is missing expected H atoms. Skipping. Residue ILE 318 is missing expected H atoms. Skipping. Residue LEU 321 is missing expected H atoms. Skipping. Residue VAL 326 is missing expected H atoms. Skipping. Residue LEU 332 is missing expected H atoms. Skipping. Residue ALA 335 is missing expected H atoms. Skipping. Residue ALA 339 is missing expected H atoms. Skipping. Residue ALA 342 is missing expected H atoms. Skipping. Residue LEU 346 is missing expected H atoms. Skipping. Residue LEU 348 is missing expected H atoms. Skipping. Residue LEU 349 is missing expected H atoms. Skipping. Residue ALA 350 is missing expected H atoms. Skipping. Residue ALA 352 is missing expected H atoms. Skipping. Residue LEU 353 is missing expected H atoms. Skipping. Residue THR 356 is missing expected H atoms. Skipping. Residue LEU 361 is missing expected H atoms. Skipping. Residue ALA 362 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue MET 369 is missing expected H atoms. Skipping. Residue ALA 374 is missing expected H atoms. Skipping. Residue ILE 386 is missing expected H atoms. Skipping. Residue ALA 392 is missing expected H atoms. Skipping. Residue ILE 403 is missing expected H atoms. Skipping. Residue LEU 405 is missing expected H atoms. Skipping. Residue MET 406 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 415 is missing expected H atoms. Skipping. Residue ILE 417 is missing expected H atoms. Skipping. Residue VAL 420 is missing expected H atoms. Skipping. Residue VAL 423 is missing expected H atoms. Skipping. Residue LEU 429 is missing expected H atoms. Skipping. Residue ALA 430 is missing expected H atoms. Skipping. Residue ALA 433 is missing expected H atoms. Skipping. Residue THR 435 is missing expected H atoms. Skipping. Residue LEU 436 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue MET 445 is missing expected H atoms. Skipping. Residue THR 447 is missing expected H atoms. Skipping. Residue MET 456 is missing expected H atoms. Skipping. Residue LEU 458 is missing expected H atoms. Skipping. Residue ALA 459 is missing expected H atoms. Skipping. Residue ILE 469 is missing expected H atoms. Skipping. Residue LEU 478 is missing expected H atoms. Skipping. Residue VAL 481 is missing expected H atoms. Skipping. Residue ILE 482 is missing expected H atoms. Skipping. Residue ALA 483 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue LEU 488 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue LEU 495 is missing expected H atoms. Skipping. Residue ILE 496 is missing expected H atoms. Skipping. Residue ALA 497 is missing expected H atoms. Skipping. Residue VAL 501 is missing expected H atoms. Skipping. Residue LEU 506 is missing expected H atoms. Skipping. Residue THR 508 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue LEU 515 is missing expected H atoms. Skipping. Residue VAL 518 is missing expected H atoms. Skipping. Residue VAL 523 is missing expected H atoms. Skipping. Residue ALA 525 is missing expected H atoms. Skipping. Residue ALA 16 is missing expected H atoms. Skipping. Residue ALA 19 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue VAL 23 is missing expected H atoms. Skipping. Residue ALA 25 is missing expected H atoms. Skipping. Residue VAL 28 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue THR 44 is missing expected H atoms. Skipping. Residue ALA 47 is missing expected H atoms. Skipping. Residue THR 48 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ALA 53 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue ALA 64 is missing expected H atoms. Skipping. Residue ALA 68 is missing expected H atoms. Skipping. Residue MET 70 is missing expected H atoms. Skipping. Residue ALA 72 is missing expected H atoms. Skipping. Residue VAL 73 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue ALA 85 is missing expected H atoms. Skipping. Residue LEU 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue ALA 91 is missing expected H atoms. Skipping. Residue VAL 93 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue THR 102 is missing expected H atoms. Skipping. Residue MET 103 is missing expected H atoms. Skipping. Residue VAL 105 is missing expected H atoms. Skipping. Residue VAL 106 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue VAL 112 is missing expected H atoms. Skipping. Residue ALA 117 is missing expected H atoms. Skipping. Residue ILE 118 is missing expected H atoms. Skipping. Residue ALA 119 is missing expected H atoms. Skipping. Residue ALA 120 is missing expected H atoms. Skipping. Residue THR 121 is missing expected H atoms. Skipping. Residue MET 123 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Residue ALA 128 is missing expected H atoms. Skipping. Residue ALA 130 is missing expected H atoms. Skipping. Residue ALA 131 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue ALA 139 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue THR 148 is missing expected H atoms. Skipping. Residue ALA 152 is missing expected H atoms. Skipping. Residue VAL 154 is missing expected H atoms. Skipping. Residue ALA 159 is missing expected H atoms. Skipping. Residue ALA 166 is missing expected H atoms. Skipping. Residue ALA 171 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue ILE 177 is missing expected H atoms. Skipping. Residue LEU 180 is missing expected H atoms. Skipping. Residue MET 184 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue ILE 193 is missing expected H atoms. Skipping. Residue ALA 197 is missing expected H atoms. Skipping. Residue VAL 198 is missing expected H atoms. Skipping. Residue LEU 202 is missing expected H atoms. Skipping. Residue LEU 204 is missing expected H atoms. Skipping. Residue LEU 206 is missing expected H atoms. Skipping. Residue VAL 207 is missing expected H atoms. Skipping. Residue ALA 210 is missing expected H atoms. Skipping. Residue THR 213 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue ILE 217 is missing expected H atoms. Skipping. Residue VAL 218 is missing expected H atoms. Skipping. Residue ALA 219 is missing expected H atoms. Skipping. Residue VAL 220 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue ALA 224 is missing expected H atoms. Skipping. Residue ALA 225 is missing expected H atoms. Skipping. Residue ALA 226 is missing expected H atoms. Skipping. Residue ILE 231 is missing expected H atoms. Skipping. Residue THR 232 is missing expected H atoms. Skipping. Residue THR 234 is missing expected H atoms. Skipping. Residue VAL 235 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue ILE 239 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LEU 244 is missing expected H atoms. Skipping. Residue MET 247 is missing expected H atoms. Skipping. Residue ALA 248 is missing expected H atoms. Skipping. Residue THR 253 is missing expected H atoms. Skipping. Residue VAL 254 is missing expected H atoms. Skipping. Residue VAL 255 is missing expected H atoms. Skipping. Residue ILE 257 is missing expected H atoms. Skipping. Residue ALA 258 is missing expected H atoms. Skipping. Residue ALA 262 is missing expected H atoms. Skipping. Residue ALA 264 is missing expected H atoms. Skipping. Residue LEU 267 is missing expected H atoms. Skipping. Residue THR 269 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue ALA 274 is missing expected H atoms. Skipping. Residue THR 277 is missing expected H atoms. Skipping. Residue THR 283 is missing expected H atoms. Skipping. Residue VAL 285 is missing expected H atoms. Skipping. Residue LEU 286 is missing expected H atoms. Skipping. Residue MET 288 is missing expected H atoms. Skipping. Residue LEU 289 is missing expected H atoms. Skipping. Residue VAL 298 is missing expected H atoms. Skipping. Residue VAL 302 is missing expected H atoms. Skipping. Residue THR 304 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Residue ILE 316 is missing expected H atoms. Skipping. Residue ILE 318 is missing expected H atoms. Skipping. Residue LEU 321 is missing expected H atoms. Skipping. Residue VAL 326 is missing expected H atoms. Skipping. Residue LEU 332 is missing expected H atoms. Skipping. Residue ALA 335 is missing expected H atoms. Skipping. Residue ALA 339 is missing expected H atoms. Skipping. Residue ALA 342 is missing expected H atoms. Skipping. Residue LEU 346 is missing expected H atoms. Skipping. Residue LEU 348 is missing expected H atoms. Skipping. Residue LEU 349 is missing expected H atoms. Skipping. Residue ALA 350 is missing expected H atoms. Skipping. Residue ALA 352 is missing expected H atoms. Skipping. Residue LEU 353 is missing expected H atoms. Skipping. Residue THR 356 is missing expected H atoms. Skipping. Residue LEU 361 is missing expected H atoms. Skipping. Residue ALA 362 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue MET 369 is missing expected H atoms. Skipping. Residue ALA 374 is missing expected H atoms. Skipping. Residue ILE 386 is missing expected H atoms. Skipping. Residue ALA 392 is missing expected H atoms. Skipping. Residue ILE 403 is missing expected H atoms. Skipping. Residue LEU 405 is missing expected H atoms. Skipping. Residue MET 406 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 415 is missing expected H atoms. Skipping. Residue ILE 417 is missing expected H atoms. Skipping. Residue VAL 420 is missing expected H atoms. Skipping. Residue VAL 423 is missing expected H atoms. Skipping. Residue LEU 429 is missing expected H atoms. Skipping. Residue ALA 430 is missing expected H atoms. Skipping. Residue ALA 433 is missing expected H atoms. Skipping. Residue THR 435 is missing expected H atoms. Skipping. Residue LEU 436 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue MET 445 is missing expected H atoms. Skipping. Residue THR 447 is missing expected H atoms. Skipping. Residue MET 456 is missing expected H atoms. Skipping. Residue LEU 458 is missing expected H atoms. Skipping. Residue ALA 459 is missing expected H atoms. Skipping. Residue ILE 469 is missing expected H atoms. Skipping. Residue LEU 478 is missing expected H atoms. Skipping. Residue VAL 481 is missing expected H atoms. Skipping. Residue ILE 482 is missing expected H atoms. Skipping. Residue ALA 483 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue LEU 488 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue LEU 495 is missing expected H atoms. Skipping. Residue ILE 496 is missing expected H atoms. Skipping. Residue ALA 497 is missing expected H atoms. Skipping. Residue VAL 501 is missing expected H atoms. Skipping. Residue LEU 506 is missing expected H atoms. Skipping. Residue THR 508 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue LEU 515 is missing expected H atoms. Skipping. Residue VAL 518 is missing expected H atoms. Skipping. Residue VAL 523 is missing expected H atoms. Skipping. Residue ALA 525 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue MET 16 is missing expected H atoms. Skipping. Residue ALA 17 is missing expected H atoms. Skipping. Residue ALA 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 20 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue ALA 23 is missing expected H atoms. Skipping. Residue LEU 24 is missing expected H atoms. Skipping. Residue ALA 27 is missing expected H atoms. Skipping. Residue LEU 29 is missing expected H atoms. Skipping. Residue MET 35 is missing expected H atoms. Skipping. Residue VAL 39 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue THR 47 is missing expected H atoms. Skipping. Residue ALA 51 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue THR 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ALA 56 is missing expected H atoms. Skipping. Residue ALA 60 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue ALA 64 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue THR 92 is missing expected H atoms. Skipping. Residue VAL 93 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue ALA 107 is missing expected H atoms. Skipping. Residue VAL 110 is missing expected H atoms. Skipping. Residue ALA 114 is missing expected H atoms. Skipping. Residue THR 120 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Residue ALA 129 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue ALA 135 is missing expected H atoms. Skipping. Residue MET 136 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue ALA 151 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue ALA 162 is missing expected H atoms. Skipping. Residue ALA 167 is missing expected H atoms. Skipping. Residue ALA 170 is missing expected H atoms. Skipping. Residue LEU 171 is missing expected H atoms. Skipping. Residue VAL 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue ALA 180 is missing expected H atoms. Skipping. Residue ILE 187 is missing expected H atoms. Skipping. Residue ILE 189 is missing expected H atoms. Skipping. Residue ALA 190 is missing expected H atoms. Skipping. Residue MET 192 is missing expected H atoms. Skipping. Residue ILE 193 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue LEU 200 is missing expected H atoms. Skipping. Residue ALA 201 is missing expected H atoms. Skipping. Residue ILE 203 is missing expected H atoms. Skipping. Residue VAL 204 is missing expected H atoms. Skipping. Residue THR 211 is missing expected H atoms. Skipping. Residue ALA 212 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue ALA 216 is missing expected H atoms. Skipping. Residue THR 219 is missing expected H atoms. Skipping. Residue VAL 223 is missing expected H atoms. Skipping. Residue ALA 227 is missing expected H atoms. Skipping. Residue LEU 229 is missing expected H atoms. Skipping. Residue ALA 230 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue VAL 238 is missing expected H atoms. Skipping. Residue ALA 245 is missing expected H atoms. Skipping. Residue VAL 248 is missing expected H atoms. Skipping. Residue ALA 250 is missing expected H atoms. Skipping. Residue VAL 251 is missing expected H atoms. Skipping. Residue ALA 254 is missing expected H atoms. Skipping. Residue LEU 255 is missing expected H atoms. Skipping. Residue VAL 260 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue ALA 269 is missing expected H atoms. Skipping. Residue LEU 276 is missing expected H atoms. Skipping. Residue THR 277 is missing expected H atoms. Skipping. Residue ILE 281 is missing expected H atoms. Skipping. Residue ALA 284 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue ILE 290 is missing expected H atoms. Skipping. Residue ALA 291 is missing expected H atoms. Skipping. Residue VAL 295 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LEU 303 is missing expected H atoms. Skipping. Residue THR 315 is missing expected H atoms. Skipping. Residue VAL 316 is missing expected H atoms. Skipping. Residue MET 317 is missing expected H atoms. Skipping. Residue THR 321 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue THR 328 is missing expected H atoms. Skipping. Residue ILE 329 is missing expected H atoms. Skipping. Residue ALA 330 is missing expected H atoms. Skipping. Residue ALA 331 is missing expected H atoms. Skipping. Residue LEU 332 is missing expected H atoms. Skipping. Residue MET 336 is missing expected H atoms. Skipping. Residue LEU 338 is missing expected H atoms. Skipping. Residue ALA 340 is missing expected H atoms. Skipping. Residue LEU 342 is missing expected H atoms. Skipping. Residue ALA 344 is missing expected H atoms. Skipping. Residue THR 346 is missing expected H atoms. Skipping. Residue THR 347 is missing expected H atoms. Skipping. Residue ILE 352 is missing expected H atoms. Skipping. Residue THR 353 is missing expected H atoms. Skipping. Residue ALA 354 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue VAL 360 is missing expected H atoms. Skipping. Residue ILE 364 is missing expected H atoms. Skipping. Residue ALA 368 is missing expected H atoms. Skipping. Residue ILE 371 is missing expected H atoms. Skipping. Residue ALA 375 is missing expected H atoms. Skipping. Residue ILE 380 is missing expected H atoms. Skipping. Residue VAL 381 is missing expected H atoms. Skipping. Residue ALA 383 is missing expected H atoms. Skipping. Residue VAL 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue ALA 386 is missing expected H atoms. Skipping. Residue LEU 388 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue ILE 6 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue ILE 19 is missing expected H atoms. Skipping. Residue ALA 20 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue THR 24 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue ALA 28 is missing expected H atoms. Skipping. Residue ALA 29 is missing expected H atoms. Skipping. Residue MET 31 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue MET 37 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue THR 41 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue ILE 56 is missing expected H atoms. Skipping. Residue ALA 58 is missing expected H atoms. Skipping. Residue LEU 60 is missing expected H atoms. Skipping. Residue VAL 64 is missing expected H atoms. Skipping. Residue ALA 65 is missing expected H atoms. Skipping. Residue VAL 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue ALA 69 is missing expected H atoms. Skipping. Residue ALA 71 is missing expected H atoms. Skipping. Residue VAL 75 is missing expected H atoms. Skipping. Residue THR 81 is missing expected H atoms. Skipping. Residue ALA 82 is missing expected H atoms. Skipping. Residue ALA 87 is missing expected H atoms. Skipping. Residue VAL 90 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue THR 94 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue MET 98 is missing expected H atoms. Skipping. Residue ALA 100 is missing expected H atoms. Skipping. Residue ALA 101 is missing expected H atoms. Skipping. Residue ALA 107 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 112 is missing expected H atoms. Skipping. Residue ALA 117 is missing expected H atoms. Skipping. Residue ILE 122 is missing expected H atoms. Skipping. Residue MET 123 is missing expected H atoms. Skipping. Residue VAL 125 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue THR 137 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue MET 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue THR 150 is missing expected H atoms. Skipping. Residue LEU 152 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue VAL 161 is missing expected H atoms. Skipping. Residue VAL 163 is missing expected H atoms. Skipping. Residue VAL 164 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue ILE 6 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue ILE 19 is missing expected H atoms. Skipping. Residue ALA 20 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue THR 24 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue ALA 28 is missing expected H atoms. Skipping. Residue ALA 29 is missing expected H atoms. Skipping. Residue MET 31 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue MET 37 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue THR 41 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue ILE 56 is missing expected H atoms. Skipping. Residue ALA 58 is missing expected H atoms. Skipping. Residue LEU 60 is missing expected H atoms. Skipping. Residue VAL 64 is missing expected H atoms. Skipping. Residue ALA 65 is missing expected H atoms. Skipping. Residue VAL 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue ALA 69 is missing expected H atoms. Skipping. Residue ALA 71 is missing expected H atoms. Skipping. Residue VAL 75 is missing expected H atoms. Skipping. Residue THR 81 is missing expected H atoms. Skipping. Residue ALA 82 is missing expected H atoms. Skipping. Residue ALA 87 is missing expected H atoms. Skipping. Residue VAL 90 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue THR 94 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue MET 98 is missing expected H atoms. Skipping. Residue ALA 100 is missing expected H atoms. Skipping. Residue ALA 101 is missing expected H atoms. Skipping. Residue ALA 107 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 112 is missing expected H atoms. Skipping. Residue ALA 117 is missing expected H atoms. Skipping. Residue ILE 122 is missing expected H atoms. Skipping. Residue MET 123 is missing expected H atoms. Skipping. Residue VAL 125 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue THR 137 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue MET 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue THR 150 is missing expected H atoms. Skipping. Residue LEU 152 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue VAL 161 is missing expected H atoms. Skipping. Residue VAL 163 is missing expected H atoms. Skipping. Residue VAL 164 is missing expected H atoms. Skipping. Evaluate side-chains 185 residues out of total 1782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 164 time to evaluate : 2.450 Fit side-chains revert: symmetry clash REVERT: D 40 LYS cc_start: 0.8519 (tmmt) cc_final: 0.8192 (tttm) REVERT: D 55 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7753 (pm20) REVERT: D 444 GLN cc_start: 0.8766 (OUTLIER) cc_final: 0.7218 (tt0) REVERT: E 30 ARG cc_start: 0.8372 (tmt-80) cc_final: 0.8037 (tmt-80) REVERT: E 520 LYS cc_start: 0.8146 (mttm) cc_final: 0.7720 (mtpt) REVERT: B 7 ARG cc_start: 0.7388 (OUTLIER) cc_final: 0.6350 (mmm-85) REVERT: B 86 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.8332 (pt0) REVERT: B 308 GLU cc_start: 0.7821 (tt0) cc_final: 0.7353 (tp30) REVERT: C 130 ASP cc_start: 0.8705 (OUTLIER) cc_final: 0.8415 (t70) REVERT: C 165 GLN cc_start: 0.8810 (OUTLIER) cc_final: 0.7696 (tm-30) REVERT: C 225 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8409 (tttm) REVERT: C 271 ARG cc_start: 0.8330 (OUTLIER) cc_final: 0.7412 (mtt-85) REVERT: G 26 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.7202 (tt0) REVERT: G 74 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7480 (mt-10) REVERT: H 21 GLN cc_start: 0.8308 (OUTLIER) cc_final: 0.7939 (mp10) outliers start: 21 outliers final: 4 residues processed: 180 average time/residue: 2.0565 time to fit residues: 404.5420 Evaluate side-chains 166 residues out of total 1782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 151 time to evaluate : 2.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 55 GLU Chi-restraints excluded: chain D residue 76 GLU Chi-restraints excluded: chain D residue 444 GLN Chi-restraints excluded: chain E residue 307 ARG Chi-restraints excluded: chain B residue 7 ARG Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 173 ASP Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 165 GLN Chi-restraints excluded: chain C residue 225 LYS Chi-restraints excluded: chain C residue 271 ARG Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain G residue 41 THR Chi-restraints excluded: chain G residue 74 GLU Chi-restraints excluded: chain H residue 21 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 108 optimal weight: 7.9990 chunk 102 optimal weight: 1.9990 chunk 190 optimal weight: 4.9990 chunk 30 optimal weight: 10.0000 chunk 184 optimal weight: 2.9990 chunk 25 optimal weight: 7.9990 chunk 203 optimal weight: 10.0000 chunk 143 optimal weight: 6.9990 chunk 149 optimal weight: 4.9990 chunk 166 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 59 GLN ** D 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 140 GLN D 205 GLN E 203 ASN E 278 GLN G 17 ASN ** G 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.090699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.080835 restraints weight = 33021.094| |-----------------------------------------------------------------------------| r_work (start): 0.2735 rms_B_bonded: 1.02 r_work: 0.2650 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.2551 rms_B_bonded: 2.56 restraints_weight: 0.2500 r_work (final): 0.2551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 17861 Z= 0.274 Angle : 0.529 6.455 24231 Z= 0.293 Chirality : 0.044 0.177 2461 Planarity : 0.005 0.046 3153 Dihedral : 5.119 71.716 2346 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.74 % Allowed : 9.03 % Favored : 89.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.19), residues: 2101 helix: 1.15 (0.14), residues: 1361 sheet: 1.87 (0.81), residues: 44 loop : -0.19 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 125 HIS 0.009 0.002 HIS D 382 PHE 0.019 0.002 PHE E 39 TYR 0.017 0.002 TYR B 299 ARG 0.005 0.001 ARG C 104 Details of bonding type rmsd hydrogen bonds : bond 0.06053 ( 993) hydrogen bonds : angle 5.20659 ( 2883) covalent geometry : bond 0.00648 (17861) covalent geometry : angle 0.52910 (24231) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 19 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue VAL 23 is missing expected H atoms. Skipping. Residue ALA 25 is missing expected H atoms. Skipping. Residue VAL 28 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue THR 44 is missing expected H atoms. Skipping. Residue ALA 47 is missing expected H atoms. Skipping. Residue THR 48 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ALA 53 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue ALA 64 is missing expected H atoms. Skipping. Residue ALA 68 is missing expected H atoms. Skipping. Residue MET 70 is missing expected H atoms. Skipping. Residue ALA 72 is missing expected H atoms. Skipping. Residue VAL 73 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue ALA 85 is missing expected H atoms. Skipping. Residue LEU 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue ALA 91 is missing expected H atoms. Skipping. Residue VAL 93 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue THR 102 is missing expected H atoms. Skipping. Residue MET 103 is missing expected H atoms. Skipping. Residue VAL 105 is missing expected H atoms. Skipping. Residue VAL 106 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue VAL 112 is missing expected H atoms. Skipping. Residue ALA 117 is missing expected H atoms. Skipping. Residue ILE 118 is missing expected H atoms. Skipping. Residue ALA 119 is missing expected H atoms. Skipping. Residue ALA 120 is missing expected H atoms. Skipping. Residue THR 121 is missing expected H atoms. Skipping. Residue MET 123 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Residue ALA 128 is missing expected H atoms. Skipping. Residue ALA 130 is missing expected H atoms. Skipping. Residue ALA 131 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue ALA 139 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue THR 148 is missing expected H atoms. Skipping. Residue ALA 152 is missing expected H atoms. Skipping. Residue VAL 154 is missing expected H atoms. Skipping. Residue ALA 159 is missing expected H atoms. Skipping. Residue ALA 166 is missing expected H atoms. Skipping. Residue ALA 171 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue ILE 177 is missing expected H atoms. Skipping. Residue LEU 180 is missing expected H atoms. Skipping. Residue MET 184 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue ILE 193 is missing expected H atoms. Skipping. Residue ALA 197 is missing expected H atoms. Skipping. Residue VAL 198 is missing expected H atoms. Skipping. Residue LEU 202 is missing expected H atoms. Skipping. Residue LEU 204 is missing expected H atoms. Skipping. Residue LEU 206 is missing expected H atoms. Skipping. Residue VAL 207 is missing expected H atoms. Skipping. Residue ALA 210 is missing expected H atoms. Skipping. Residue THR 213 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue ILE 217 is missing expected H atoms. Skipping. Residue VAL 218 is missing expected H atoms. Skipping. Residue ALA 219 is missing expected H atoms. Skipping. Residue VAL 220 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue ALA 224 is missing expected H atoms. Skipping. Residue ALA 225 is missing expected H atoms. Skipping. Residue ALA 226 is missing expected H atoms. Skipping. Residue ILE 231 is missing expected H atoms. Skipping. Residue THR 232 is missing expected H atoms. Skipping. Residue THR 234 is missing expected H atoms. Skipping. Residue VAL 235 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue ILE 239 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LEU 244 is missing expected H atoms. Skipping. Residue MET 247 is missing expected H atoms. Skipping. Residue ALA 248 is missing expected H atoms. Skipping. Residue THR 253 is missing expected H atoms. Skipping. Residue VAL 254 is missing expected H atoms. Skipping. Residue VAL 255 is missing expected H atoms. Skipping. Residue ILE 257 is missing expected H atoms. Skipping. Residue ALA 258 is missing expected H atoms. Skipping. Residue ALA 262 is missing expected H atoms. Skipping. Residue ALA 264 is missing expected H atoms. Skipping. Residue LEU 267 is missing expected H atoms. Skipping. Residue THR 269 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue ALA 274 is missing expected H atoms. Skipping. Residue THR 277 is missing expected H atoms. Skipping. Residue THR 283 is missing expected H atoms. Skipping. Residue VAL 285 is missing expected H atoms. Skipping. Residue LEU 286 is missing expected H atoms. Skipping. Residue MET 288 is missing expected H atoms. Skipping. Residue LEU 289 is missing expected H atoms. Skipping. Residue VAL 298 is missing expected H atoms. Skipping. Residue VAL 302 is missing expected H atoms. Skipping. Residue THR 304 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Residue ILE 316 is missing expected H atoms. Skipping. Residue ILE 318 is missing expected H atoms. Skipping. Residue LEU 321 is missing expected H atoms. Skipping. Residue VAL 326 is missing expected H atoms. Skipping. Residue LEU 332 is missing expected H atoms. Skipping. Residue ALA 335 is missing expected H atoms. Skipping. Residue ALA 339 is missing expected H atoms. Skipping. Residue ALA 342 is missing expected H atoms. Skipping. Residue LEU 346 is missing expected H atoms. Skipping. Residue LEU 348 is missing expected H atoms. Skipping. Residue LEU 349 is missing expected H atoms. Skipping. Residue ALA 350 is missing expected H atoms. Skipping. Residue ALA 352 is missing expected H atoms. Skipping. Residue LEU 353 is missing expected H atoms. Skipping. Residue THR 356 is missing expected H atoms. Skipping. Residue LEU 361 is missing expected H atoms. Skipping. Residue ALA 362 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue MET 369 is missing expected H atoms. Skipping. Residue ALA 374 is missing expected H atoms. Skipping. Residue ILE 386 is missing expected H atoms. Skipping. Residue ALA 392 is missing expected H atoms. Skipping. Residue ILE 403 is missing expected H atoms. Skipping. Residue LEU 405 is missing expected H atoms. Skipping. Residue MET 406 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 415 is missing expected H atoms. Skipping. Residue ILE 417 is missing expected H atoms. Skipping. Residue VAL 420 is missing expected H atoms. Skipping. Residue VAL 423 is missing expected H atoms. Skipping. Residue LEU 429 is missing expected H atoms. Skipping. Residue ALA 430 is missing expected H atoms. Skipping. Residue ALA 433 is missing expected H atoms. Skipping. Residue THR 435 is missing expected H atoms. Skipping. Residue LEU 436 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue MET 445 is missing expected H atoms. Skipping. Residue THR 447 is missing expected H atoms. Skipping. Residue MET 456 is missing expected H atoms. Skipping. Residue LEU 458 is missing expected H atoms. Skipping. Residue ALA 459 is missing expected H atoms. Skipping. Residue ILE 469 is missing expected H atoms. Skipping. Residue LEU 478 is missing expected H atoms. Skipping. Residue VAL 481 is missing expected H atoms. Skipping. Residue ILE 482 is missing expected H atoms. Skipping. Residue ALA 483 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue LEU 488 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue LEU 495 is missing expected H atoms. Skipping. Residue ILE 496 is missing expected H atoms. Skipping. Residue ALA 497 is missing expected H atoms. Skipping. Residue VAL 501 is missing expected H atoms. Skipping. Residue LEU 506 is missing expected H atoms. Skipping. Residue THR 508 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue LEU 515 is missing expected H atoms. Skipping. Residue VAL 518 is missing expected H atoms. Skipping. Residue VAL 523 is missing expected H atoms. Skipping. Residue ALA 525 is missing expected H atoms. Skipping. Residue ALA 16 is missing expected H atoms. Skipping. Residue ALA 19 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue VAL 23 is missing expected H atoms. Skipping. Residue ALA 25 is missing expected H atoms. Skipping. Residue VAL 28 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue THR 44 is missing expected H atoms. Skipping. Residue ALA 47 is missing expected H atoms. Skipping. Residue THR 48 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ALA 53 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue ALA 64 is missing expected H atoms. Skipping. Residue ALA 68 is missing expected H atoms. Skipping. Residue MET 70 is missing expected H atoms. Skipping. Residue ALA 72 is missing expected H atoms. Skipping. Residue VAL 73 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue ALA 85 is missing expected H atoms. Skipping. Residue LEU 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue ALA 91 is missing expected H atoms. Skipping. Residue VAL 93 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue THR 102 is missing expected H atoms. Skipping. Residue MET 103 is missing expected H atoms. Skipping. Residue VAL 105 is missing expected H atoms. Skipping. Residue VAL 106 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue VAL 112 is missing expected H atoms. Skipping. Residue ALA 117 is missing expected H atoms. Skipping. Residue ILE 118 is missing expected H atoms. Skipping. Residue ALA 119 is missing expected H atoms. Skipping. Residue ALA 120 is missing expected H atoms. Skipping. Residue THR 121 is missing expected H atoms. Skipping. Residue MET 123 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Residue ALA 128 is missing expected H atoms. Skipping. Residue ALA 130 is missing expected H atoms. Skipping. Residue ALA 131 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue ALA 139 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue THR 148 is missing expected H atoms. Skipping. Residue ALA 152 is missing expected H atoms. Skipping. Residue VAL 154 is missing expected H atoms. Skipping. Residue ALA 159 is missing expected H atoms. Skipping. Residue ALA 166 is missing expected H atoms. Skipping. Residue ALA 171 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue ILE 177 is missing expected H atoms. Skipping. Residue LEU 180 is missing expected H atoms. Skipping. Residue MET 184 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue ILE 193 is missing expected H atoms. Skipping. Residue ALA 197 is missing expected H atoms. Skipping. Residue VAL 198 is missing expected H atoms. Skipping. Residue LEU 202 is missing expected H atoms. Skipping. Residue LEU 204 is missing expected H atoms. Skipping. Residue LEU 206 is missing expected H atoms. Skipping. Residue VAL 207 is missing expected H atoms. Skipping. Residue ALA 210 is missing expected H atoms. Skipping. Residue THR 213 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue ILE 217 is missing expected H atoms. Skipping. Residue VAL 218 is missing expected H atoms. Skipping. Residue ALA 219 is missing expected H atoms. Skipping. Residue VAL 220 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue ALA 224 is missing expected H atoms. Skipping. Residue ALA 225 is missing expected H atoms. Skipping. Residue ALA 226 is missing expected H atoms. Skipping. Residue ILE 231 is missing expected H atoms. Skipping. Residue THR 232 is missing expected H atoms. Skipping. Residue THR 234 is missing expected H atoms. Skipping. Residue VAL 235 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue ILE 239 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LEU 244 is missing expected H atoms. Skipping. Residue MET 247 is missing expected H atoms. Skipping. Residue ALA 248 is missing expected H atoms. Skipping. Residue THR 253 is missing expected H atoms. Skipping. Residue VAL 254 is missing expected H atoms. Skipping. Residue VAL 255 is missing expected H atoms. Skipping. Residue ILE 257 is missing expected H atoms. Skipping. Residue ALA 258 is missing expected H atoms. Skipping. Residue ALA 262 is missing expected H atoms. Skipping. Residue ALA 264 is missing expected H atoms. Skipping. Residue LEU 267 is missing expected H atoms. Skipping. Residue THR 269 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue ALA 274 is missing expected H atoms. Skipping. Residue THR 277 is missing expected H atoms. Skipping. Residue THR 283 is missing expected H atoms. Skipping. Residue VAL 285 is missing expected H atoms. Skipping. Residue LEU 286 is missing expected H atoms. Skipping. Residue MET 288 is missing expected H atoms. Skipping. Residue LEU 289 is missing expected H atoms. Skipping. Residue VAL 298 is missing expected H atoms. Skipping. Residue VAL 302 is missing expected H atoms. Skipping. Residue THR 304 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Residue ILE 316 is missing expected H atoms. Skipping. Residue ILE 318 is missing expected H atoms. Skipping. Residue LEU 321 is missing expected H atoms. Skipping. Residue VAL 326 is missing expected H atoms. Skipping. Residue LEU 332 is missing expected H atoms. Skipping. Residue ALA 335 is missing expected H atoms. Skipping. Residue ALA 339 is missing expected H atoms. Skipping. Residue ALA 342 is missing expected H atoms. Skipping. Residue LEU 346 is missing expected H atoms. Skipping. Residue LEU 348 is missing expected H atoms. Skipping. Residue LEU 349 is missing expected H atoms. Skipping. Residue ALA 350 is missing expected H atoms. Skipping. Residue ALA 352 is missing expected H atoms. Skipping. Residue LEU 353 is missing expected H atoms. Skipping. Residue THR 356 is missing expected H atoms. Skipping. Residue LEU 361 is missing expected H atoms. Skipping. Residue ALA 362 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue MET 369 is missing expected H atoms. Skipping. Residue ALA 374 is missing expected H atoms. Skipping. Residue ILE 386 is missing expected H atoms. Skipping. Residue ALA 392 is missing expected H atoms. Skipping. Residue ILE 403 is missing expected H atoms. Skipping. Residue LEU 405 is missing expected H atoms. Skipping. Residue MET 406 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 415 is missing expected H atoms. Skipping. Residue ILE 417 is missing expected H atoms. Skipping. Residue VAL 420 is missing expected H atoms. Skipping. Residue VAL 423 is missing expected H atoms. Skipping. Residue LEU 429 is missing expected H atoms. Skipping. Residue ALA 430 is missing expected H atoms. Skipping. Residue ALA 433 is missing expected H atoms. Skipping. Residue THR 435 is missing expected H atoms. Skipping. Residue LEU 436 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue MET 445 is missing expected H atoms. Skipping. Residue THR 447 is missing expected H atoms. Skipping. Residue MET 456 is missing expected H atoms. Skipping. Residue LEU 458 is missing expected H atoms. Skipping. Residue ALA 459 is missing expected H atoms. Skipping. Residue ILE 469 is missing expected H atoms. Skipping. Residue LEU 478 is missing expected H atoms. Skipping. Residue VAL 481 is missing expected H atoms. Skipping. Residue ILE 482 is missing expected H atoms. Skipping. Residue ALA 483 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue LEU 488 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue LEU 495 is missing expected H atoms. Skipping. Residue ILE 496 is missing expected H atoms. Skipping. Residue ALA 497 is missing expected H atoms. Skipping. Residue VAL 501 is missing expected H atoms. Skipping. Residue LEU 506 is missing expected H atoms. Skipping. Residue THR 508 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue LEU 515 is missing expected H atoms. Skipping. Residue VAL 518 is missing expected H atoms. Skipping. Residue VAL 523 is missing expected H atoms. Skipping. Residue ALA 525 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue MET 16 is missing expected H atoms. Skipping. Residue ALA 17 is missing expected H atoms. Skipping. Residue ALA 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 20 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue ALA 23 is missing expected H atoms. Skipping. Residue LEU 24 is missing expected H atoms. Skipping. Residue ALA 27 is missing expected H atoms. Skipping. Residue LEU 29 is missing expected H atoms. Skipping. Residue MET 35 is missing expected H atoms. Skipping. Residue VAL 39 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue THR 47 is missing expected H atoms. Skipping. Residue ALA 51 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue THR 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ALA 56 is missing expected H atoms. Skipping. Residue ALA 60 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue ALA 64 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue THR 92 is missing expected H atoms. Skipping. Residue VAL 93 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue ALA 107 is missing expected H atoms. Skipping. Residue VAL 110 is missing expected H atoms. Skipping. Residue ALA 114 is missing expected H atoms. Skipping. Residue THR 120 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Residue ALA 129 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue ALA 135 is missing expected H atoms. Skipping. Residue MET 136 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue ALA 151 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue ALA 162 is missing expected H atoms. Skipping. Residue ALA 167 is missing expected H atoms. Skipping. Residue ALA 170 is missing expected H atoms. Skipping. Residue LEU 171 is missing expected H atoms. Skipping. Residue VAL 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue ALA 180 is missing expected H atoms. Skipping. Residue ILE 187 is missing expected H atoms. Skipping. Residue ILE 189 is missing expected H atoms. Skipping. Residue ALA 190 is missing expected H atoms. Skipping. Residue MET 192 is missing expected H atoms. Skipping. Residue ILE 193 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue LEU 200 is missing expected H atoms. Skipping. Residue ALA 201 is missing expected H atoms. Skipping. Residue ILE 203 is missing expected H atoms. Skipping. Residue VAL 204 is missing expected H atoms. Skipping. Residue THR 211 is missing expected H atoms. Skipping. Residue ALA 212 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue ALA 216 is missing expected H atoms. Skipping. Residue THR 219 is missing expected H atoms. Skipping. Residue VAL 223 is missing expected H atoms. Skipping. Residue ALA 227 is missing expected H atoms. Skipping. Residue LEU 229 is missing expected H atoms. Skipping. Residue ALA 230 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue VAL 238 is missing expected H atoms. Skipping. Residue ALA 245 is missing expected H atoms. Skipping. Residue VAL 248 is missing expected H atoms. Skipping. Residue ALA 250 is missing expected H atoms. Skipping. Residue VAL 251 is missing expected H atoms. Skipping. Residue ALA 254 is missing expected H atoms. Skipping. Residue LEU 255 is missing expected H atoms. Skipping. Residue VAL 260 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue ALA 269 is missing expected H atoms. Skipping. Residue LEU 276 is missing expected H atoms. Skipping. Residue THR 277 is missing expected H atoms. Skipping. Residue ILE 281 is missing expected H atoms. Skipping. Residue ALA 284 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue ILE 290 is missing expected H atoms. Skipping. Residue ALA 291 is missing expected H atoms. Skipping. Residue VAL 295 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LEU 303 is missing expected H atoms. Skipping. Residue THR 315 is missing expected H atoms. Skipping. Residue VAL 316 is missing expected H atoms. Skipping. Residue MET 317 is missing expected H atoms. Skipping. Residue THR 321 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue THR 328 is missing expected H atoms. Skipping. Residue ILE 329 is missing expected H atoms. Skipping. Residue ALA 330 is missing expected H atoms. Skipping. Residue ALA 331 is missing expected H atoms. Skipping. Residue LEU 332 is missing expected H atoms. Skipping. Residue MET 336 is missing expected H atoms. Skipping. Residue LEU 338 is missing expected H atoms. Skipping. Residue ALA 340 is missing expected H atoms. Skipping. Residue LEU 342 is missing expected H atoms. Skipping. Residue ALA 344 is missing expected H atoms. Skipping. Residue THR 346 is missing expected H atoms. Skipping. Residue THR 347 is missing expected H atoms. Skipping. Residue ILE 352 is missing expected H atoms. Skipping. Residue THR 353 is missing expected H atoms. Skipping. Residue ALA 354 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue VAL 360 is missing expected H atoms. Skipping. Residue ILE 364 is missing expected H atoms. Skipping. Residue ALA 368 is missing expected H atoms. Skipping. Residue ILE 371 is missing expected H atoms. Skipping. Residue ALA 375 is missing expected H atoms. Skipping. Residue ILE 380 is missing expected H atoms. Skipping. Residue VAL 381 is missing expected H atoms. Skipping. Residue ALA 383 is missing expected H atoms. Skipping. Residue VAL 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue ALA 386 is missing expected H atoms. Skipping. Residue LEU 388 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue ILE 6 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue ILE 19 is missing expected H atoms. Skipping. Residue ALA 20 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue THR 24 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue ALA 28 is missing expected H atoms. Skipping. Residue ALA 29 is missing expected H atoms. Skipping. Residue MET 31 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue MET 37 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue THR 41 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue ILE 56 is missing expected H atoms. Skipping. Residue ALA 58 is missing expected H atoms. Skipping. Residue LEU 60 is missing expected H atoms. Skipping. Residue VAL 64 is missing expected H atoms. Skipping. Residue ALA 65 is missing expected H atoms. Skipping. Residue VAL 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue ALA 69 is missing expected H atoms. Skipping. Residue ALA 71 is missing expected H atoms. Skipping. Residue VAL 75 is missing expected H atoms. Skipping. Residue THR 81 is missing expected H atoms. Skipping. Residue ALA 82 is missing expected H atoms. Skipping. Residue ALA 87 is missing expected H atoms. Skipping. Residue VAL 90 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue THR 94 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue MET 98 is missing expected H atoms. Skipping. Residue ALA 100 is missing expected H atoms. Skipping. Residue ALA 101 is missing expected H atoms. Skipping. Residue ALA 107 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 112 is missing expected H atoms. Skipping. Residue ALA 117 is missing expected H atoms. Skipping. Residue ILE 122 is missing expected H atoms. Skipping. Residue MET 123 is missing expected H atoms. Skipping. Residue VAL 125 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue THR 137 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue MET 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue THR 150 is missing expected H atoms. Skipping. Residue LEU 152 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue VAL 161 is missing expected H atoms. Skipping. Residue VAL 163 is missing expected H atoms. Skipping. Residue VAL 164 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue ILE 6 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue ILE 19 is missing expected H atoms. Skipping. Residue ALA 20 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue THR 24 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue ALA 28 is missing expected H atoms. Skipping. Residue ALA 29 is missing expected H atoms. Skipping. Residue MET 31 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue MET 37 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue THR 41 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue ILE 56 is missing expected H atoms. Skipping. Residue ALA 58 is missing expected H atoms. Skipping. Residue LEU 60 is missing expected H atoms. Skipping. Residue VAL 64 is missing expected H atoms. Skipping. Residue ALA 65 is missing expected H atoms. Skipping. Residue VAL 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue ALA 69 is missing expected H atoms. Skipping. Residue ALA 71 is missing expected H atoms. Skipping. Residue VAL 75 is missing expected H atoms. Skipping. Residue THR 81 is missing expected H atoms. Skipping. Residue ALA 82 is missing expected H atoms. Skipping. Residue ALA 87 is missing expected H atoms. Skipping. Residue VAL 90 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue THR 94 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue MET 98 is missing expected H atoms. Skipping. Residue ALA 100 is missing expected H atoms. Skipping. Residue ALA 101 is missing expected H atoms. Skipping. Residue ALA 107 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 112 is missing expected H atoms. Skipping. Residue ALA 117 is missing expected H atoms. Skipping. Residue ILE 122 is missing expected H atoms. Skipping. Residue MET 123 is missing expected H atoms. Skipping. Residue VAL 125 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue THR 137 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue MET 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue THR 150 is missing expected H atoms. Skipping. Residue LEU 152 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue VAL 161 is missing expected H atoms. Skipping. Residue VAL 163 is missing expected H atoms. Skipping. Residue VAL 164 is missing expected H atoms. Skipping. Evaluate side-chains 176 residues out of total 1782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 145 time to evaluate : 2.001 Fit side-chains revert: symmetry clash REVERT: D 55 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7731 (pm20) REVERT: D 311 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.6848 (mm-30) REVERT: E 30 ARG cc_start: 0.8456 (tmt-80) cc_final: 0.7268 (ttm110) REVERT: E 520 LYS cc_start: 0.8145 (mttm) cc_final: 0.7750 (mtmt) REVERT: B 7 ARG cc_start: 0.7428 (OUTLIER) cc_final: 0.6520 (mmm-85) REVERT: B 86 GLU cc_start: 0.8806 (OUTLIER) cc_final: 0.8440 (pt0) REVERT: B 103 ARG cc_start: 0.8686 (OUTLIER) cc_final: 0.7112 (mtp180) REVERT: B 308 GLU cc_start: 0.7777 (tt0) cc_final: 0.7240 (tp30) REVERT: C 130 ASP cc_start: 0.8737 (OUTLIER) cc_final: 0.8382 (t70) REVERT: C 165 GLN cc_start: 0.8810 (OUTLIER) cc_final: 0.7553 (tm-30) REVERT: C 271 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.7490 (mtt-85) REVERT: G 74 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7598 (mt-10) REVERT: H 21 GLN cc_start: 0.8345 (OUTLIER) cc_final: 0.7953 (mp10) REVERT: H 41 THR cc_start: 0.7366 (OUTLIER) cc_final: 0.7054 (p) outliers start: 31 outliers final: 13 residues processed: 167 average time/residue: 2.1125 time to fit residues: 385.2202 Evaluate side-chains 164 residues out of total 1782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 140 time to evaluate : 2.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 40 LYS Chi-restraints excluded: chain D residue 55 GLU Chi-restraints excluded: chain D residue 76 GLU Chi-restraints excluded: chain D residue 125 TRP Chi-restraints excluded: chain D residue 311 GLU Chi-restraints excluded: chain D residue 409 ILE Chi-restraints excluded: chain D residue 444 GLN Chi-restraints excluded: chain D residue 460 GLU Chi-restraints excluded: chain D residue 517 CYS Chi-restraints excluded: chain E residue 125 TRP Chi-restraints excluded: chain E residue 307 ARG Chi-restraints excluded: chain E residue 474 GLU Chi-restraints excluded: chain B residue 7 ARG Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 103 ARG Chi-restraints excluded: chain B residue 173 ASP Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 165 GLN Chi-restraints excluded: chain C residue 271 ARG Chi-restraints excluded: chain G residue 41 THR Chi-restraints excluded: chain G residue 74 GLU Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain H residue 21 GLN Chi-restraints excluded: chain H residue 41 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 16 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 152 optimal weight: 0.9990 chunk 144 optimal weight: 0.5980 chunk 34 optimal weight: 0.8980 chunk 161 optimal weight: 3.9990 chunk 75 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 chunk 158 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 138 optimal weight: 0.0870 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 59 GLN ** D 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.094711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.084899 restraints weight = 32801.177| |-----------------------------------------------------------------------------| r_work (start): 0.2817 rms_B_bonded: 1.01 r_work: 0.2734 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.2635 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 17861 Z= 0.099 Angle : 0.405 4.713 24231 Z= 0.230 Chirality : 0.036 0.133 2461 Planarity : 0.004 0.043 3153 Dihedral : 4.828 68.660 2346 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.29 % Allowed : 9.26 % Favored : 89.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.19), residues: 2101 helix: 1.47 (0.15), residues: 1359 sheet: 1.90 (0.81), residues: 44 loop : -0.02 (0.24), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 43 HIS 0.006 0.001 HIS D 343 PHE 0.009 0.001 PHE E 39 TYR 0.014 0.001 TYR D 156 ARG 0.005 0.000 ARG E 320 Details of bonding type rmsd hydrogen bonds : bond 0.04501 ( 993) hydrogen bonds : angle 4.85167 ( 2883) covalent geometry : bond 0.00197 (17861) covalent geometry : angle 0.40476 (24231) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 19 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue VAL 23 is missing expected H atoms. Skipping. Residue ALA 25 is missing expected H atoms. Skipping. Residue VAL 28 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue THR 44 is missing expected H atoms. Skipping. Residue ALA 47 is missing expected H atoms. Skipping. Residue THR 48 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ALA 53 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue ALA 64 is missing expected H atoms. Skipping. Residue ALA 68 is missing expected H atoms. Skipping. Residue MET 70 is missing expected H atoms. Skipping. Residue ALA 72 is missing expected H atoms. Skipping. Residue VAL 73 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue ALA 85 is missing expected H atoms. Skipping. Residue LEU 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue ALA 91 is missing expected H atoms. Skipping. Residue VAL 93 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue THR 102 is missing expected H atoms. Skipping. Residue MET 103 is missing expected H atoms. Skipping. Residue VAL 105 is missing expected H atoms. Skipping. Residue VAL 106 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue VAL 112 is missing expected H atoms. Skipping. Residue ALA 117 is missing expected H atoms. Skipping. Residue ILE 118 is missing expected H atoms. Skipping. Residue ALA 119 is missing expected H atoms. Skipping. Residue ALA 120 is missing expected H atoms. Skipping. Residue THR 121 is missing expected H atoms. Skipping. Residue MET 123 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Residue ALA 128 is missing expected H atoms. Skipping. Residue ALA 130 is missing expected H atoms. Skipping. Residue ALA 131 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue ALA 139 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue THR 148 is missing expected H atoms. Skipping. Residue ALA 152 is missing expected H atoms. Skipping. Residue VAL 154 is missing expected H atoms. Skipping. Residue ALA 159 is missing expected H atoms. Skipping. Residue ALA 166 is missing expected H atoms. Skipping. Residue ALA 171 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue ILE 177 is missing expected H atoms. Skipping. Residue LEU 180 is missing expected H atoms. Skipping. Residue MET 184 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue ILE 193 is missing expected H atoms. Skipping. Residue ALA 197 is missing expected H atoms. Skipping. Residue VAL 198 is missing expected H atoms. Skipping. Residue LEU 202 is missing expected H atoms. Skipping. Residue LEU 204 is missing expected H atoms. Skipping. Residue LEU 206 is missing expected H atoms. Skipping. Residue VAL 207 is missing expected H atoms. Skipping. Residue ALA 210 is missing expected H atoms. Skipping. Residue THR 213 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue ILE 217 is missing expected H atoms. Skipping. Residue VAL 218 is missing expected H atoms. Skipping. Residue ALA 219 is missing expected H atoms. Skipping. Residue VAL 220 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue ALA 224 is missing expected H atoms. Skipping. Residue ALA 225 is missing expected H atoms. Skipping. Residue ALA 226 is missing expected H atoms. Skipping. Residue ILE 231 is missing expected H atoms. Skipping. Residue THR 232 is missing expected H atoms. Skipping. Residue THR 234 is missing expected H atoms. Skipping. Residue VAL 235 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue ILE 239 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LEU 244 is missing expected H atoms. Skipping. Residue MET 247 is missing expected H atoms. Skipping. Residue ALA 248 is missing expected H atoms. Skipping. Residue THR 253 is missing expected H atoms. Skipping. Residue VAL 254 is missing expected H atoms. Skipping. Residue VAL 255 is missing expected H atoms. Skipping. Residue ILE 257 is missing expected H atoms. Skipping. Residue ALA 258 is missing expected H atoms. Skipping. Residue ALA 262 is missing expected H atoms. Skipping. Residue ALA 264 is missing expected H atoms. Skipping. Residue LEU 267 is missing expected H atoms. Skipping. Residue THR 269 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue ALA 274 is missing expected H atoms. Skipping. Residue THR 277 is missing expected H atoms. Skipping. Residue THR 283 is missing expected H atoms. Skipping. Residue VAL 285 is missing expected H atoms. Skipping. Residue LEU 286 is missing expected H atoms. Skipping. Residue MET 288 is missing expected H atoms. Skipping. Residue LEU 289 is missing expected H atoms. Skipping. Residue VAL 298 is missing expected H atoms. Skipping. Residue VAL 302 is missing expected H atoms. Skipping. Residue THR 304 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Residue ILE 316 is missing expected H atoms. Skipping. Residue ILE 318 is missing expected H atoms. Skipping. Residue LEU 321 is missing expected H atoms. Skipping. Residue VAL 326 is missing expected H atoms. Skipping. Residue LEU 332 is missing expected H atoms. Skipping. Residue ALA 335 is missing expected H atoms. Skipping. Residue ALA 339 is missing expected H atoms. Skipping. Residue ALA 342 is missing expected H atoms. Skipping. Residue LEU 346 is missing expected H atoms. Skipping. Residue LEU 348 is missing expected H atoms. Skipping. Residue LEU 349 is missing expected H atoms. Skipping. Residue ALA 350 is missing expected H atoms. Skipping. Residue ALA 352 is missing expected H atoms. Skipping. Residue LEU 353 is missing expected H atoms. Skipping. Residue THR 356 is missing expected H atoms. Skipping. Residue LEU 361 is missing expected H atoms. Skipping. Residue ALA 362 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue MET 369 is missing expected H atoms. Skipping. Residue ALA 374 is missing expected H atoms. Skipping. Residue ILE 386 is missing expected H atoms. Skipping. Residue ALA 392 is missing expected H atoms. Skipping. Residue ILE 403 is missing expected H atoms. Skipping. Residue LEU 405 is missing expected H atoms. Skipping. Residue MET 406 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 415 is missing expected H atoms. Skipping. Residue ILE 417 is missing expected H atoms. Skipping. Residue VAL 420 is missing expected H atoms. Skipping. Residue VAL 423 is missing expected H atoms. Skipping. Residue LEU 429 is missing expected H atoms. Skipping. Residue ALA 430 is missing expected H atoms. Skipping. Residue ALA 433 is missing expected H atoms. Skipping. Residue THR 435 is missing expected H atoms. Skipping. Residue LEU 436 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue MET 445 is missing expected H atoms. Skipping. Residue THR 447 is missing expected H atoms. Skipping. Residue MET 456 is missing expected H atoms. Skipping. Residue LEU 458 is missing expected H atoms. Skipping. Residue ALA 459 is missing expected H atoms. Skipping. Residue ILE 469 is missing expected H atoms. Skipping. Residue LEU 478 is missing expected H atoms. Skipping. Residue VAL 481 is missing expected H atoms. Skipping. Residue ILE 482 is missing expected H atoms. Skipping. Residue ALA 483 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue LEU 488 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue LEU 495 is missing expected H atoms. Skipping. Residue ILE 496 is missing expected H atoms. Skipping. Residue ALA 497 is missing expected H atoms. Skipping. Residue VAL 501 is missing expected H atoms. Skipping. Residue LEU 506 is missing expected H atoms. Skipping. Residue THR 508 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue LEU 515 is missing expected H atoms. Skipping. Residue VAL 518 is missing expected H atoms. Skipping. Residue VAL 523 is missing expected H atoms. Skipping. Residue ALA 525 is missing expected H atoms. Skipping. Residue ALA 16 is missing expected H atoms. Skipping. Residue ALA 19 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue VAL 23 is missing expected H atoms. Skipping. Residue ALA 25 is missing expected H atoms. Skipping. Residue VAL 28 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue THR 44 is missing expected H atoms. Skipping. Residue ALA 47 is missing expected H atoms. Skipping. Residue THR 48 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ALA 53 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue ALA 64 is missing expected H atoms. Skipping. Residue ALA 68 is missing expected H atoms. Skipping. Residue MET 70 is missing expected H atoms. Skipping. Residue ALA 72 is missing expected H atoms. Skipping. Residue VAL 73 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue ALA 85 is missing expected H atoms. Skipping. Residue LEU 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue ALA 91 is missing expected H atoms. Skipping. Residue VAL 93 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue THR 102 is missing expected H atoms. Skipping. Residue MET 103 is missing expected H atoms. Skipping. Residue VAL 105 is missing expected H atoms. Skipping. Residue VAL 106 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue VAL 112 is missing expected H atoms. Skipping. Residue ALA 117 is missing expected H atoms. Skipping. Residue ILE 118 is missing expected H atoms. Skipping. Residue ALA 119 is missing expected H atoms. Skipping. Residue ALA 120 is missing expected H atoms. Skipping. Residue THR 121 is missing expected H atoms. Skipping. Residue MET 123 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Residue ALA 128 is missing expected H atoms. Skipping. Residue ALA 130 is missing expected H atoms. Skipping. Residue ALA 131 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue ALA 139 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue THR 148 is missing expected H atoms. Skipping. Residue ALA 152 is missing expected H atoms. Skipping. Residue VAL 154 is missing expected H atoms. Skipping. Residue ALA 159 is missing expected H atoms. Skipping. Residue ALA 166 is missing expected H atoms. Skipping. Residue ALA 171 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue ILE 177 is missing expected H atoms. Skipping. Residue LEU 180 is missing expected H atoms. Skipping. Residue MET 184 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue ILE 193 is missing expected H atoms. Skipping. Residue ALA 197 is missing expected H atoms. Skipping. Residue VAL 198 is missing expected H atoms. Skipping. Residue LEU 202 is missing expected H atoms. Skipping. Residue LEU 204 is missing expected H atoms. Skipping. Residue LEU 206 is missing expected H atoms. Skipping. Residue VAL 207 is missing expected H atoms. Skipping. Residue ALA 210 is missing expected H atoms. Skipping. Residue THR 213 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue ILE 217 is missing expected H atoms. Skipping. Residue VAL 218 is missing expected H atoms. Skipping. Residue ALA 219 is missing expected H atoms. Skipping. Residue VAL 220 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue ALA 224 is missing expected H atoms. Skipping. Residue ALA 225 is missing expected H atoms. Skipping. Residue ALA 226 is missing expected H atoms. Skipping. Residue ILE 231 is missing expected H atoms. Skipping. Residue THR 232 is missing expected H atoms. Skipping. Residue THR 234 is missing expected H atoms. Skipping. Residue VAL 235 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue ILE 239 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LEU 244 is missing expected H atoms. Skipping. Residue MET 247 is missing expected H atoms. Skipping. Residue ALA 248 is missing expected H atoms. Skipping. Residue THR 253 is missing expected H atoms. Skipping. Residue VAL 254 is missing expected H atoms. Skipping. Residue VAL 255 is missing expected H atoms. Skipping. Residue ILE 257 is missing expected H atoms. Skipping. Residue ALA 258 is missing expected H atoms. Skipping. Residue ALA 262 is missing expected H atoms. Skipping. Residue ALA 264 is missing expected H atoms. Skipping. Residue LEU 267 is missing expected H atoms. Skipping. Residue THR 269 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue ALA 274 is missing expected H atoms. Skipping. Residue THR 277 is missing expected H atoms. Skipping. Residue THR 283 is missing expected H atoms. Skipping. Residue VAL 285 is missing expected H atoms. Skipping. Residue LEU 286 is missing expected H atoms. Skipping. Residue MET 288 is missing expected H atoms. Skipping. Residue LEU 289 is missing expected H atoms. Skipping. Residue VAL 298 is missing expected H atoms. Skipping. Residue VAL 302 is missing expected H atoms. Skipping. Residue THR 304 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Residue ILE 316 is missing expected H atoms. Skipping. Residue ILE 318 is missing expected H atoms. Skipping. Residue LEU 321 is missing expected H atoms. Skipping. Residue VAL 326 is missing expected H atoms. Skipping. Residue LEU 332 is missing expected H atoms. Skipping. Residue ALA 335 is missing expected H atoms. Skipping. Residue ALA 339 is missing expected H atoms. Skipping. Residue ALA 342 is missing expected H atoms. Skipping. Residue LEU 346 is missing expected H atoms. Skipping. Residue LEU 348 is missing expected H atoms. Skipping. Residue LEU 349 is missing expected H atoms. Skipping. Residue ALA 350 is missing expected H atoms. Skipping. Residue ALA 352 is missing expected H atoms. Skipping. Residue LEU 353 is missing expected H atoms. Skipping. Residue THR 356 is missing expected H atoms. Skipping. Residue LEU 361 is missing expected H atoms. Skipping. Residue ALA 362 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue MET 369 is missing expected H atoms. Skipping. Residue ALA 374 is missing expected H atoms. Skipping. Residue ILE 386 is missing expected H atoms. Skipping. Residue ALA 392 is missing expected H atoms. Skipping. Residue ILE 403 is missing expected H atoms. Skipping. Residue LEU 405 is missing expected H atoms. Skipping. Residue MET 406 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 415 is missing expected H atoms. Skipping. Residue ILE 417 is missing expected H atoms. Skipping. Residue VAL 420 is missing expected H atoms. Skipping. Residue VAL 423 is missing expected H atoms. Skipping. Residue LEU 429 is missing expected H atoms. Skipping. Residue ALA 430 is missing expected H atoms. Skipping. Residue ALA 433 is missing expected H atoms. Skipping. Residue THR 435 is missing expected H atoms. Skipping. Residue LEU 436 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue MET 445 is missing expected H atoms. Skipping. Residue THR 447 is missing expected H atoms. Skipping. Residue MET 456 is missing expected H atoms. Skipping. Residue LEU 458 is missing expected H atoms. Skipping. Residue ALA 459 is missing expected H atoms. Skipping. Residue ILE 469 is missing expected H atoms. Skipping. Residue LEU 478 is missing expected H atoms. Skipping. Residue VAL 481 is missing expected H atoms. Skipping. Residue ILE 482 is missing expected H atoms. Skipping. Residue ALA 483 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue LEU 488 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue LEU 495 is missing expected H atoms. Skipping. Residue ILE 496 is missing expected H atoms. Skipping. Residue ALA 497 is missing expected H atoms. Skipping. Residue VAL 501 is missing expected H atoms. Skipping. Residue LEU 506 is missing expected H atoms. Skipping. Residue THR 508 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue LEU 515 is missing expected H atoms. Skipping. Residue VAL 518 is missing expected H atoms. Skipping. Residue VAL 523 is missing expected H atoms. Skipping. Residue ALA 525 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue MET 16 is missing expected H atoms. Skipping. Residue ALA 17 is missing expected H atoms. Skipping. Residue ALA 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 20 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue ALA 23 is missing expected H atoms. Skipping. Residue LEU 24 is missing expected H atoms. Skipping. Residue ALA 27 is missing expected H atoms. Skipping. Residue LEU 29 is missing expected H atoms. Skipping. Residue MET 35 is missing expected H atoms. Skipping. Residue VAL 39 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue THR 47 is missing expected H atoms. Skipping. Residue ALA 51 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue THR 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ALA 56 is missing expected H atoms. Skipping. Residue ALA 60 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue ALA 64 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue THR 92 is missing expected H atoms. Skipping. Residue VAL 93 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue ALA 107 is missing expected H atoms. Skipping. Residue VAL 110 is missing expected H atoms. Skipping. Residue ALA 114 is missing expected H atoms. Skipping. Residue THR 120 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Residue ALA 129 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue ALA 135 is missing expected H atoms. Skipping. Residue MET 136 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue ALA 151 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue ALA 162 is missing expected H atoms. Skipping. Residue ALA 167 is missing expected H atoms. Skipping. Residue ALA 170 is missing expected H atoms. Skipping. Residue LEU 171 is missing expected H atoms. Skipping. Residue VAL 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue ALA 180 is missing expected H atoms. Skipping. Residue ILE 187 is missing expected H atoms. Skipping. Residue ILE 189 is missing expected H atoms. Skipping. Residue ALA 190 is missing expected H atoms. Skipping. Residue MET 192 is missing expected H atoms. Skipping. Residue ILE 193 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue LEU 200 is missing expected H atoms. Skipping. Residue ALA 201 is missing expected H atoms. Skipping. Residue ILE 203 is missing expected H atoms. Skipping. Residue VAL 204 is missing expected H atoms. Skipping. Residue THR 211 is missing expected H atoms. Skipping. Residue ALA 212 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue ALA 216 is missing expected H atoms. Skipping. Residue THR 219 is missing expected H atoms. Skipping. Residue VAL 223 is missing expected H atoms. Skipping. Residue ALA 227 is missing expected H atoms. Skipping. Residue LEU 229 is missing expected H atoms. Skipping. Residue ALA 230 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue VAL 238 is missing expected H atoms. Skipping. Residue ALA 245 is missing expected H atoms. Skipping. Residue VAL 248 is missing expected H atoms. Skipping. Residue ALA 250 is missing expected H atoms. Skipping. Residue VAL 251 is missing expected H atoms. Skipping. Residue ALA 254 is missing expected H atoms. Skipping. Residue LEU 255 is missing expected H atoms. Skipping. Residue VAL 260 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue ALA 269 is missing expected H atoms. Skipping. Residue LEU 276 is missing expected H atoms. Skipping. Residue THR 277 is missing expected H atoms. Skipping. Residue ILE 281 is missing expected H atoms. Skipping. Residue ALA 284 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue ILE 290 is missing expected H atoms. Skipping. Residue ALA 291 is missing expected H atoms. Skipping. Residue VAL 295 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LEU 303 is missing expected H atoms. Skipping. Residue THR 315 is missing expected H atoms. Skipping. Residue VAL 316 is missing expected H atoms. Skipping. Residue MET 317 is missing expected H atoms. Skipping. Residue THR 321 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue THR 328 is missing expected H atoms. Skipping. Residue ILE 329 is missing expected H atoms. Skipping. Residue ALA 330 is missing expected H atoms. Skipping. Residue ALA 331 is missing expected H atoms. Skipping. Residue LEU 332 is missing expected H atoms. Skipping. Residue MET 336 is missing expected H atoms. Skipping. Residue LEU 338 is missing expected H atoms. Skipping. Residue ALA 340 is missing expected H atoms. Skipping. Residue LEU 342 is missing expected H atoms. Skipping. Residue ALA 344 is missing expected H atoms. Skipping. Residue THR 346 is missing expected H atoms. Skipping. Residue THR 347 is missing expected H atoms. Skipping. Residue ILE 352 is missing expected H atoms. Skipping. Residue THR 353 is missing expected H atoms. Skipping. Residue ALA 354 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue VAL 360 is missing expected H atoms. Skipping. Residue ILE 364 is missing expected H atoms. Skipping. Residue ALA 368 is missing expected H atoms. Skipping. Residue ILE 371 is missing expected H atoms. Skipping. Residue ALA 375 is missing expected H atoms. Skipping. Residue ILE 380 is missing expected H atoms. Skipping. Residue VAL 381 is missing expected H atoms. Skipping. Residue ALA 383 is missing expected H atoms. Skipping. Residue VAL 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue ALA 386 is missing expected H atoms. Skipping. Residue LEU 388 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue ILE 6 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue ILE 19 is missing expected H atoms. Skipping. Residue ALA 20 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue THR 24 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue ALA 28 is missing expected H atoms. Skipping. Residue ALA 29 is missing expected H atoms. Skipping. Residue MET 31 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue MET 37 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue THR 41 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue ILE 56 is missing expected H atoms. Skipping. Residue ALA 58 is missing expected H atoms. Skipping. Residue LEU 60 is missing expected H atoms. Skipping. Residue VAL 64 is missing expected H atoms. Skipping. Residue ALA 65 is missing expected H atoms. Skipping. Residue VAL 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue ALA 69 is missing expected H atoms. Skipping. Residue ALA 71 is missing expected H atoms. Skipping. Residue VAL 75 is missing expected H atoms. Skipping. Residue THR 81 is missing expected H atoms. Skipping. Residue ALA 82 is missing expected H atoms. Skipping. Residue ALA 87 is missing expected H atoms. Skipping. Residue VAL 90 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue THR 94 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue MET 98 is missing expected H atoms. Skipping. Residue ALA 100 is missing expected H atoms. Skipping. Residue ALA 101 is missing expected H atoms. Skipping. Residue ALA 107 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 112 is missing expected H atoms. Skipping. Residue ALA 117 is missing expected H atoms. Skipping. Residue ILE 122 is missing expected H atoms. Skipping. Residue MET 123 is missing expected H atoms. Skipping. Residue VAL 125 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue THR 137 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue MET 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue THR 150 is missing expected H atoms. Skipping. Residue LEU 152 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue VAL 161 is missing expected H atoms. Skipping. Residue VAL 163 is missing expected H atoms. Skipping. Residue VAL 164 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue ILE 6 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue ILE 19 is missing expected H atoms. Skipping. Residue ALA 20 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue THR 24 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue ALA 28 is missing expected H atoms. Skipping. Residue ALA 29 is missing expected H atoms. Skipping. Residue MET 31 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue MET 37 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue THR 41 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue ILE 56 is missing expected H atoms. Skipping. Residue ALA 58 is missing expected H atoms. Skipping. Residue LEU 60 is missing expected H atoms. Skipping. Residue VAL 64 is missing expected H atoms. Skipping. Residue ALA 65 is missing expected H atoms. Skipping. Residue VAL 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue ALA 69 is missing expected H atoms. Skipping. Residue ALA 71 is missing expected H atoms. Skipping. Residue VAL 75 is missing expected H atoms. Skipping. Residue THR 81 is missing expected H atoms. Skipping. Residue ALA 82 is missing expected H atoms. Skipping. Residue ALA 87 is missing expected H atoms. Skipping. Residue VAL 90 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue THR 94 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue MET 98 is missing expected H atoms. Skipping. Residue ALA 100 is missing expected H atoms. Skipping. Residue ALA 101 is missing expected H atoms. Skipping. Residue ALA 107 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 112 is missing expected H atoms. Skipping. Residue ALA 117 is missing expected H atoms. Skipping. Residue ILE 122 is missing expected H atoms. Skipping. Residue MET 123 is missing expected H atoms. Skipping. Residue VAL 125 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue THR 137 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue MET 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue THR 150 is missing expected H atoms. Skipping. Residue LEU 152 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue VAL 161 is missing expected H atoms. Skipping. Residue VAL 163 is missing expected H atoms. Skipping. Residue VAL 164 is missing expected H atoms. Skipping. Evaluate side-chains 178 residues out of total 1782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 155 time to evaluate : 2.103 Fit side-chains revert: symmetry clash REVERT: D 40 LYS cc_start: 0.8516 (tmmt) cc_final: 0.8192 (tttm) REVERT: D 444 GLN cc_start: 0.8748 (OUTLIER) cc_final: 0.7218 (tt0) REVERT: E 30 ARG cc_start: 0.8431 (tmt-80) cc_final: 0.8056 (tmt-80) REVERT: E 323 LYS cc_start: 0.7973 (OUTLIER) cc_final: 0.7766 (pttp) REVERT: E 520 LYS cc_start: 0.8153 (mttm) cc_final: 0.7715 (mtpt) REVERT: B 7 ARG cc_start: 0.7358 (OUTLIER) cc_final: 0.6405 (mmm-85) REVERT: B 86 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.8340 (pt0) REVERT: B 308 GLU cc_start: 0.7767 (tt0) cc_final: 0.7287 (tp30) REVERT: C 130 ASP cc_start: 0.8716 (OUTLIER) cc_final: 0.8427 (t70) REVERT: C 165 GLN cc_start: 0.8857 (OUTLIER) cc_final: 0.7385 (tm-30) REVERT: C 271 ARG cc_start: 0.8312 (OUTLIER) cc_final: 0.7393 (mtt-85) REVERT: G 26 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.7156 (tt0) REVERT: G 74 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7479 (mt-10) REVERT: H 21 GLN cc_start: 0.8283 (OUTLIER) cc_final: 0.7912 (mp10) REVERT: H 41 THR cc_start: 0.6815 (OUTLIER) cc_final: 0.6455 (p) outliers start: 23 outliers final: 7 residues processed: 172 average time/residue: 2.1368 time to fit residues: 402.1775 Evaluate side-chains 168 residues out of total 1782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 150 time to evaluate : 2.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 76 GLU Chi-restraints excluded: chain D residue 444 GLN Chi-restraints excluded: chain D residue 460 GLU Chi-restraints excluded: chain D residue 517 CYS Chi-restraints excluded: chain E residue 307 ARG Chi-restraints excluded: chain E residue 323 LYS Chi-restraints excluded: chain B residue 7 ARG Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 173 ASP Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 165 GLN Chi-restraints excluded: chain C residue 271 ARG Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain G residue 41 THR Chi-restraints excluded: chain G residue 74 GLU Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain H residue 21 GLN Chi-restraints excluded: chain H residue 41 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 6 optimal weight: 3.9990 chunk 182 optimal weight: 6.9990 chunk 150 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 194 optimal weight: 6.9990 chunk 189 optimal weight: 0.0970 chunk 108 optimal weight: 5.9990 chunk 139 optimal weight: 5.9990 chunk 160 optimal weight: 0.9990 chunk 91 optimal weight: 0.8980 chunk 162 optimal weight: 5.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 59 GLN ** D 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 17 ASN ** G 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.093330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.083479 restraints weight = 33008.970| |-----------------------------------------------------------------------------| r_work (start): 0.2793 rms_B_bonded: 1.02 r_work: 0.2709 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.2609 rms_B_bonded: 2.59 restraints_weight: 0.2500 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 17861 Z= 0.158 Angle : 0.441 4.985 24231 Z= 0.246 Chirality : 0.039 0.148 2461 Planarity : 0.004 0.044 3153 Dihedral : 4.853 68.524 2346 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.57 % Allowed : 9.26 % Favored : 89.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.19), residues: 2101 helix: 1.46 (0.14), residues: 1359 sheet: 1.95 (0.82), residues: 44 loop : -0.05 (0.24), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 125 HIS 0.006 0.001 HIS D 382 PHE 0.014 0.001 PHE E 39 TYR 0.017 0.001 TYR D 156 ARG 0.004 0.000 ARG E 320 Details of bonding type rmsd hydrogen bonds : bond 0.04976 ( 993) hydrogen bonds : angle 4.91038 ( 2883) covalent geometry : bond 0.00357 (17861) covalent geometry : angle 0.44059 (24231) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 19 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue VAL 23 is missing expected H atoms. Skipping. Residue ALA 25 is missing expected H atoms. Skipping. Residue VAL 28 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue THR 44 is missing expected H atoms. Skipping. Residue ALA 47 is missing expected H atoms. Skipping. Residue THR 48 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ALA 53 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue ALA 64 is missing expected H atoms. Skipping. Residue ALA 68 is missing expected H atoms. Skipping. Residue MET 70 is missing expected H atoms. Skipping. Residue ALA 72 is missing expected H atoms. Skipping. Residue VAL 73 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue ALA 85 is missing expected H atoms. Skipping. Residue LEU 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue ALA 91 is missing expected H atoms. Skipping. Residue VAL 93 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue THR 102 is missing expected H atoms. Skipping. Residue MET 103 is missing expected H atoms. Skipping. Residue VAL 105 is missing expected H atoms. Skipping. Residue VAL 106 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue VAL 112 is missing expected H atoms. Skipping. Residue ALA 117 is missing expected H atoms. Skipping. Residue ILE 118 is missing expected H atoms. Skipping. Residue ALA 119 is missing expected H atoms. Skipping. Residue ALA 120 is missing expected H atoms. Skipping. Residue THR 121 is missing expected H atoms. Skipping. Residue MET 123 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Residue ALA 128 is missing expected H atoms. Skipping. Residue ALA 130 is missing expected H atoms. Skipping. Residue ALA 131 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue ALA 139 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue THR 148 is missing expected H atoms. Skipping. Residue ALA 152 is missing expected H atoms. Skipping. Residue VAL 154 is missing expected H atoms. Skipping. Residue ALA 159 is missing expected H atoms. Skipping. Residue ALA 166 is missing expected H atoms. Skipping. Residue ALA 171 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue ILE 177 is missing expected H atoms. Skipping. Residue LEU 180 is missing expected H atoms. Skipping. Residue MET 184 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue ILE 193 is missing expected H atoms. Skipping. Residue ALA 197 is missing expected H atoms. Skipping. Residue VAL 198 is missing expected H atoms. Skipping. Residue LEU 202 is missing expected H atoms. Skipping. Residue LEU 204 is missing expected H atoms. Skipping. Residue LEU 206 is missing expected H atoms. Skipping. Residue VAL 207 is missing expected H atoms. Skipping. Residue ALA 210 is missing expected H atoms. Skipping. Residue THR 213 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue ILE 217 is missing expected H atoms. Skipping. Residue VAL 218 is missing expected H atoms. Skipping. Residue ALA 219 is missing expected H atoms. Skipping. Residue VAL 220 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue ALA 224 is missing expected H atoms. Skipping. Residue ALA 225 is missing expected H atoms. Skipping. Residue ALA 226 is missing expected H atoms. Skipping. Residue ILE 231 is missing expected H atoms. Skipping. Residue THR 232 is missing expected H atoms. Skipping. Residue THR 234 is missing expected H atoms. Skipping. Residue VAL 235 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue ILE 239 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LEU 244 is missing expected H atoms. Skipping. Residue MET 247 is missing expected H atoms. Skipping. Residue ALA 248 is missing expected H atoms. Skipping. Residue THR 253 is missing expected H atoms. Skipping. Residue VAL 254 is missing expected H atoms. Skipping. Residue VAL 255 is missing expected H atoms. Skipping. Residue ILE 257 is missing expected H atoms. Skipping. Residue ALA 258 is missing expected H atoms. Skipping. Residue ALA 262 is missing expected H atoms. Skipping. Residue ALA 264 is missing expected H atoms. Skipping. Residue LEU 267 is missing expected H atoms. Skipping. Residue THR 269 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue ALA 274 is missing expected H atoms. Skipping. Residue THR 277 is missing expected H atoms. Skipping. Residue THR 283 is missing expected H atoms. Skipping. Residue VAL 285 is missing expected H atoms. Skipping. Residue LEU 286 is missing expected H atoms. Skipping. Residue MET 288 is missing expected H atoms. Skipping. Residue LEU 289 is missing expected H atoms. Skipping. Residue VAL 298 is missing expected H atoms. Skipping. Residue VAL 302 is missing expected H atoms. Skipping. Residue THR 304 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Residue ILE 316 is missing expected H atoms. Skipping. Residue ILE 318 is missing expected H atoms. Skipping. Residue LEU 321 is missing expected H atoms. Skipping. Residue VAL 326 is missing expected H atoms. Skipping. Residue LEU 332 is missing expected H atoms. Skipping. Residue ALA 335 is missing expected H atoms. Skipping. Residue ALA 339 is missing expected H atoms. Skipping. Residue ALA 342 is missing expected H atoms. Skipping. Residue LEU 346 is missing expected H atoms. Skipping. Residue LEU 348 is missing expected H atoms. Skipping. Residue LEU 349 is missing expected H atoms. Skipping. Residue ALA 350 is missing expected H atoms. Skipping. Residue ALA 352 is missing expected H atoms. Skipping. Residue LEU 353 is missing expected H atoms. Skipping. Residue THR 356 is missing expected H atoms. Skipping. Residue LEU 361 is missing expected H atoms. Skipping. Residue ALA 362 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue MET 369 is missing expected H atoms. Skipping. Residue ALA 374 is missing expected H atoms. Skipping. Residue ILE 386 is missing expected H atoms. Skipping. Residue ALA 392 is missing expected H atoms. Skipping. Residue ILE 403 is missing expected H atoms. Skipping. Residue LEU 405 is missing expected H atoms. Skipping. Residue MET 406 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 415 is missing expected H atoms. Skipping. Residue ILE 417 is missing expected H atoms. Skipping. Residue VAL 420 is missing expected H atoms. Skipping. Residue VAL 423 is missing expected H atoms. Skipping. Residue LEU 429 is missing expected H atoms. Skipping. Residue ALA 430 is missing expected H atoms. Skipping. Residue ALA 433 is missing expected H atoms. Skipping. Residue THR 435 is missing expected H atoms. Skipping. Residue LEU 436 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue MET 445 is missing expected H atoms. Skipping. Residue THR 447 is missing expected H atoms. Skipping. Residue MET 456 is missing expected H atoms. Skipping. Residue LEU 458 is missing expected H atoms. Skipping. Residue ALA 459 is missing expected H atoms. Skipping. Residue ILE 469 is missing expected H atoms. Skipping. Residue LEU 478 is missing expected H atoms. Skipping. Residue VAL 481 is missing expected H atoms. Skipping. Residue ILE 482 is missing expected H atoms. Skipping. Residue ALA 483 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue LEU 488 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue LEU 495 is missing expected H atoms. Skipping. Residue ILE 496 is missing expected H atoms. Skipping. Residue ALA 497 is missing expected H atoms. Skipping. Residue VAL 501 is missing expected H atoms. Skipping. Residue LEU 506 is missing expected H atoms. Skipping. Residue THR 508 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue LEU 515 is missing expected H atoms. Skipping. Residue VAL 518 is missing expected H atoms. Skipping. Residue VAL 523 is missing expected H atoms. Skipping. Residue ALA 525 is missing expected H atoms. Skipping. Residue ALA 16 is missing expected H atoms. Skipping. Residue ALA 19 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue VAL 23 is missing expected H atoms. Skipping. Residue ALA 25 is missing expected H atoms. Skipping. Residue VAL 28 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue THR 44 is missing expected H atoms. Skipping. Residue ALA 47 is missing expected H atoms. Skipping. Residue THR 48 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ALA 53 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue ALA 64 is missing expected H atoms. Skipping. Residue ALA 68 is missing expected H atoms. Skipping. Residue MET 70 is missing expected H atoms. Skipping. Residue ALA 72 is missing expected H atoms. Skipping. Residue VAL 73 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue ALA 85 is missing expected H atoms. Skipping. Residue LEU 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue ALA 91 is missing expected H atoms. Skipping. Residue VAL 93 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue THR 102 is missing expected H atoms. Skipping. Residue MET 103 is missing expected H atoms. Skipping. Residue VAL 105 is missing expected H atoms. Skipping. Residue VAL 106 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue VAL 112 is missing expected H atoms. Skipping. Residue ALA 117 is missing expected H atoms. Skipping. Residue ILE 118 is missing expected H atoms. Skipping. Residue ALA 119 is missing expected H atoms. Skipping. Residue ALA 120 is missing expected H atoms. Skipping. Residue THR 121 is missing expected H atoms. Skipping. Residue MET 123 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Residue ALA 128 is missing expected H atoms. Skipping. Residue ALA 130 is missing expected H atoms. Skipping. Residue ALA 131 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue ALA 139 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue THR 148 is missing expected H atoms. Skipping. Residue ALA 152 is missing expected H atoms. Skipping. Residue VAL 154 is missing expected H atoms. Skipping. Residue ALA 159 is missing expected H atoms. Skipping. Residue ALA 166 is missing expected H atoms. Skipping. Residue ALA 171 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue ILE 177 is missing expected H atoms. Skipping. Residue LEU 180 is missing expected H atoms. Skipping. Residue MET 184 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue ILE 193 is missing expected H atoms. Skipping. Residue ALA 197 is missing expected H atoms. Skipping. Residue VAL 198 is missing expected H atoms. Skipping. Residue LEU 202 is missing expected H atoms. Skipping. Residue LEU 204 is missing expected H atoms. Skipping. Residue LEU 206 is missing expected H atoms. Skipping. Residue VAL 207 is missing expected H atoms. Skipping. Residue ALA 210 is missing expected H atoms. Skipping. Residue THR 213 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue ILE 217 is missing expected H atoms. Skipping. Residue VAL 218 is missing expected H atoms. Skipping. Residue ALA 219 is missing expected H atoms. Skipping. Residue VAL 220 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue ALA 224 is missing expected H atoms. Skipping. Residue ALA 225 is missing expected H atoms. Skipping. Residue ALA 226 is missing expected H atoms. Skipping. Residue ILE 231 is missing expected H atoms. Skipping. Residue THR 232 is missing expected H atoms. Skipping. Residue THR 234 is missing expected H atoms. Skipping. Residue VAL 235 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue ILE 239 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LEU 244 is missing expected H atoms. Skipping. Residue MET 247 is missing expected H atoms. Skipping. Residue ALA 248 is missing expected H atoms. Skipping. Residue THR 253 is missing expected H atoms. Skipping. Residue VAL 254 is missing expected H atoms. Skipping. Residue VAL 255 is missing expected H atoms. Skipping. Residue ILE 257 is missing expected H atoms. Skipping. Residue ALA 258 is missing expected H atoms. Skipping. Residue ALA 262 is missing expected H atoms. Skipping. Residue ALA 264 is missing expected H atoms. Skipping. Residue LEU 267 is missing expected H atoms. Skipping. Residue THR 269 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue ALA 274 is missing expected H atoms. Skipping. Residue THR 277 is missing expected H atoms. Skipping. Residue THR 283 is missing expected H atoms. Skipping. Residue VAL 285 is missing expected H atoms. Skipping. Residue LEU 286 is missing expected H atoms. Skipping. Residue MET 288 is missing expected H atoms. Skipping. Residue LEU 289 is missing expected H atoms. Skipping. Residue VAL 298 is missing expected H atoms. Skipping. Residue VAL 302 is missing expected H atoms. Skipping. Residue THR 304 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Residue ILE 316 is missing expected H atoms. Skipping. Residue ILE 318 is missing expected H atoms. Skipping. Residue LEU 321 is missing expected H atoms. Skipping. Residue VAL 326 is missing expected H atoms. Skipping. Residue LEU 332 is missing expected H atoms. Skipping. Residue ALA 335 is missing expected H atoms. Skipping. Residue ALA 339 is missing expected H atoms. Skipping. Residue ALA 342 is missing expected H atoms. Skipping. Residue LEU 346 is missing expected H atoms. Skipping. Residue LEU 348 is missing expected H atoms. Skipping. Residue LEU 349 is missing expected H atoms. Skipping. Residue ALA 350 is missing expected H atoms. Skipping. Residue ALA 352 is missing expected H atoms. Skipping. Residue LEU 353 is missing expected H atoms. Skipping. Residue THR 356 is missing expected H atoms. Skipping. Residue LEU 361 is missing expected H atoms. Skipping. Residue ALA 362 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue MET 369 is missing expected H atoms. Skipping. Residue ALA 374 is missing expected H atoms. Skipping. Residue ILE 386 is missing expected H atoms. Skipping. Residue ALA 392 is missing expected H atoms. Skipping. Residue ILE 403 is missing expected H atoms. Skipping. Residue LEU 405 is missing expected H atoms. Skipping. Residue MET 406 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 415 is missing expected H atoms. Skipping. Residue ILE 417 is missing expected H atoms. Skipping. Residue VAL 420 is missing expected H atoms. Skipping. Residue VAL 423 is missing expected H atoms. Skipping. Residue LEU 429 is missing expected H atoms. Skipping. Residue ALA 430 is missing expected H atoms. Skipping. Residue ALA 433 is missing expected H atoms. Skipping. Residue THR 435 is missing expected H atoms. Skipping. Residue LEU 436 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue MET 445 is missing expected H atoms. Skipping. Residue THR 447 is missing expected H atoms. Skipping. Residue MET 456 is missing expected H atoms. Skipping. Residue LEU 458 is missing expected H atoms. Skipping. Residue ALA 459 is missing expected H atoms. Skipping. Residue ILE 469 is missing expected H atoms. Skipping. Residue LEU 478 is missing expected H atoms. Skipping. Residue VAL 481 is missing expected H atoms. Skipping. Residue ILE 482 is missing expected H atoms. Skipping. Residue ALA 483 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue LEU 488 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue LEU 495 is missing expected H atoms. Skipping. Residue ILE 496 is missing expected H atoms. Skipping. Residue ALA 497 is missing expected H atoms. Skipping. Residue VAL 501 is missing expected H atoms. Skipping. Residue LEU 506 is missing expected H atoms. Skipping. Residue THR 508 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue LEU 515 is missing expected H atoms. Skipping. Residue VAL 518 is missing expected H atoms. Skipping. Residue VAL 523 is missing expected H atoms. Skipping. Residue ALA 525 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue MET 16 is missing expected H atoms. Skipping. Residue ALA 17 is missing expected H atoms. Skipping. Residue ALA 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 20 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue ALA 23 is missing expected H atoms. Skipping. Residue LEU 24 is missing expected H atoms. Skipping. Residue ALA 27 is missing expected H atoms. Skipping. Residue LEU 29 is missing expected H atoms. Skipping. Residue MET 35 is missing expected H atoms. Skipping. Residue VAL 39 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue THR 47 is missing expected H atoms. Skipping. Residue ALA 51 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue THR 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ALA 56 is missing expected H atoms. Skipping. Residue ALA 60 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue ALA 64 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue THR 92 is missing expected H atoms. Skipping. Residue VAL 93 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue ALA 107 is missing expected H atoms. Skipping. Residue VAL 110 is missing expected H atoms. Skipping. Residue ALA 114 is missing expected H atoms. Skipping. Residue THR 120 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Residue ALA 129 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue ALA 135 is missing expected H atoms. Skipping. Residue MET 136 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue ALA 151 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue ALA 162 is missing expected H atoms. Skipping. Residue ALA 167 is missing expected H atoms. Skipping. Residue ALA 170 is missing expected H atoms. Skipping. Residue LEU 171 is missing expected H atoms. Skipping. Residue VAL 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue ALA 180 is missing expected H atoms. Skipping. Residue ILE 187 is missing expected H atoms. Skipping. Residue ILE 189 is missing expected H atoms. Skipping. Residue ALA 190 is missing expected H atoms. Skipping. Residue MET 192 is missing expected H atoms. Skipping. Residue ILE 193 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue LEU 200 is missing expected H atoms. Skipping. Residue ALA 201 is missing expected H atoms. Skipping. Residue ILE 203 is missing expected H atoms. Skipping. Residue VAL 204 is missing expected H atoms. Skipping. Residue THR 211 is missing expected H atoms. Skipping. Residue ALA 212 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue ALA 216 is missing expected H atoms. Skipping. Residue THR 219 is missing expected H atoms. Skipping. Residue VAL 223 is missing expected H atoms. Skipping. Residue ALA 227 is missing expected H atoms. Skipping. Residue LEU 229 is missing expected H atoms. Skipping. Residue ALA 230 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue VAL 238 is missing expected H atoms. Skipping. Residue ALA 245 is missing expected H atoms. Skipping. Residue VAL 248 is missing expected H atoms. Skipping. Residue ALA 250 is missing expected H atoms. Skipping. Residue VAL 251 is missing expected H atoms. Skipping. Residue ALA 254 is missing expected H atoms. Skipping. Residue LEU 255 is missing expected H atoms. Skipping. Residue VAL 260 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue ALA 269 is missing expected H atoms. Skipping. Residue LEU 276 is missing expected H atoms. Skipping. Residue THR 277 is missing expected H atoms. Skipping. Residue ILE 281 is missing expected H atoms. Skipping. Residue ALA 284 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue ILE 290 is missing expected H atoms. Skipping. Residue ALA 291 is missing expected H atoms. Skipping. Residue VAL 295 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LEU 303 is missing expected H atoms. Skipping. Residue THR 315 is missing expected H atoms. Skipping. Residue VAL 316 is missing expected H atoms. Skipping. Residue MET 317 is missing expected H atoms. Skipping. Residue THR 321 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue THR 328 is missing expected H atoms. Skipping. Residue ILE 329 is missing expected H atoms. Skipping. Residue ALA 330 is missing expected H atoms. Skipping. Residue ALA 331 is missing expected H atoms. Skipping. Residue LEU 332 is missing expected H atoms. Skipping. Residue MET 336 is missing expected H atoms. Skipping. Residue LEU 338 is missing expected H atoms. Skipping. Residue ALA 340 is missing expected H atoms. Skipping. Residue LEU 342 is missing expected H atoms. Skipping. Residue ALA 344 is missing expected H atoms. Skipping. Residue THR 346 is missing expected H atoms. Skipping. Residue THR 347 is missing expected H atoms. Skipping. Residue ILE 352 is missing expected H atoms. Skipping. Residue THR 353 is missing expected H atoms. Skipping. Residue ALA 354 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue VAL 360 is missing expected H atoms. Skipping. Residue ILE 364 is missing expected H atoms. Skipping. Residue ALA 368 is missing expected H atoms. Skipping. Residue ILE 371 is missing expected H atoms. Skipping. Residue ALA 375 is missing expected H atoms. Skipping. Residue ILE 380 is missing expected H atoms. Skipping. Residue VAL 381 is missing expected H atoms. Skipping. Residue ALA 383 is missing expected H atoms. Skipping. Residue VAL 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue ALA 386 is missing expected H atoms. Skipping. Residue LEU 388 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue ILE 6 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue ILE 19 is missing expected H atoms. Skipping. Residue ALA 20 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue THR 24 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue ALA 28 is missing expected H atoms. Skipping. Residue ALA 29 is missing expected H atoms. Skipping. Residue MET 31 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue MET 37 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue THR 41 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue ILE 56 is missing expected H atoms. Skipping. Residue ALA 58 is missing expected H atoms. Skipping. Residue LEU 60 is missing expected H atoms. Skipping. Residue VAL 64 is missing expected H atoms. Skipping. Residue ALA 65 is missing expected H atoms. Skipping. Residue VAL 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue ALA 69 is missing expected H atoms. Skipping. Residue ALA 71 is missing expected H atoms. Skipping. Residue VAL 75 is missing expected H atoms. Skipping. Residue THR 81 is missing expected H atoms. Skipping. Residue ALA 82 is missing expected H atoms. Skipping. Residue ALA 87 is missing expected H atoms. Skipping. Residue VAL 90 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue THR 94 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue MET 98 is missing expected H atoms. Skipping. Residue ALA 100 is missing expected H atoms. Skipping. Residue ALA 101 is missing expected H atoms. Skipping. Residue ALA 107 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 112 is missing expected H atoms. Skipping. Residue ALA 117 is missing expected H atoms. Skipping. Residue ILE 122 is missing expected H atoms. Skipping. Residue MET 123 is missing expected H atoms. Skipping. Residue VAL 125 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue THR 137 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue MET 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue THR 150 is missing expected H atoms. Skipping. Residue LEU 152 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue VAL 161 is missing expected H atoms. Skipping. Residue VAL 163 is missing expected H atoms. Skipping. Residue VAL 164 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue ILE 6 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue ILE 19 is missing expected H atoms. Skipping. Residue ALA 20 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue THR 24 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue ALA 28 is missing expected H atoms. Skipping. Residue ALA 29 is missing expected H atoms. Skipping. Residue MET 31 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue MET 37 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue THR 41 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue ILE 56 is missing expected H atoms. Skipping. Residue ALA 58 is missing expected H atoms. Skipping. Residue LEU 60 is missing expected H atoms. Skipping. Residue VAL 64 is missing expected H atoms. Skipping. Residue ALA 65 is missing expected H atoms. Skipping. Residue VAL 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue ALA 69 is missing expected H atoms. Skipping. Residue ALA 71 is missing expected H atoms. Skipping. Residue VAL 75 is missing expected H atoms. Skipping. Residue THR 81 is missing expected H atoms. Skipping. Residue ALA 82 is missing expected H atoms. Skipping. Residue ALA 87 is missing expected H atoms. Skipping. Residue VAL 90 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue THR 94 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue MET 98 is missing expected H atoms. Skipping. Residue ALA 100 is missing expected H atoms. Skipping. Residue ALA 101 is missing expected H atoms. Skipping. Residue ALA 107 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 112 is missing expected H atoms. Skipping. Residue ALA 117 is missing expected H atoms. Skipping. Residue ILE 122 is missing expected H atoms. Skipping. Residue MET 123 is missing expected H atoms. Skipping. Residue VAL 125 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue THR 137 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue MET 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue THR 150 is missing expected H atoms. Skipping. Residue LEU 152 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue VAL 161 is missing expected H atoms. Skipping. Residue VAL 163 is missing expected H atoms. Skipping. Residue VAL 164 is missing expected H atoms. Skipping. Evaluate side-chains 178 residues out of total 1782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 150 time to evaluate : 2.127 Fit side-chains revert: symmetry clash REVERT: D 40 LYS cc_start: 0.8524 (OUTLIER) cc_final: 0.8201 (tttm) REVERT: D 55 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7659 (pm20) REVERT: D 175 ARG cc_start: 0.8666 (OUTLIER) cc_final: 0.8202 (ptp-170) REVERT: D 444 GLN cc_start: 0.8777 (OUTLIER) cc_final: 0.7290 (tt0) REVERT: E 30 ARG cc_start: 0.8420 (tmt-80) cc_final: 0.7262 (ttm110) REVERT: E 323 LYS cc_start: 0.7951 (OUTLIER) cc_final: 0.7721 (pttp) REVERT: E 520 LYS cc_start: 0.8163 (mttm) cc_final: 0.7796 (mtmt) REVERT: B 7 ARG cc_start: 0.7394 (OUTLIER) cc_final: 0.6461 (mmm-85) REVERT: B 86 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.8374 (pt0) REVERT: B 308 GLU cc_start: 0.7769 (tt0) cc_final: 0.7315 (tp30) REVERT: C 130 ASP cc_start: 0.8669 (OUTLIER) cc_final: 0.8364 (t70) REVERT: C 165 GLN cc_start: 0.8825 (OUTLIER) cc_final: 0.7424 (tm-30) REVERT: C 225 LYS cc_start: 0.8668 (OUTLIER) cc_final: 0.8425 (tttm) REVERT: C 271 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.7406 (mtt-85) REVERT: G 26 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.7211 (tt0) REVERT: G 74 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7513 (mt-10) REVERT: H 21 GLN cc_start: 0.8338 (OUTLIER) cc_final: 0.7970 (mp10) REVERT: H 41 THR cc_start: 0.7080 (OUTLIER) cc_final: 0.6737 (p) outliers start: 28 outliers final: 9 residues processed: 168 average time/residue: 2.1748 time to fit residues: 398.7176 Evaluate side-chains 167 residues out of total 1782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 143 time to evaluate : 2.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 40 LYS Chi-restraints excluded: chain D residue 55 GLU Chi-restraints excluded: chain D residue 76 GLU Chi-restraints excluded: chain D residue 175 ARG Chi-restraints excluded: chain D residue 444 GLN Chi-restraints excluded: chain D residue 460 GLU Chi-restraints excluded: chain D residue 517 CYS Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 307 ARG Chi-restraints excluded: chain E residue 323 LYS Chi-restraints excluded: chain E residue 474 GLU Chi-restraints excluded: chain B residue 7 ARG Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 173 ASP Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 165 GLN Chi-restraints excluded: chain C residue 225 LYS Chi-restraints excluded: chain C residue 271 ARG Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain G residue 41 THR Chi-restraints excluded: chain G residue 74 GLU Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain H residue 21 GLN Chi-restraints excluded: chain H residue 41 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 59 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 114 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 chunk 141 optimal weight: 3.9990 chunk 198 optimal weight: 0.9980 chunk 89 optimal weight: 8.9990 chunk 1 optimal weight: 6.9990 chunk 116 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 59 GLN ** D 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.092471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.082588 restraints weight = 33123.848| |-----------------------------------------------------------------------------| r_work (start): 0.2763 rms_B_bonded: 1.02 r_work: 0.2678 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.2578 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.2578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 17861 Z= 0.180 Angle : 0.461 5.276 24231 Z= 0.258 Chirality : 0.040 0.153 2461 Planarity : 0.004 0.044 3153 Dihedral : 4.929 68.988 2346 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.52 % Allowed : 9.37 % Favored : 89.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.19), residues: 2101 helix: 1.37 (0.14), residues: 1360 sheet: 1.98 (0.82), residues: 44 loop : -0.10 (0.24), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 125 HIS 0.006 0.001 HIS D 382 PHE 0.016 0.001 PHE D 188 TYR 0.016 0.001 TYR D 156 ARG 0.005 0.000 ARG E 320 Details of bonding type rmsd hydrogen bonds : bond 0.05265 ( 993) hydrogen bonds : angle 4.99607 ( 2883) covalent geometry : bond 0.00414 (17861) covalent geometry : angle 0.46076 (24231) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 19 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue VAL 23 is missing expected H atoms. Skipping. Residue ALA 25 is missing expected H atoms. Skipping. Residue VAL 28 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue THR 44 is missing expected H atoms. Skipping. Residue ALA 47 is missing expected H atoms. Skipping. Residue THR 48 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ALA 53 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue ALA 64 is missing expected H atoms. Skipping. Residue ALA 68 is missing expected H atoms. Skipping. Residue MET 70 is missing expected H atoms. Skipping. Residue ALA 72 is missing expected H atoms. Skipping. Residue VAL 73 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue ALA 85 is missing expected H atoms. Skipping. Residue LEU 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue ALA 91 is missing expected H atoms. Skipping. Residue VAL 93 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue THR 102 is missing expected H atoms. Skipping. Residue MET 103 is missing expected H atoms. Skipping. Residue VAL 105 is missing expected H atoms. Skipping. Residue VAL 106 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue VAL 112 is missing expected H atoms. Skipping. Residue ALA 117 is missing expected H atoms. Skipping. Residue ILE 118 is missing expected H atoms. Skipping. Residue ALA 119 is missing expected H atoms. Skipping. Residue ALA 120 is missing expected H atoms. Skipping. Residue THR 121 is missing expected H atoms. Skipping. Residue MET 123 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Residue ALA 128 is missing expected H atoms. Skipping. Residue ALA 130 is missing expected H atoms. Skipping. Residue ALA 131 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue ALA 139 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue THR 148 is missing expected H atoms. Skipping. Residue ALA 152 is missing expected H atoms. Skipping. Residue VAL 154 is missing expected H atoms. Skipping. Residue ALA 159 is missing expected H atoms. Skipping. Residue ALA 166 is missing expected H atoms. Skipping. Residue ALA 171 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue ILE 177 is missing expected H atoms. Skipping. Residue LEU 180 is missing expected H atoms. Skipping. Residue MET 184 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue ILE 193 is missing expected H atoms. Skipping. Residue ALA 197 is missing expected H atoms. Skipping. Residue VAL 198 is missing expected H atoms. Skipping. Residue LEU 202 is missing expected H atoms. Skipping. Residue LEU 204 is missing expected H atoms. Skipping. Residue LEU 206 is missing expected H atoms. Skipping. Residue VAL 207 is missing expected H atoms. Skipping. Residue ALA 210 is missing expected H atoms. Skipping. Residue THR 213 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue ILE 217 is missing expected H atoms. Skipping. Residue VAL 218 is missing expected H atoms. Skipping. Residue ALA 219 is missing expected H atoms. Skipping. Residue VAL 220 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue ALA 224 is missing expected H atoms. Skipping. Residue ALA 225 is missing expected H atoms. Skipping. Residue ALA 226 is missing expected H atoms. Skipping. Residue ILE 231 is missing expected H atoms. Skipping. Residue THR 232 is missing expected H atoms. Skipping. Residue THR 234 is missing expected H atoms. Skipping. Residue VAL 235 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue ILE 239 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LEU 244 is missing expected H atoms. Skipping. Residue MET 247 is missing expected H atoms. Skipping. Residue ALA 248 is missing expected H atoms. Skipping. Residue THR 253 is missing expected H atoms. Skipping. Residue VAL 254 is missing expected H atoms. Skipping. Residue VAL 255 is missing expected H atoms. Skipping. Residue ILE 257 is missing expected H atoms. Skipping. Residue ALA 258 is missing expected H atoms. Skipping. Residue ALA 262 is missing expected H atoms. Skipping. Residue ALA 264 is missing expected H atoms. Skipping. Residue LEU 267 is missing expected H atoms. Skipping. Residue THR 269 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue ALA 274 is missing expected H atoms. Skipping. Residue THR 277 is missing expected H atoms. Skipping. Residue THR 283 is missing expected H atoms. Skipping. Residue VAL 285 is missing expected H atoms. Skipping. Residue LEU 286 is missing expected H atoms. Skipping. Residue MET 288 is missing expected H atoms. Skipping. Residue LEU 289 is missing expected H atoms. Skipping. Residue VAL 298 is missing expected H atoms. Skipping. Residue VAL 302 is missing expected H atoms. Skipping. Residue THR 304 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Residue ILE 316 is missing expected H atoms. Skipping. Residue ILE 318 is missing expected H atoms. Skipping. Residue LEU 321 is missing expected H atoms. Skipping. Residue VAL 326 is missing expected H atoms. Skipping. Residue LEU 332 is missing expected H atoms. Skipping. Residue ALA 335 is missing expected H atoms. Skipping. Residue ALA 339 is missing expected H atoms. Skipping. Residue ALA 342 is missing expected H atoms. Skipping. Residue LEU 346 is missing expected H atoms. Skipping. Residue LEU 348 is missing expected H atoms. Skipping. Residue LEU 349 is missing expected H atoms. Skipping. Residue ALA 350 is missing expected H atoms. Skipping. Residue ALA 352 is missing expected H atoms. Skipping. Residue LEU 353 is missing expected H atoms. Skipping. Residue THR 356 is missing expected H atoms. Skipping. Residue LEU 361 is missing expected H atoms. Skipping. Residue ALA 362 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue MET 369 is missing expected H atoms. Skipping. Residue ALA 374 is missing expected H atoms. Skipping. Residue ILE 386 is missing expected H atoms. Skipping. Residue ALA 392 is missing expected H atoms. Skipping. Residue ILE 403 is missing expected H atoms. Skipping. Residue LEU 405 is missing expected H atoms. Skipping. Residue MET 406 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 415 is missing expected H atoms. Skipping. Residue ILE 417 is missing expected H atoms. Skipping. Residue VAL 420 is missing expected H atoms. Skipping. Residue VAL 423 is missing expected H atoms. Skipping. Residue LEU 429 is missing expected H atoms. Skipping. Residue ALA 430 is missing expected H atoms. Skipping. Residue ALA 433 is missing expected H atoms. Skipping. Residue THR 435 is missing expected H atoms. Skipping. Residue LEU 436 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue MET 445 is missing expected H atoms. Skipping. Residue THR 447 is missing expected H atoms. Skipping. Residue MET 456 is missing expected H atoms. Skipping. Residue LEU 458 is missing expected H atoms. Skipping. Residue ALA 459 is missing expected H atoms. Skipping. Residue ILE 469 is missing expected H atoms. Skipping. Residue LEU 478 is missing expected H atoms. Skipping. Residue VAL 481 is missing expected H atoms. Skipping. Residue ILE 482 is missing expected H atoms. Skipping. Residue ALA 483 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue LEU 488 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue LEU 495 is missing expected H atoms. Skipping. Residue ILE 496 is missing expected H atoms. Skipping. Residue ALA 497 is missing expected H atoms. Skipping. Residue VAL 501 is missing expected H atoms. Skipping. Residue LEU 506 is missing expected H atoms. Skipping. Residue THR 508 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue LEU 515 is missing expected H atoms. Skipping. Residue VAL 518 is missing expected H atoms. Skipping. Residue VAL 523 is missing expected H atoms. Skipping. Residue ALA 525 is missing expected H atoms. Skipping. Residue ALA 16 is missing expected H atoms. Skipping. Residue ALA 19 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue VAL 23 is missing expected H atoms. Skipping. Residue ALA 25 is missing expected H atoms. Skipping. Residue VAL 28 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue THR 44 is missing expected H atoms. Skipping. Residue ALA 47 is missing expected H atoms. Skipping. Residue THR 48 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ALA 53 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue ALA 64 is missing expected H atoms. Skipping. Residue ALA 68 is missing expected H atoms. Skipping. Residue MET 70 is missing expected H atoms. Skipping. Residue ALA 72 is missing expected H atoms. Skipping. Residue VAL 73 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue ALA 85 is missing expected H atoms. Skipping. Residue LEU 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue ALA 91 is missing expected H atoms. Skipping. Residue VAL 93 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue THR 102 is missing expected H atoms. Skipping. Residue MET 103 is missing expected H atoms. Skipping. Residue VAL 105 is missing expected H atoms. Skipping. Residue VAL 106 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue VAL 112 is missing expected H atoms. Skipping. Residue ALA 117 is missing expected H atoms. Skipping. Residue ILE 118 is missing expected H atoms. Skipping. Residue ALA 119 is missing expected H atoms. Skipping. Residue ALA 120 is missing expected H atoms. Skipping. Residue THR 121 is missing expected H atoms. Skipping. Residue MET 123 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Residue ALA 128 is missing expected H atoms. Skipping. Residue ALA 130 is missing expected H atoms. Skipping. Residue ALA 131 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue ALA 139 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue THR 148 is missing expected H atoms. Skipping. Residue ALA 152 is missing expected H atoms. Skipping. Residue VAL 154 is missing expected H atoms. Skipping. Residue ALA 159 is missing expected H atoms. Skipping. Residue ALA 166 is missing expected H atoms. Skipping. Residue ALA 171 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue ILE 177 is missing expected H atoms. Skipping. Residue LEU 180 is missing expected H atoms. Skipping. Residue MET 184 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue ILE 193 is missing expected H atoms. Skipping. Residue ALA 197 is missing expected H atoms. Skipping. Residue VAL 198 is missing expected H atoms. Skipping. Residue LEU 202 is missing expected H atoms. Skipping. Residue LEU 204 is missing expected H atoms. Skipping. Residue LEU 206 is missing expected H atoms. Skipping. Residue VAL 207 is missing expected H atoms. Skipping. Residue ALA 210 is missing expected H atoms. Skipping. Residue THR 213 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue ILE 217 is missing expected H atoms. Skipping. Residue VAL 218 is missing expected H atoms. Skipping. Residue ALA 219 is missing expected H atoms. Skipping. Residue VAL 220 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue ALA 224 is missing expected H atoms. Skipping. Residue ALA 225 is missing expected H atoms. Skipping. Residue ALA 226 is missing expected H atoms. Skipping. Residue ILE 231 is missing expected H atoms. Skipping. Residue THR 232 is missing expected H atoms. Skipping. Residue THR 234 is missing expected H atoms. Skipping. Residue VAL 235 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue ILE 239 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LEU 244 is missing expected H atoms. Skipping. Residue MET 247 is missing expected H atoms. Skipping. Residue ALA 248 is missing expected H atoms. Skipping. Residue THR 253 is missing expected H atoms. Skipping. Residue VAL 254 is missing expected H atoms. Skipping. Residue VAL 255 is missing expected H atoms. Skipping. Residue ILE 257 is missing expected H atoms. Skipping. Residue ALA 258 is missing expected H atoms. Skipping. Residue ALA 262 is missing expected H atoms. Skipping. Residue ALA 264 is missing expected H atoms. Skipping. Residue LEU 267 is missing expected H atoms. Skipping. Residue THR 269 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue ALA 274 is missing expected H atoms. Skipping. Residue THR 277 is missing expected H atoms. Skipping. Residue THR 283 is missing expected H atoms. Skipping. Residue VAL 285 is missing expected H atoms. Skipping. Residue LEU 286 is missing expected H atoms. Skipping. Residue MET 288 is missing expected H atoms. Skipping. Residue LEU 289 is missing expected H atoms. Skipping. Residue VAL 298 is missing expected H atoms. Skipping. Residue VAL 302 is missing expected H atoms. Skipping. Residue THR 304 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Residue ILE 316 is missing expected H atoms. Skipping. Residue ILE 318 is missing expected H atoms. Skipping. Residue LEU 321 is missing expected H atoms. Skipping. Residue VAL 326 is missing expected H atoms. Skipping. Residue LEU 332 is missing expected H atoms. Skipping. Residue ALA 335 is missing expected H atoms. Skipping. Residue ALA 339 is missing expected H atoms. Skipping. Residue ALA 342 is missing expected H atoms. Skipping. Residue LEU 346 is missing expected H atoms. Skipping. Residue LEU 348 is missing expected H atoms. Skipping. Residue LEU 349 is missing expected H atoms. Skipping. Residue ALA 350 is missing expected H atoms. Skipping. Residue ALA 352 is missing expected H atoms. Skipping. Residue LEU 353 is missing expected H atoms. Skipping. Residue THR 356 is missing expected H atoms. Skipping. Residue LEU 361 is missing expected H atoms. Skipping. Residue ALA 362 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue MET 369 is missing expected H atoms. Skipping. Residue ALA 374 is missing expected H atoms. Skipping. Residue ILE 386 is missing expected H atoms. Skipping. Residue ALA 392 is missing expected H atoms. Skipping. Residue ILE 403 is missing expected H atoms. Skipping. Residue LEU 405 is missing expected H atoms. Skipping. Residue MET 406 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 415 is missing expected H atoms. Skipping. Residue ILE 417 is missing expected H atoms. Skipping. Residue VAL 420 is missing expected H atoms. Skipping. Residue VAL 423 is missing expected H atoms. Skipping. Residue LEU 429 is missing expected H atoms. Skipping. Residue ALA 430 is missing expected H atoms. Skipping. Residue ALA 433 is missing expected H atoms. Skipping. Residue THR 435 is missing expected H atoms. Skipping. Residue LEU 436 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue MET 445 is missing expected H atoms. Skipping. Residue THR 447 is missing expected H atoms. Skipping. Residue MET 456 is missing expected H atoms. Skipping. Residue LEU 458 is missing expected H atoms. Skipping. Residue ALA 459 is missing expected H atoms. Skipping. Residue ILE 469 is missing expected H atoms. Skipping. Residue LEU 478 is missing expected H atoms. Skipping. Residue VAL 481 is missing expected H atoms. Skipping. Residue ILE 482 is missing expected H atoms. Skipping. Residue ALA 483 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue LEU 488 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue LEU 495 is missing expected H atoms. Skipping. Residue ILE 496 is missing expected H atoms. Skipping. Residue ALA 497 is missing expected H atoms. Skipping. Residue VAL 501 is missing expected H atoms. Skipping. Residue LEU 506 is missing expected H atoms. Skipping. Residue THR 508 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue LEU 515 is missing expected H atoms. Skipping. Residue VAL 518 is missing expected H atoms. Skipping. Residue VAL 523 is missing expected H atoms. Skipping. Residue ALA 525 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue MET 16 is missing expected H atoms. Skipping. Residue ALA 17 is missing expected H atoms. Skipping. Residue ALA 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 20 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue ALA 23 is missing expected H atoms. Skipping. Residue LEU 24 is missing expected H atoms. Skipping. Residue ALA 27 is missing expected H atoms. Skipping. Residue LEU 29 is missing expected H atoms. Skipping. Residue MET 35 is missing expected H atoms. Skipping. Residue VAL 39 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue THR 47 is missing expected H atoms. Skipping. Residue ALA 51 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue THR 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ALA 56 is missing expected H atoms. Skipping. Residue ALA 60 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue ALA 64 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue THR 92 is missing expected H atoms. Skipping. Residue VAL 93 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue ALA 107 is missing expected H atoms. Skipping. Residue VAL 110 is missing expected H atoms. Skipping. Residue ALA 114 is missing expected H atoms. Skipping. Residue THR 120 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Residue ALA 129 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue ALA 135 is missing expected H atoms. Skipping. Residue MET 136 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue ALA 151 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue ALA 162 is missing expected H atoms. Skipping. Residue ALA 167 is missing expected H atoms. Skipping. Residue ALA 170 is missing expected H atoms. Skipping. Residue LEU 171 is missing expected H atoms. Skipping. Residue VAL 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue ALA 180 is missing expected H atoms. Skipping. Residue ILE 187 is missing expected H atoms. Skipping. Residue ILE 189 is missing expected H atoms. Skipping. Residue ALA 190 is missing expected H atoms. Skipping. Residue MET 192 is missing expected H atoms. Skipping. Residue ILE 193 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue LEU 200 is missing expected H atoms. Skipping. Residue ALA 201 is missing expected H atoms. Skipping. Residue ILE 203 is missing expected H atoms. Skipping. Residue VAL 204 is missing expected H atoms. Skipping. Residue THR 211 is missing expected H atoms. Skipping. Residue ALA 212 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue ALA 216 is missing expected H atoms. Skipping. Residue THR 219 is missing expected H atoms. Skipping. Residue VAL 223 is missing expected H atoms. Skipping. Residue ALA 227 is missing expected H atoms. Skipping. Residue LEU 229 is missing expected H atoms. Skipping. Residue ALA 230 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue VAL 238 is missing expected H atoms. Skipping. Residue ALA 245 is missing expected H atoms. Skipping. Residue VAL 248 is missing expected H atoms. Skipping. Residue ALA 250 is missing expected H atoms. Skipping. Residue VAL 251 is missing expected H atoms. Skipping. Residue ALA 254 is missing expected H atoms. Skipping. Residue LEU 255 is missing expected H atoms. Skipping. Residue VAL 260 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue ALA 269 is missing expected H atoms. Skipping. Residue LEU 276 is missing expected H atoms. Skipping. Residue THR 277 is missing expected H atoms. Skipping. Residue ILE 281 is missing expected H atoms. Skipping. Residue ALA 284 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue ILE 290 is missing expected H atoms. Skipping. Residue ALA 291 is missing expected H atoms. Skipping. Residue VAL 295 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LEU 303 is missing expected H atoms. Skipping. Residue THR 315 is missing expected H atoms. Skipping. Residue VAL 316 is missing expected H atoms. Skipping. Residue MET 317 is missing expected H atoms. Skipping. Residue THR 321 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue THR 328 is missing expected H atoms. Skipping. Residue ILE 329 is missing expected H atoms. Skipping. Residue ALA 330 is missing expected H atoms. Skipping. Residue ALA 331 is missing expected H atoms. Skipping. Residue LEU 332 is missing expected H atoms. Skipping. Residue MET 336 is missing expected H atoms. Skipping. Residue LEU 338 is missing expected H atoms. Skipping. Residue ALA 340 is missing expected H atoms. Skipping. Residue LEU 342 is missing expected H atoms. Skipping. Residue ALA 344 is missing expected H atoms. Skipping. Residue THR 346 is missing expected H atoms. Skipping. Residue THR 347 is missing expected H atoms. Skipping. Residue ILE 352 is missing expected H atoms. Skipping. Residue THR 353 is missing expected H atoms. Skipping. Residue ALA 354 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue VAL 360 is missing expected H atoms. Skipping. Residue ILE 364 is missing expected H atoms. Skipping. Residue ALA 368 is missing expected H atoms. Skipping. Residue ILE 371 is missing expected H atoms. Skipping. Residue ALA 375 is missing expected H atoms. Skipping. Residue ILE 380 is missing expected H atoms. Skipping. Residue VAL 381 is missing expected H atoms. Skipping. Residue ALA 383 is missing expected H atoms. Skipping. Residue VAL 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue ALA 386 is missing expected H atoms. Skipping. Residue LEU 388 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue ILE 6 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue ILE 19 is missing expected H atoms. Skipping. Residue ALA 20 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue THR 24 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue ALA 28 is missing expected H atoms. Skipping. Residue ALA 29 is missing expected H atoms. Skipping. Residue MET 31 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue MET 37 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue THR 41 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue ILE 56 is missing expected H atoms. Skipping. Residue ALA 58 is missing expected H atoms. Skipping. Residue LEU 60 is missing expected H atoms. Skipping. Residue VAL 64 is missing expected H atoms. Skipping. Residue ALA 65 is missing expected H atoms. Skipping. Residue VAL 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue ALA 69 is missing expected H atoms. Skipping. Residue ALA 71 is missing expected H atoms. Skipping. Residue VAL 75 is missing expected H atoms. Skipping. Residue THR 81 is missing expected H atoms. Skipping. Residue ALA 82 is missing expected H atoms. Skipping. Residue ALA 87 is missing expected H atoms. Skipping. Residue VAL 90 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue THR 94 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue MET 98 is missing expected H atoms. Skipping. Residue ALA 100 is missing expected H atoms. Skipping. Residue ALA 101 is missing expected H atoms. Skipping. Residue ALA 107 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 112 is missing expected H atoms. Skipping. Residue ALA 117 is missing expected H atoms. Skipping. Residue ILE 122 is missing expected H atoms. Skipping. Residue MET 123 is missing expected H atoms. Skipping. Residue VAL 125 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue THR 137 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue MET 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue THR 150 is missing expected H atoms. Skipping. Residue LEU 152 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue VAL 161 is missing expected H atoms. Skipping. Residue VAL 163 is missing expected H atoms. Skipping. Residue VAL 164 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue ILE 6 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue ILE 19 is missing expected H atoms. Skipping. Residue ALA 20 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue THR 24 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue ALA 28 is missing expected H atoms. Skipping. Residue ALA 29 is missing expected H atoms. Skipping. Residue MET 31 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue MET 37 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue THR 41 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue ILE 56 is missing expected H atoms. Skipping. Residue ALA 58 is missing expected H atoms. Skipping. Residue LEU 60 is missing expected H atoms. Skipping. Residue VAL 64 is missing expected H atoms. Skipping. Residue ALA 65 is missing expected H atoms. Skipping. Residue VAL 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue ALA 69 is missing expected H atoms. Skipping. Residue ALA 71 is missing expected H atoms. Skipping. Residue VAL 75 is missing expected H atoms. Skipping. Residue THR 81 is missing expected H atoms. Skipping. Residue ALA 82 is missing expected H atoms. Skipping. Residue ALA 87 is missing expected H atoms. Skipping. Residue VAL 90 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue THR 94 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue MET 98 is missing expected H atoms. Skipping. Residue ALA 100 is missing expected H atoms. Skipping. Residue ALA 101 is missing expected H atoms. Skipping. Residue ALA 107 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 112 is missing expected H atoms. Skipping. Residue ALA 117 is missing expected H atoms. Skipping. Residue ILE 122 is missing expected H atoms. Skipping. Residue MET 123 is missing expected H atoms. Skipping. Residue VAL 125 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue THR 137 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue MET 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue THR 150 is missing expected H atoms. Skipping. Residue LEU 152 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue VAL 161 is missing expected H atoms. Skipping. Residue VAL 163 is missing expected H atoms. Skipping. Residue VAL 164 is missing expected H atoms. Skipping. Evaluate side-chains 174 residues out of total 1782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 147 time to evaluate : 2.416 Fit side-chains revert: symmetry clash REVERT: D 55 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7663 (pm20) REVERT: D 175 ARG cc_start: 0.8699 (OUTLIER) cc_final: 0.8242 (ptp-170) REVERT: D 444 GLN cc_start: 0.8791 (OUTLIER) cc_final: 0.7323 (tt0) REVERT: E 30 ARG cc_start: 0.8423 (tmt-80) cc_final: 0.7281 (ttm110) REVERT: E 520 LYS cc_start: 0.8187 (mttm) cc_final: 0.7811 (mtmt) REVERT: B 7 ARG cc_start: 0.7415 (OUTLIER) cc_final: 0.6546 (mmm-85) REVERT: B 86 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.8405 (pt0) REVERT: B 308 GLU cc_start: 0.7778 (tt0) cc_final: 0.7321 (tp30) REVERT: C 130 ASP cc_start: 0.8697 (OUTLIER) cc_final: 0.8377 (t70) REVERT: C 165 GLN cc_start: 0.8813 (OUTLIER) cc_final: 0.7524 (tm-30) REVERT: C 225 LYS cc_start: 0.8680 (OUTLIER) cc_final: 0.8434 (tttm) REVERT: C 271 ARG cc_start: 0.8349 (OUTLIER) cc_final: 0.7433 (mtt-85) REVERT: G 26 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7250 (tt0) REVERT: G 74 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7573 (mt-10) REVERT: H 21 GLN cc_start: 0.8357 (OUTLIER) cc_final: 0.7994 (mp10) REVERT: H 41 THR cc_start: 0.7152 (OUTLIER) cc_final: 0.6799 (p) outliers start: 27 outliers final: 11 residues processed: 166 average time/residue: 2.6351 time to fit residues: 477.5365 Evaluate side-chains 167 residues out of total 1782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 143 time to evaluate : 3.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 40 LYS Chi-restraints excluded: chain D residue 55 GLU Chi-restraints excluded: chain D residue 76 GLU Chi-restraints excluded: chain D residue 175 ARG Chi-restraints excluded: chain D residue 444 GLN Chi-restraints excluded: chain D residue 460 GLU Chi-restraints excluded: chain D residue 517 CYS Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 307 ARG Chi-restraints excluded: chain E residue 474 GLU Chi-restraints excluded: chain B residue 7 ARG Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 173 ASP Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 165 GLN Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 225 LYS Chi-restraints excluded: chain C residue 271 ARG Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain G residue 41 THR Chi-restraints excluded: chain G residue 74 GLU Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain H residue 21 GLN Chi-restraints excluded: chain H residue 41 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 99 optimal weight: 0.0030 chunk 8 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 4 optimal weight: 6.9990 chunk 34 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 117 optimal weight: 6.9990 overall best weight: 1.1596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 59 GLN ** D 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 17 ASN ** G 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.094738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.084718 restraints weight = 32856.154| |-----------------------------------------------------------------------------| r_work (start): 0.2817 rms_B_bonded: 1.04 r_work: 0.2733 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2633 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 17861 Z= 0.112 Angle : 0.407 4.757 24231 Z= 0.229 Chirality : 0.036 0.132 2461 Planarity : 0.004 0.044 3153 Dihedral : 4.750 66.497 2346 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.40 % Allowed : 9.71 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.19), residues: 2101 helix: 1.55 (0.15), residues: 1359 sheet: 2.01 (0.83), residues: 44 loop : 0.01 (0.25), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 99 HIS 0.005 0.001 HIS D 343 PHE 0.010 0.001 PHE E 39 TYR 0.016 0.001 TYR D 156 ARG 0.005 0.000 ARG E 320 Details of bonding type rmsd hydrogen bonds : bond 0.04510 ( 993) hydrogen bonds : angle 4.80047 ( 2883) covalent geometry : bond 0.00241 (17861) covalent geometry : angle 0.40692 (24231) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 19 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue VAL 23 is missing expected H atoms. Skipping. Residue ALA 25 is missing expected H atoms. Skipping. Residue VAL 28 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue THR 44 is missing expected H atoms. Skipping. Residue ALA 47 is missing expected H atoms. Skipping. Residue THR 48 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ALA 53 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue ALA 64 is missing expected H atoms. Skipping. Residue ALA 68 is missing expected H atoms. Skipping. Residue MET 70 is missing expected H atoms. Skipping. Residue ALA 72 is missing expected H atoms. Skipping. Residue VAL 73 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue ALA 85 is missing expected H atoms. Skipping. Residue LEU 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue ALA 91 is missing expected H atoms. Skipping. Residue VAL 93 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue THR 102 is missing expected H atoms. Skipping. Residue MET 103 is missing expected H atoms. Skipping. Residue VAL 105 is missing expected H atoms. Skipping. Residue VAL 106 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue VAL 112 is missing expected H atoms. Skipping. Residue ALA 117 is missing expected H atoms. Skipping. Residue ILE 118 is missing expected H atoms. Skipping. Residue ALA 119 is missing expected H atoms. Skipping. Residue ALA 120 is missing expected H atoms. Skipping. Residue THR 121 is missing expected H atoms. Skipping. Residue MET 123 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Residue ALA 128 is missing expected H atoms. Skipping. Residue ALA 130 is missing expected H atoms. Skipping. Residue ALA 131 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue ALA 139 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue THR 148 is missing expected H atoms. Skipping. Residue ALA 152 is missing expected H atoms. Skipping. Residue VAL 154 is missing expected H atoms. Skipping. Residue ALA 159 is missing expected H atoms. Skipping. Residue ALA 166 is missing expected H atoms. Skipping. Residue ALA 171 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue ILE 177 is missing expected H atoms. Skipping. Residue LEU 180 is missing expected H atoms. Skipping. Residue MET 184 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue ILE 193 is missing expected H atoms. Skipping. Residue ALA 197 is missing expected H atoms. Skipping. Residue VAL 198 is missing expected H atoms. Skipping. Residue LEU 202 is missing expected H atoms. Skipping. Residue LEU 204 is missing expected H atoms. Skipping. Residue LEU 206 is missing expected H atoms. Skipping. Residue VAL 207 is missing expected H atoms. Skipping. Residue ALA 210 is missing expected H atoms. Skipping. Residue THR 213 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue ILE 217 is missing expected H atoms. Skipping. Residue VAL 218 is missing expected H atoms. Skipping. Residue ALA 219 is missing expected H atoms. Skipping. Residue VAL 220 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue ALA 224 is missing expected H atoms. Skipping. Residue ALA 225 is missing expected H atoms. Skipping. Residue ALA 226 is missing expected H atoms. Skipping. Residue ILE 231 is missing expected H atoms. Skipping. Residue THR 232 is missing expected H atoms. Skipping. Residue THR 234 is missing expected H atoms. Skipping. Residue VAL 235 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue ILE 239 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LEU 244 is missing expected H atoms. Skipping. Residue MET 247 is missing expected H atoms. Skipping. Residue ALA 248 is missing expected H atoms. Skipping. Residue THR 253 is missing expected H atoms. Skipping. Residue VAL 254 is missing expected H atoms. Skipping. Residue VAL 255 is missing expected H atoms. Skipping. Residue ILE 257 is missing expected H atoms. Skipping. Residue ALA 258 is missing expected H atoms. Skipping. Residue ALA 262 is missing expected H atoms. Skipping. Residue ALA 264 is missing expected H atoms. Skipping. Residue LEU 267 is missing expected H atoms. Skipping. Residue THR 269 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue ALA 274 is missing expected H atoms. Skipping. Residue THR 277 is missing expected H atoms. Skipping. Residue THR 283 is missing expected H atoms. Skipping. Residue VAL 285 is missing expected H atoms. Skipping. Residue LEU 286 is missing expected H atoms. Skipping. Residue MET 288 is missing expected H atoms. Skipping. Residue LEU 289 is missing expected H atoms. Skipping. Residue VAL 298 is missing expected H atoms. Skipping. Residue VAL 302 is missing expected H atoms. Skipping. Residue THR 304 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Residue ILE 316 is missing expected H atoms. Skipping. Residue ILE 318 is missing expected H atoms. Skipping. Residue LEU 321 is missing expected H atoms. Skipping. Residue VAL 326 is missing expected H atoms. Skipping. Residue LEU 332 is missing expected H atoms. Skipping. Residue ALA 335 is missing expected H atoms. Skipping. Residue ALA 339 is missing expected H atoms. Skipping. Residue ALA 342 is missing expected H atoms. Skipping. Residue LEU 346 is missing expected H atoms. Skipping. Residue LEU 348 is missing expected H atoms. Skipping. Residue LEU 349 is missing expected H atoms. Skipping. Residue ALA 350 is missing expected H atoms. Skipping. Residue ALA 352 is missing expected H atoms. Skipping. Residue LEU 353 is missing expected H atoms. Skipping. Residue THR 356 is missing expected H atoms. Skipping. Residue LEU 361 is missing expected H atoms. Skipping. Residue ALA 362 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue MET 369 is missing expected H atoms. Skipping. Residue ALA 374 is missing expected H atoms. Skipping. Residue ILE 386 is missing expected H atoms. Skipping. Residue ALA 392 is missing expected H atoms. Skipping. Residue ILE 403 is missing expected H atoms. Skipping. Residue LEU 405 is missing expected H atoms. Skipping. Residue MET 406 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 415 is missing expected H atoms. Skipping. Residue ILE 417 is missing expected H atoms. Skipping. Residue VAL 420 is missing expected H atoms. Skipping. Residue VAL 423 is missing expected H atoms. Skipping. Residue LEU 429 is missing expected H atoms. Skipping. Residue ALA 430 is missing expected H atoms. Skipping. Residue ALA 433 is missing expected H atoms. Skipping. Residue THR 435 is missing expected H atoms. Skipping. Residue LEU 436 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue MET 445 is missing expected H atoms. Skipping. Residue THR 447 is missing expected H atoms. Skipping. Residue MET 456 is missing expected H atoms. Skipping. Residue LEU 458 is missing expected H atoms. Skipping. Residue ALA 459 is missing expected H atoms. Skipping. Residue ILE 469 is missing expected H atoms. Skipping. Residue LEU 478 is missing expected H atoms. Skipping. Residue VAL 481 is missing expected H atoms. Skipping. Residue ILE 482 is missing expected H atoms. Skipping. Residue ALA 483 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue LEU 488 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue LEU 495 is missing expected H atoms. Skipping. Residue ILE 496 is missing expected H atoms. Skipping. Residue ALA 497 is missing expected H atoms. Skipping. Residue VAL 501 is missing expected H atoms. Skipping. Residue LEU 506 is missing expected H atoms. Skipping. Residue THR 508 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue LEU 515 is missing expected H atoms. Skipping. Residue VAL 518 is missing expected H atoms. Skipping. Residue VAL 523 is missing expected H atoms. Skipping. Residue ALA 525 is missing expected H atoms. Skipping. Residue ALA 16 is missing expected H atoms. Skipping. Residue ALA 19 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue VAL 23 is missing expected H atoms. Skipping. Residue ALA 25 is missing expected H atoms. Skipping. Residue VAL 28 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue THR 44 is missing expected H atoms. Skipping. Residue ALA 47 is missing expected H atoms. Skipping. Residue THR 48 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ALA 53 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue ALA 64 is missing expected H atoms. Skipping. Residue ALA 68 is missing expected H atoms. Skipping. Residue MET 70 is missing expected H atoms. Skipping. Residue ALA 72 is missing expected H atoms. Skipping. Residue VAL 73 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue ALA 85 is missing expected H atoms. Skipping. Residue LEU 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue ALA 91 is missing expected H atoms. Skipping. Residue VAL 93 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue THR 102 is missing expected H atoms. Skipping. Residue MET 103 is missing expected H atoms. Skipping. Residue VAL 105 is missing expected H atoms. Skipping. Residue VAL 106 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue VAL 112 is missing expected H atoms. Skipping. Residue ALA 117 is missing expected H atoms. Skipping. Residue ILE 118 is missing expected H atoms. Skipping. Residue ALA 119 is missing expected H atoms. Skipping. Residue ALA 120 is missing expected H atoms. Skipping. Residue THR 121 is missing expected H atoms. Skipping. Residue MET 123 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Residue ALA 128 is missing expected H atoms. Skipping. Residue ALA 130 is missing expected H atoms. Skipping. Residue ALA 131 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue ALA 139 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue THR 148 is missing expected H atoms. Skipping. Residue ALA 152 is missing expected H atoms. Skipping. Residue VAL 154 is missing expected H atoms. Skipping. Residue ALA 159 is missing expected H atoms. Skipping. Residue ALA 166 is missing expected H atoms. Skipping. Residue ALA 171 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue ILE 177 is missing expected H atoms. Skipping. Residue LEU 180 is missing expected H atoms. Skipping. Residue MET 184 is missing expected H atoms. Skipping. Residue VAL 187 is missing expected H atoms. Skipping. Residue ILE 193 is missing expected H atoms. Skipping. Residue ALA 197 is missing expected H atoms. Skipping. Residue VAL 198 is missing expected H atoms. Skipping. Residue LEU 202 is missing expected H atoms. Skipping. Residue LEU 204 is missing expected H atoms. Skipping. Residue LEU 206 is missing expected H atoms. Skipping. Residue VAL 207 is missing expected H atoms. Skipping. Residue ALA 210 is missing expected H atoms. Skipping. Residue THR 213 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue ILE 217 is missing expected H atoms. Skipping. Residue VAL 218 is missing expected H atoms. Skipping. Residue ALA 219 is missing expected H atoms. Skipping. Residue VAL 220 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue ALA 224 is missing expected H atoms. Skipping. Residue ALA 225 is missing expected H atoms. Skipping. Residue ALA 226 is missing expected H atoms. Skipping. Residue ILE 231 is missing expected H atoms. Skipping. Residue THR 232 is missing expected H atoms. Skipping. Residue THR 234 is missing expected H atoms. Skipping. Residue VAL 235 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue ILE 239 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LEU 244 is missing expected H atoms. Skipping. Residue MET 247 is missing expected H atoms. Skipping. Residue ALA 248 is missing expected H atoms. Skipping. Residue THR 253 is missing expected H atoms. Skipping. Residue VAL 254 is missing expected H atoms. Skipping. Residue VAL 255 is missing expected H atoms. Skipping. Residue ILE 257 is missing expected H atoms. Skipping. Residue ALA 258 is missing expected H atoms. Skipping. Residue ALA 262 is missing expected H atoms. Skipping. Residue ALA 264 is missing expected H atoms. Skipping. Residue LEU 267 is missing expected H atoms. Skipping. Residue THR 269 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue ALA 274 is missing expected H atoms. Skipping. Residue THR 277 is missing expected H atoms. Skipping. Residue THR 283 is missing expected H atoms. Skipping. Residue VAL 285 is missing expected H atoms. Skipping. Residue LEU 286 is missing expected H atoms. Skipping. Residue MET 288 is missing expected H atoms. Skipping. Residue LEU 289 is missing expected H atoms. Skipping. Residue VAL 298 is missing expected H atoms. Skipping. Residue VAL 302 is missing expected H atoms. Skipping. Residue THR 304 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Residue ILE 316 is missing expected H atoms. Skipping. Residue ILE 318 is missing expected H atoms. Skipping. Residue LEU 321 is missing expected H atoms. Skipping. Residue VAL 326 is missing expected H atoms. Skipping. Residue LEU 332 is missing expected H atoms. Skipping. Residue ALA 335 is missing expected H atoms. Skipping. Residue ALA 339 is missing expected H atoms. Skipping. Residue ALA 342 is missing expected H atoms. Skipping. Residue LEU 346 is missing expected H atoms. Skipping. Residue LEU 348 is missing expected H atoms. Skipping. Residue LEU 349 is missing expected H atoms. Skipping. Residue ALA 350 is missing expected H atoms. Skipping. Residue ALA 352 is missing expected H atoms. Skipping. Residue LEU 353 is missing expected H atoms. Skipping. Residue THR 356 is missing expected H atoms. Skipping. Residue LEU 361 is missing expected H atoms. Skipping. Residue ALA 362 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue MET 369 is missing expected H atoms. Skipping. Residue ALA 374 is missing expected H atoms. Skipping. Residue ILE 386 is missing expected H atoms. Skipping. Residue ALA 392 is missing expected H atoms. Skipping. Residue ILE 403 is missing expected H atoms. Skipping. Residue LEU 405 is missing expected H atoms. Skipping. Residue MET 406 is missing expected H atoms. Skipping. Residue ILE 409 is missing expected H atoms. Skipping. Residue ILE 415 is missing expected H atoms. Skipping. Residue ILE 417 is missing expected H atoms. Skipping. Residue VAL 420 is missing expected H atoms. Skipping. Residue VAL 423 is missing expected H atoms. Skipping. Residue LEU 429 is missing expected H atoms. Skipping. Residue ALA 430 is missing expected H atoms. Skipping. Residue ALA 433 is missing expected H atoms. Skipping. Residue THR 435 is missing expected H atoms. Skipping. Residue LEU 436 is missing expected H atoms. Skipping. Residue VAL 438 is missing expected H atoms. Skipping. Residue MET 445 is missing expected H atoms. Skipping. Residue THR 447 is missing expected H atoms. Skipping. Residue MET 456 is missing expected H atoms. Skipping. Residue LEU 458 is missing expected H atoms. Skipping. Residue ALA 459 is missing expected H atoms. Skipping. Residue ILE 469 is missing expected H atoms. Skipping. Residue LEU 478 is missing expected H atoms. Skipping. Residue VAL 481 is missing expected H atoms. Skipping. Residue ILE 482 is missing expected H atoms. Skipping. Residue ALA 483 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue LEU 488 is missing expected H atoms. Skipping. Residue THR 494 is missing expected H atoms. Skipping. Residue LEU 495 is missing expected H atoms. Skipping. Residue ILE 496 is missing expected H atoms. Skipping. Residue ALA 497 is missing expected H atoms. Skipping. Residue VAL 501 is missing expected H atoms. Skipping. Residue LEU 506 is missing expected H atoms. Skipping. Residue THR 508 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 512 is missing expected H atoms. Skipping. Residue LEU 515 is missing expected H atoms. Skipping. Residue VAL 518 is missing expected H atoms. Skipping. Residue VAL 523 is missing expected H atoms. Skipping. Residue ALA 525 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue MET 16 is missing expected H atoms. Skipping. Residue ALA 17 is missing expected H atoms. Skipping. Residue ALA 18 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue ILE 20 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue ALA 23 is missing expected H atoms. Skipping. Residue LEU 24 is missing expected H atoms. Skipping. Residue ALA 27 is missing expected H atoms. Skipping. Residue LEU 29 is missing expected H atoms. Skipping. Residue MET 35 is missing expected H atoms. Skipping. Residue VAL 39 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue THR 47 is missing expected H atoms. Skipping. Residue ALA 51 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue THR 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ALA 56 is missing expected H atoms. Skipping. Residue ALA 60 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue ALA 64 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue LEU 90 is missing expected H atoms. Skipping. Residue THR 92 is missing expected H atoms. Skipping. Residue VAL 93 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue ALA 107 is missing expected H atoms. Skipping. Residue VAL 110 is missing expected H atoms. Skipping. Residue ALA 114 is missing expected H atoms. Skipping. Residue THR 120 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Residue ALA 129 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue ALA 135 is missing expected H atoms. Skipping. Residue MET 136 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue ALA 151 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue ALA 162 is missing expected H atoms. Skipping. Residue ALA 167 is missing expected H atoms. Skipping. Residue ALA 170 is missing expected H atoms. Skipping. Residue LEU 171 is missing expected H atoms. Skipping. Residue VAL 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue ALA 180 is missing expected H atoms. Skipping. Residue ILE 187 is missing expected H atoms. Skipping. Residue ILE 189 is missing expected H atoms. Skipping. Residue ALA 190 is missing expected H atoms. Skipping. Residue MET 192 is missing expected H atoms. Skipping. Residue ILE 193 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue LEU 200 is missing expected H atoms. Skipping. Residue ALA 201 is missing expected H atoms. Skipping. Residue ILE 203 is missing expected H atoms. Skipping. Residue VAL 204 is missing expected H atoms. Skipping. Residue THR 211 is missing expected H atoms. Skipping. Residue ALA 212 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue ALA 216 is missing expected H atoms. Skipping. Residue THR 219 is missing expected H atoms. Skipping. Residue VAL 223 is missing expected H atoms. Skipping. Residue ALA 227 is missing expected H atoms. Skipping. Residue LEU 229 is missing expected H atoms. Skipping. Residue ALA 230 is missing expected H atoms. Skipping. Residue VAL 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue VAL 238 is missing expected H atoms. Skipping. Residue ALA 245 is missing expected H atoms. Skipping. Residue VAL 248 is missing expected H atoms. Skipping. Residue ALA 250 is missing expected H atoms. Skipping. Residue VAL 251 is missing expected H atoms. Skipping. Residue ALA 254 is missing expected H atoms. Skipping. Residue LEU 255 is missing expected H atoms. Skipping. Residue VAL 260 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue ALA 269 is missing expected H atoms. Skipping. Residue LEU 276 is missing expected H atoms. Skipping. Residue THR 277 is missing expected H atoms. Skipping. Residue ILE 281 is missing expected H atoms. Skipping. Residue ALA 284 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue ILE 290 is missing expected H atoms. Skipping. Residue ALA 291 is missing expected H atoms. Skipping. Residue VAL 295 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue LEU 303 is missing expected H atoms. Skipping. Residue THR 315 is missing expected H atoms. Skipping. Residue VAL 316 is missing expected H atoms. Skipping. Residue MET 317 is missing expected H atoms. Skipping. Residue THR 321 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue THR 328 is missing expected H atoms. Skipping. Residue ILE 329 is missing expected H atoms. Skipping. Residue ALA 330 is missing expected H atoms. Skipping. Residue ALA 331 is missing expected H atoms. Skipping. Residue LEU 332 is missing expected H atoms. Skipping. Residue MET 336 is missing expected H atoms. Skipping. Residue LEU 338 is missing expected H atoms. Skipping. Residue ALA 340 is missing expected H atoms. Skipping. Residue LEU 342 is missing expected H atoms. Skipping. Residue ALA 344 is missing expected H atoms. Skipping. Residue THR 346 is missing expected H atoms. Skipping. Residue THR 347 is missing expected H atoms. Skipping. Residue ILE 352 is missing expected H atoms. Skipping. Residue THR 353 is missing expected H atoms. Skipping. Residue ALA 354 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue VAL 359 is missing expected H atoms. Skipping. Residue VAL 360 is missing expected H atoms. Skipping. Residue ILE 364 is missing expected H atoms. Skipping. Residue ALA 368 is missing expected H atoms. Skipping. Residue ILE 371 is missing expected H atoms. Skipping. Residue ALA 375 is missing expected H atoms. Skipping. Residue ILE 380 is missing expected H atoms. Skipping. Residue VAL 381 is missing expected H atoms. Skipping. Residue ALA 383 is missing expected H atoms. Skipping. Residue VAL 384 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue ALA 386 is missing expected H atoms. Skipping. Residue LEU 388 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue ILE 6 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue ILE 19 is missing expected H atoms. Skipping. Residue ALA 20 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue THR 24 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue ALA 28 is missing expected H atoms. Skipping. Residue ALA 29 is missing expected H atoms. Skipping. Residue MET 31 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue MET 37 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue THR 41 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue ILE 56 is missing expected H atoms. Skipping. Residue ALA 58 is missing expected H atoms. Skipping. Residue LEU 60 is missing expected H atoms. Skipping. Residue VAL 64 is missing expected H atoms. Skipping. Residue ALA 65 is missing expected H atoms. Skipping. Residue VAL 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue ALA 69 is missing expected H atoms. Skipping. Residue ALA 71 is missing expected H atoms. Skipping. Residue VAL 75 is missing expected H atoms. Skipping. Residue THR 81 is missing expected H atoms. Skipping. Residue ALA 82 is missing expected H atoms. Skipping. Residue ALA 87 is missing expected H atoms. Skipping. Residue VAL 90 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue THR 94 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue MET 98 is missing expected H atoms. Skipping. Residue ALA 100 is missing expected H atoms. Skipping. Residue ALA 101 is missing expected H atoms. Skipping. Residue ALA 107 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 112 is missing expected H atoms. Skipping. Residue ALA 117 is missing expected H atoms. Skipping. Residue ILE 122 is missing expected H atoms. Skipping. Residue MET 123 is missing expected H atoms. Skipping. Residue VAL 125 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue THR 137 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue MET 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue THR 150 is missing expected H atoms. Skipping. Residue LEU 152 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue VAL 161 is missing expected H atoms. Skipping. Residue VAL 163 is missing expected H atoms. Skipping. Residue VAL 164 is missing expected H atoms. Skipping. Residue LEU 4 is missing expected H atoms. Skipping. Residue ILE 6 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue ILE 19 is missing expected H atoms. Skipping. Residue ALA 20 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue THR 24 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue ALA 28 is missing expected H atoms. Skipping. Residue ALA 29 is missing expected H atoms. Skipping. Residue MET 31 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue MET 37 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue THR 41 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue ILE 56 is missing expected H atoms. Skipping. Residue ALA 58 is missing expected H atoms. Skipping. Residue LEU 60 is missing expected H atoms. Skipping. Residue VAL 64 is missing expected H atoms. Skipping. Residue ALA 65 is missing expected H atoms. Skipping. Residue VAL 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue ALA 69 is missing expected H atoms. Skipping. Residue ALA 71 is missing expected H atoms. Skipping. Residue VAL 75 is missing expected H atoms. Skipping. Residue THR 81 is missing expected H atoms. Skipping. Residue ALA 82 is missing expected H atoms. Skipping. Residue ALA 87 is missing expected H atoms. Skipping. Residue VAL 90 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue THR 94 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue MET 98 is missing expected H atoms. Skipping. Residue ALA 100 is missing expected H atoms. Skipping. Residue ALA 101 is missing expected H atoms. Skipping. Residue ALA 107 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 112 is missing expected H atoms. Skipping. Residue ALA 117 is missing expected H atoms. Skipping. Residue ILE 122 is missing expected H atoms. Skipping. Residue MET 123 is missing expected H atoms. Skipping. Residue VAL 125 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue THR 137 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue MET 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue THR 150 is missing expected H atoms. Skipping. Residue LEU 152 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue VAL 161 is missing expected H atoms. Skipping. Residue VAL 163 is missing expected H atoms. Skipping. Residue VAL 164 is missing expected H atoms. Skipping. Evaluate side-chains 177 residues out of total 1782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 152 time to evaluate : 2.235 Fit side-chains revert: symmetry clash REVERT: D 40 LYS cc_start: 0.8535 (OUTLIER) cc_final: 0.8214 (tttm) REVERT: D 55 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7663 (pm20) REVERT: D 175 ARG cc_start: 0.8656 (OUTLIER) cc_final: 0.8184 (ptp-170) REVERT: D 444 GLN cc_start: 0.8756 (OUTLIER) cc_final: 0.7249 (tt0) REVERT: E 30 ARG cc_start: 0.8345 (tmt-80) cc_final: 0.7983 (tmt-80) REVERT: E 520 LYS cc_start: 0.8174 (mttm) cc_final: 0.7741 (mtpt) REVERT: B 7 ARG cc_start: 0.7385 (OUTLIER) cc_final: 0.6515 (mmm-85) REVERT: B 86 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.8358 (pt0) REVERT: B 308 GLU cc_start: 0.7765 (tt0) cc_final: 0.7308 (tp30) REVERT: C 130 ASP cc_start: 0.8716 (OUTLIER) cc_final: 0.8444 (t70) REVERT: C 165 GLN cc_start: 0.8860 (OUTLIER) cc_final: 0.7442 (tm-30) REVERT: C 225 LYS cc_start: 0.8654 (OUTLIER) cc_final: 0.8424 (tttm) REVERT: C 271 ARG cc_start: 0.8312 (OUTLIER) cc_final: 0.7382 (mtt-85) REVERT: G 26 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7226 (tt0) REVERT: G 74 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7500 (mt-10) REVERT: H 21 GLN cc_start: 0.8317 (OUTLIER) cc_final: 0.7962 (mp10) REVERT: H 41 THR cc_start: 0.6768 (OUTLIER) cc_final: 0.6388 (p) outliers start: 25 outliers final: 9 residues processed: 170 average time/residue: 2.1271 time to fit residues: 395.0449 Evaluate side-chains 171 residues out of total 1782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 148 time to evaluate : 2.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 40 LYS Chi-restraints excluded: chain D residue 55 GLU Chi-restraints excluded: chain D residue 76 GLU Chi-restraints excluded: chain D residue 175 ARG Chi-restraints excluded: chain D residue 444 GLN Chi-restraints excluded: chain D residue 460 GLU Chi-restraints excluded: chain D residue 517 CYS Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 307 ARG Chi-restraints excluded: chain B residue 7 ARG Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 173 ASP Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 165 GLN Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 225 LYS Chi-restraints excluded: chain C residue 271 ARG Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain G residue 41 THR Chi-restraints excluded: chain G residue 74 GLU Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain H residue 21 GLN Chi-restraints excluded: chain H residue 41 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 7 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 198 optimal weight: 5.9990 chunk 4 optimal weight: 0.5980 chunk 124 optimal weight: 6.9990 chunk 186 optimal weight: 7.9990 chunk 161 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 1 optimal weight: 0.0980 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 59 GLN ** D 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 9 ASN ** G 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.092007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.082147 restraints weight = 33084.035| |-----------------------------------------------------------------------------| r_work (start): 0.2753 rms_B_bonded: 1.02 r_work: 0.2668 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.2568 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.2568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 17861 Z= 0.213 Angle : 0.484 5.954 24231 Z= 0.269 Chirality : 0.041 0.163 2461 Planarity : 0.004 0.044 3153 Dihedral : 4.941 67.675 2346 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.46 % Allowed : 9.88 % Favored : 88.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.19), residues: 2101 helix: 1.35 (0.14), residues: 1361 sheet: 1.98 (0.82), residues: 44 loop : -0.11 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 125 HIS 0.007 0.001 HIS D 382 PHE 0.018 0.002 PHE D 188 TYR 0.015 0.002 TYR B 299 ARG 0.005 0.001 ARG E 320 Details of bonding type rmsd hydrogen bonds : bond 0.05511 ( 993) hydrogen bonds : angle 5.03411 ( 2883) covalent geometry : bond 0.00495 (17861) covalent geometry : angle 0.48388 (24231) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12721.69 seconds wall clock time: 219 minutes 14.98 seconds (13154.98 seconds total)