Starting phenix.real_space_refine on Mon Mar 18 09:39:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tc8_25805/03_2024/7tc8_25805.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tc8_25805/03_2024/7tc8_25805.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tc8_25805/03_2024/7tc8_25805.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tc8_25805/03_2024/7tc8_25805.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tc8_25805/03_2024/7tc8_25805.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tc8_25805/03_2024/7tc8_25805.pdb" } resolution = 2.4 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= -0.002 sd= 0.264 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 Residue "D GLU 76": "OE1" <-> "OE2" Residue "D GLU 199": "OE1" <-> "OE2" Residue "D ASP 365": "OD1" <-> "OD2" Residue "D GLU 367": "OE1" <-> "OE2" Residue "D GLU 440": "OE1" <-> "OE2" Residue "D GLU 460": "OE1" <-> "OE2" Residue "D ASP 510": "OD1" <-> "OD2" Residue "E GLU 76": "OE1" <-> "OE2" Residue "E GLU 111": "OE1" <-> "OE2" Residue "E TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 334": "OD1" <-> "OD2" Residue "E TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 368": "OE1" <-> "OE2" Residue "E ASP 381": "OD1" <-> "OD2" Residue "E GLU 388": "OE1" <-> "OE2" Residue "E GLU 410": "OE1" <-> "OE2" Residue "E GLU 440": "OE1" <-> "OE2" Residue "B ASP 121": "OD1" <-> "OD2" Residue "B ASP 130": "OD1" <-> "OD2" Residue "B ASP 188": "OD1" <-> "OD2" Residue "B ASP 376": "OD1" <-> "OD2" Residue "B ASP 378": "OD1" <-> "OD2" Residue "C GLU 15": "OE1" <-> "OE2" Residue "C TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 173": "OD1" <-> "OD2" Residue "C GLU 237": "OE1" <-> "OE2" Residue "G ASP 10": "OD1" <-> "OD2" Residue "G GLU 26": "OE1" <-> "OE2" Residue "G ASP 50": "OD1" <-> "OD2" Residue "G ASP 52": "OD1" <-> "OD2" Residue "G GLU 74": "OE1" <-> "OE2" Residue "G ASP 86": "OD1" <-> "OD2" Residue "G TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 153": "OE1" <-> "OE2" Residue "H PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 76": "OD1" <-> "OD2" Residue "H ASP 103": "OD1" <-> "OD2" Residue "H GLU 154": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 10.48, per 1000 atoms: 0.51 Number of scatterers: 20567 At special positions: 0 Unit cell: (82.602, 115.431, 138.729, 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 - 3.50 Amino acid : False - 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: 11.71 Conformation dependent library (CDL) restraints added in 3.2 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: 120 helices and 4 sheets defined 72.3% alpha, 0.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.76 Creating SS restraints... Processing helix chain 'D' and resid 24 through 30 Processing helix chain 'D' and resid 31 through 36 removed outlier: 3.665A pdb=" N ASN D 36 " --> pdb=" O GLN D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 84 removed outlier: 3.528A 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: 3.555A pdb=" N LYS D 104 " --> pdb=" O ASN D 100 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL D 105 " --> pdb=" O GLU D 101 " (cutoff:3.500A) removed outlier: 3.658A 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 176 through 178 No H-bonds generated for 'chain 'D' and resid 176 through 178' Processing helix chain 'D' and resid 179 through 189 removed outlier: 3.802A pdb=" N GLY D 183 " --> pdb=" O PRO D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 194 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: 3.929A pdb=" N SER D 238 " --> pdb=" O THR D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 258 removed outlier: 3.812A pdb=" N HIS D 246 " --> pdb=" O ASP D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 292 removed outlier: 4.076A pdb=" N ALA D 264 " --> pdb=" O ASP D 260 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N ASN D 268 " --> pdb=" O ALA D 264 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N THR D 269 " --> pdb=" O LYS D 265 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N TYR D 281 " --> pdb=" O THR D 277 " (cutoff:3.500A) Proline residue: D 284 - end of helix removed outlier: 3.729A 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 318 through 325 removed outlier: 4.802A pdb=" N LYS D 323 " --> pdb=" O ARG D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 331 through 353 removed outlier: 4.196A pdb=" N TYR D 340 " --> pdb=" O LYS D 336 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N TRP D 341 " --> pdb=" O GLN D 337 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ALA D 342 " --> pdb=" O ASP D 338 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N HIS D 343 " --> pdb=" O ALA D 339 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N HIS D 344 " --> pdb=" O TYR D 340 " (cutoff:3.500A) 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: 3.778A pdb=" N HIS D 382 " --> pdb=" O GLY D 378 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N LYS D 385 " --> pdb=" O ASP D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 401 removed outlier: 3.760A pdb=" N GLY D 401 " --> pdb=" O PRO D 398 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 411 removed outlier: 3.837A 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: 3.589A pdb=" N LEU D 515 " --> pdb=" O ASP D 511 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASN D 516 " --> pdb=" O ILE D 512 " (cutoff:3.500A) Processing helix chain 'D' and resid 521 through 526 removed outlier: 3.737A 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 36 removed outlier: 4.051A pdb=" N ASN E 36 " --> pdb=" O GLN E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 84 removed outlier: 3.660A 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: 3.594A pdb=" N VAL E 105 " --> pdb=" O GLU E 101 " (cutoff:3.500A) removed outlier: 3.701A 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: 3.858A pdb=" N GLY E 183 " --> pdb=" O PRO E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 189 through 194 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: 3.595A pdb=" N VAL E 218 " --> pdb=" O ASN E 214 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 241 removed outlier: 3.884A pdb=" N SER E 238 " --> pdb=" O THR E 234 " (cutoff:3.500A) Processing helix chain 'E' and resid 242 through 257 removed outlier: 3.723A pdb=" N HIS E 246 " --> pdb=" O ASP E 242 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 293 removed outlier: 4.298A pdb=" N ALA E 264 " --> pdb=" O ASP E 260 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS E 265 " --> pdb=" O PRO E 261 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N ASN E 268 " --> pdb=" O ALA E 264 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N THR E 269 " --> pdb=" O LYS E 265 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR E 281 " --> pdb=" O THR E 277 " (cutoff:3.500A) Proline residue: E 284 - end of helix removed outlier: 3.806A pdb=" N GLY E 287 " --> pdb=" O THR E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 300 through 309 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 353 removed outlier: 4.347A pdb=" N TYR E 340 " --> pdb=" O LYS E 336 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N TRP E 341 " --> pdb=" O GLN E 337 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA E 342 " --> pdb=" O ASP E 338 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N HIS E 343 " --> pdb=" O ALA E 339 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N HIS E 344 " --> pdb=" O TYR E 340 " (cutoff:3.500A) 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 393 removed outlier: 3.796A pdb=" N HIS E 382 " --> pdb=" O GLY E 378 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N LYS E 385 " --> pdb=" O ASP E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 397 through 401 removed outlier: 3.915A pdb=" N GLY E 401 " --> pdb=" O PRO E 398 " (cutoff:3.500A) Processing helix chain 'E' and resid 403 through 411 removed outlier: 3.765A 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: 3.686A pdb=" N ASN E 516 " --> pdb=" O ILE E 512 " (cutoff:3.500A) Processing helix chain 'E' and resid 521 through 526 removed outlier: 3.514A pdb=" N ALA E 525 " --> pdb=" O PRO E 522 " (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: 3.732A pdb=" N THR B 88 " --> pdb=" O ASN B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 98 removed outlier: 4.020A pdb=" N HIS B 98 " --> pdb=" O TRP B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 130 Processing helix chain 'B' and resid 131 through 136 Processing helix chain 'B' and resid 137 through 144 Processing helix chain 'B' and resid 147 through 162 removed outlier: 3.756A pdb=" N LEU B 153 " --> pdb=" O TRP B 149 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N PHE B 154 " --> pdb=" O GLY B 150 " (cutoff:3.500A) removed outlier: 3.847A 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 262 removed outlier: 4.424A pdb=" N GLN B 258 " --> pdb=" O ALA B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 269 Processing helix chain 'B' and resid 270 through 273 removed outlier: 3.654A pdb=" N GLY B 273 " --> pdb=" O PRO B 270 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 270 through 273' Processing helix chain 'B' and resid 275 through 300 removed outlier: 3.560A pdb=" N PHE B 279 " --> pdb=" O ASN B 275 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE B 280 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN B 283 " --> pdb=" O PHE B 279 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN B 293 " --> pdb=" O GLN B 289 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY B 294 " --> pdb=" O ILE B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 336 removed outlier: 4.051A 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 342 removed outlier: 3.587A pdb=" N ALA B 340 " --> pdb=" O GLY B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 367 Processing helix chain 'B' and resid 368 through 372 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: 3.539A 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 removed outlier: 3.568A pdb=" N ALA C 135 " --> pdb=" O GLN C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 144 Processing helix chain 'C' and resid 147 through 162 removed outlier: 3.718A pdb=" N LEU C 153 " --> pdb=" O TRP C 149 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N PHE C 154 " --> pdb=" O GLY C 150 " (cutoff:3.500A) removed outlier: 3.826A 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 Processing helix chain 'C' and resid 251 through 263 removed outlier: 4.319A 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 275 through 300 removed outlier: 3.605A pdb=" N PHE C 279 " --> pdb=" O ASN C 275 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE C 280 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLN C 283 " --> pdb=" O PHE C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 336 removed outlier: 3.990A 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: 3.531A pdb=" N ALA C 340 " --> pdb=" O GLY C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 348 through 367 Processing helix chain 'C' and resid 368 through 372 removed outlier: 3.620A pdb=" N ILE C 371 " --> pdb=" O ALA C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 386 Processing helix chain 'G' and resid 9 through 21 removed outlier: 3.611A pdb=" N GLN G 21 " --> pdb=" O ASN G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 24 through 40 removed outlier: 3.598A pdb=" N THR G 40 " --> pdb=" O ARG G 36 " (cutoff:3.500A) 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 145 removed outlier: 3.671A pdb=" N LEU G 145 " --> pdb=" O GLU G 141 " (cutoff:3.500A) 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 removed outlier: 3.508A pdb=" N THR H 40 " --> pdb=" O ARG H 36 " (cutoff:3.500A) 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 445 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 448 997 hydrogen bonds defined for protein. 2871 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: 6.77 Time building geometry restraints manager: 12.47 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: 187 1.23 - 1.42: 7810 1.42 - 1.61: 9760 1.61 - 1.81: 104 Bond restraints: 21061 Sorted by residual: bond pdb=" CZ ARG D 175 " pdb=" NH2 ARG D 175 " ideal model delta sigma weight residual 1.330 1.301 0.029 1.30e-02 5.92e+03 4.97e+00 bond pdb=" C ILE H 122 " pdb=" N MET H 123 " ideal model delta sigma weight residual 1.340 1.220 0.120 5.87e-02 2.90e+02 4.20e+00 bond pdb=" N GLU C 6 " pdb=" CA GLU C 6 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.90e-02 2.77e+03 3.38e+00 bond pdb=" CB TRP D 181 " pdb=" CG TRP D 181 " ideal model delta sigma weight residual 1.498 1.443 0.055 3.10e-02 1.04e+03 3.20e+00 bond pdb=" N LEU H 4 " pdb=" CA LEU H 4 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.72e+00 ... (remaining 21056 not shown) Histogram of bond angle deviations from ideal: 98.81 - 105.90: 294 105.90 - 112.99: 9979 112.99 - 120.08: 9568 120.08 - 127.17: 9879 127.17 - 134.26: 306 Bond angle restraints: 30026 Sorted by residual: angle pdb=" CA LEU B 153 " pdb=" CB LEU B 153 " pdb=" CG LEU B 153 " ideal model delta sigma weight residual 116.30 128.55 -12.25 3.50e+00 8.16e-02 1.23e+01 angle pdb=" CG ARG D 175 " pdb=" CD ARG D 175 " pdb=" NE ARG D 175 " ideal model delta sigma weight residual 112.00 119.40 -7.40 2.20e+00 2.07e-01 1.13e+01 angle pdb=" CA TRP E 125 " pdb=" CB TRP E 125 " pdb=" CG TRP E 125 " ideal model delta sigma weight residual 113.60 119.41 -5.81 1.90e+00 2.77e-01 9.36e+00 angle pdb=" CA LEU C 153 " pdb=" CB LEU C 153 " pdb=" CG LEU C 153 " ideal model delta sigma weight residual 116.30 126.19 -9.89 3.50e+00 8.16e-02 7.99e+00 angle pdb=" CA TRP D 125 " pdb=" CB TRP D 125 " pdb=" CG TRP D 125 " ideal model delta sigma weight residual 113.60 118.80 -5.20 1.90e+00 2.77e-01 7.50e+00 ... (remaining 30021 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.03: 11380 18.03 - 36.06: 997 36.06 - 54.08: 312 54.08 - 72.11: 107 72.11 - 90.14: 36 Dihedral angle restraints: 12832 sinusoidal: 6526 harmonic: 6306 Sorted by residual: 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 180.00 148.86 31.14 0 5.00e+00 4.00e-02 3.88e+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 180.00 155.10 24.90 0 5.00e+00 4.00e-02 2.48e+01 dihedral pdb=" CA ARG C 104 " pdb=" C ARG C 104 " pdb=" N TRP C 105 " pdb=" CA TRP C 105 " ideal model delta harmonic sigma weight residual 180.00 157.19 22.81 0 5.00e+00 4.00e-02 2.08e+01 ... (remaining 12829 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1080 0.032 - 0.064: 904 0.064 - 0.096: 340 0.096 - 0.129: 120 0.129 - 0.161: 17 Chirality restraints: 2461 Sorted by residual: chirality pdb=" CA VAL E 95 " pdb=" N VAL E 95 " pdb=" C VAL E 95 " pdb=" CB VAL E 95 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.46e-01 chirality pdb=" CA ILE E 403 " pdb=" N ILE E 403 " pdb=" C ILE E 403 " pdb=" CB ILE E 403 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.23e-01 chirality pdb=" CA PRO H 121 " pdb=" N PRO H 121 " pdb=" C PRO H 121 " pdb=" CB PRO H 121 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.12e-01 ... (remaining 2458 not shown) Planarity restraints: 4809 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP C 253 " 0.011 2.00e-02 2.50e+03 2.13e-02 4.54e+00 pdb=" C ASP C 253 " -0.037 2.00e-02 2.50e+03 pdb=" O ASP C 253 " 0.014 2.00e-02 2.50e+03 pdb=" N ALA C 254 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS D 382 " -0.011 2.00e-02 2.50e+03 2.11e-02 4.45e+00 pdb=" C HIS D 382 " 0.037 2.00e-02 2.50e+03 pdb=" O HIS D 382 " -0.014 2.00e-02 2.50e+03 pdb=" N TYR D 383 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 67 " -0.026 2.00e-02 2.50e+03 1.36e-02 3.68e+00 pdb=" CG TYR E 67 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR E 67 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR E 67 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR E 67 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR E 67 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR E 67 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR E 67 " -0.014 2.00e-02 2.50e+03 ... (remaining 4806 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 490 2.17 - 2.78: 13236 2.78 - 3.39: 37408 3.39 - 3.99: 56180 3.99 - 4.60: 80706 Nonbonded interactions: 188020 Sorted by model distance: nonbonded pdb=" HH TYR E 137 " pdb=" OG1 THR E 253 " model vdw 1.565 1.850 nonbonded pdb="HD22 ASN E 214 " pdb=" OE2 GLU E 240 " model vdw 1.567 1.850 nonbonded pdb=" O GLN E 59 " pdb=" HZ2 LYS E 61 " model vdw 1.585 1.850 nonbonded pdb=" O GLU E 144 " pdb=" HG1 THR E 148 " model vdw 1.605 1.850 nonbonded pdb=" OD1 ASP E 345 " pdb=" HH TYR E 383 " model vdw 1.625 1.850 ... (remaining 188015 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 1.410 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: 0.430 Extract box with map and model: 6.860 Check model and map are aligned: 0.320 Set scattering table: 0.170 Process input model: 58.980 Find NCS groups from input model: 1.390 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 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 : 0.008 0.120 17861 Z= 0.494 Angle : 0.681 12.252 24231 Z= 0.386 Chirality : 0.051 0.161 2461 Planarity : 0.005 0.044 3153 Dihedral : 17.518 90.138 6469 Min Nonbonded Distance : 1.659 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.31 % Allowed : 14.37 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.38 (0.18), residues: 2101 helix: 0.36 (0.13), residues: 1352 sheet: 1.14 (0.82), residues: 44 loop : 0.27 (0.24), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP E 276 HIS 0.008 0.002 HIS E 439 PHE 0.024 0.003 PHE D 275 TYR 0.027 0.004 TYR D 115 ARG 0.014 0.001 ARG D 175 *********************** 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 324 residues out of total 1782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 265 time to evaluate : 2.101 Fit side-chains REVERT: D 460 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7984 (pm20) REVERT: D 474 GLU cc_start: 0.8123 (tt0) cc_final: 0.7897 (tt0) REVERT: G 52 ASP cc_start: 0.8589 (m-30) cc_final: 0.8378 (m-30) REVERT: G 127 TYR cc_start: 0.8766 (m-80) cc_final: 0.8553 (m-80) outliers start: 59 outliers final: 53 residues processed: 318 average time/residue: 1.7912 time to fit residues: 626.4498 Evaluate side-chains 316 residues out of total 1782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 262 time to evaluate : 2.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 259 ASN Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 328 SER Chi-restraints excluded: chain D residue 346 LEU Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 460 GLU Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 505 LYS Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain E residue 186 ARG Chi-restraints excluded: chain E residue 238 SER Chi-restraints excluded: chain E residue 269 THR Chi-restraints excluded: chain E residue 328 SER Chi-restraints excluded: chain E residue 334 ASP Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain E residue 367 GLU Chi-restraints excluded: chain E residue 523 VAL Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 173 ASP Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 349 LYS Chi-restraints excluded: chain C residue 35 MET Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 173 ASP Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 388 LEU Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 97 LYS Chi-restraints excluded: chain G residue 108 GLU Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain H residue 8 SER Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain H residue 165 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 0.8980 chunk 159 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 164 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 122 optimal weight: 0.0870 chunk 190 optimal weight: 0.1980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 90 ASN ** D 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 375 ASN ** E 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 214 ASN E 337 GLN B 301 ASN C 165 GLN C 379 GLN G 158 GLN H 34 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.0868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 17861 Z= 0.123 Angle : 0.417 5.084 24231 Z= 0.237 Chirality : 0.036 0.133 2461 Planarity : 0.003 0.037 3153 Dihedral : 7.319 59.994 2440 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 16.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.09 % Allowed : 13.80 % Favored : 83.11 % 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: 1.42 (0.19), residues: 2101 helix: 1.23 (0.14), residues: 1348 sheet: 1.49 (0.80), residues: 44 loop : 0.56 (0.25), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 43 HIS 0.004 0.001 HIS E 343 PHE 0.010 0.001 PHE C 154 TYR 0.014 0.001 TYR D 347 ARG 0.003 0.000 ARG E 320 *********************** 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 335 residues out of total 1782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 280 time to evaluate : 2.279 Fit side-chains REVERT: B 34 LYS cc_start: 0.8377 (OUTLIER) cc_final: 0.8142 (mttp) REVERT: C 349 LYS cc_start: 0.8409 (OUTLIER) cc_final: 0.7957 (ttpt) REVERT: H 138 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.8190 (tpt-90) outliers start: 55 outliers final: 27 residues processed: 321 average time/residue: 1.8045 time to fit residues: 637.6317 Evaluate side-chains 306 residues out of total 1782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 276 time to evaluate : 2.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 259 ASN Chi-restraints excluded: chain D residue 328 SER Chi-restraints excluded: chain D residue 346 LEU Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 160 LYS Chi-restraints excluded: chain E residue 186 ARG Chi-restraints excluded: chain E residue 238 SER Chi-restraints excluded: chain E residue 269 THR Chi-restraints excluded: chain E residue 306 ASN Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 173 ASP Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 173 ASP Chi-restraints excluded: chain C residue 349 LYS Chi-restraints excluded: chain C residue 388 LEU Chi-restraints excluded: chain G residue 41 THR Chi-restraints excluded: chain G residue 89 SER Chi-restraints excluded: chain G residue 108 GLU Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 138 ARG Chi-restraints excluded: chain H residue 165 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 105 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 158 optimal weight: 5.9990 chunk 129 optimal weight: 5.9990 chunk 52 optimal weight: 0.9980 chunk 191 optimal weight: 5.9990 chunk 206 optimal weight: 0.7980 chunk 170 optimal weight: 0.8980 chunk 189 optimal weight: 0.6980 chunk 65 optimal weight: 0.6980 chunk 153 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 90 ASN D 155 ASN ** D 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 337 GLN B 301 ASN ** C 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 379 GLN G 158 GLN H 34 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.1073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 17861 Z= 0.130 Angle : 0.408 5.635 24231 Z= 0.230 Chirality : 0.036 0.132 2461 Planarity : 0.003 0.035 3153 Dihedral : 5.867 57.516 2377 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 16.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.69 % Allowed : 14.25 % Favored : 83.05 % 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: 1.72 (0.19), residues: 2101 helix: 1.48 (0.14), residues: 1354 sheet: 1.81 (0.83), residues: 44 loop : 0.62 (0.25), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 43 HIS 0.004 0.001 HIS D 382 PHE 0.011 0.001 PHE D 275 TYR 0.015 0.001 TYR E 156 ARG 0.003 0.000 ARG E 320 *********************** 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 324 residues out of total 1782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 276 time to evaluate : 2.213 Fit side-chains revert: symmetry clash REVERT: D 403 ILE cc_start: 0.8452 (OUTLIER) cc_final: 0.8224 (tp) REVERT: E 32 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8685 (tp) REVERT: E 460 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.8006 (mt-10) REVERT: B 34 LYS cc_start: 0.8369 (OUTLIER) cc_final: 0.8112 (mttp) REVERT: B 35 MET cc_start: 0.8593 (OUTLIER) cc_final: 0.8054 (tmt) REVERT: C 80 ARG cc_start: 0.8606 (OUTLIER) cc_final: 0.8351 (ttt180) REVERT: C 349 LYS cc_start: 0.8413 (OUTLIER) cc_final: 0.8109 (ttpt) REVERT: H 138 ARG cc_start: 0.8463 (OUTLIER) cc_final: 0.8212 (tpt-90) outliers start: 48 outliers final: 28 residues processed: 308 average time/residue: 1.8089 time to fit residues: 612.5919 Evaluate side-chains 308 residues out of total 1782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 272 time to evaluate : 2.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 213 THR Chi-restraints excluded: chain D residue 259 ASN Chi-restraints excluded: chain D residue 328 SER Chi-restraints excluded: chain D residue 346 LEU Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 160 LYS Chi-restraints excluded: chain E residue 186 ARG Chi-restraints excluded: chain E residue 306 ASN Chi-restraints excluded: chain E residue 310 TYR Chi-restraints excluded: chain E residue 381 ASP Chi-restraints excluded: chain E residue 460 GLU Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 35 MET Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 173 ASP Chi-restraints excluded: chain B residue 336 MET Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain C residue 80 ARG Chi-restraints excluded: chain C residue 173 ASP Chi-restraints excluded: chain C residue 349 LYS Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 41 THR Chi-restraints excluded: chain G residue 89 SER Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 41 THR Chi-restraints excluded: chain H residue 48 GLU Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain H residue 138 ARG Chi-restraints excluded: chain H residue 165 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 188 optimal weight: 2.9990 chunk 143 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 191 optimal weight: 5.9990 chunk 202 optimal weight: 7.9990 chunk 100 optimal weight: 0.8980 chunk 181 optimal weight: 0.7980 chunk 54 optimal weight: 4.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 90 ASN ** D 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 116 ASN ** E 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 337 GLN B 301 ASN ** C 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 379 GLN G 158 GLN H 34 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.0853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 17861 Z= 0.237 Angle : 0.483 6.761 24231 Z= 0.270 Chirality : 0.041 0.144 2461 Planarity : 0.004 0.037 3153 Dihedral : 5.841 56.153 2364 Min Nonbonded Distance : 1.769 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.97 % Allowed : 14.20 % Favored : 82.83 % 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: 1.28 (0.14), residues: 1338 sheet: 1.69 (0.84), residues: 44 loop : 0.49 (0.25), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 276 HIS 0.006 0.001 HIS D 382 PHE 0.017 0.002 PHE D 275 TYR 0.018 0.002 TYR E 115 ARG 0.006 0.001 ARG B 261 *********************** 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 323 residues out of total 1782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 270 time to evaluate : 3.062 Fit side-chains REVERT: D 186 ARG cc_start: 0.8826 (OUTLIER) cc_final: 0.8119 (tmt90) REVERT: E 460 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.7958 (mt-10) REVERT: B 34 LYS cc_start: 0.8384 (OUTLIER) cc_final: 0.8142 (mttp) REVERT: B 35 MET cc_start: 0.8610 (OUTLIER) cc_final: 0.8086 (tmt) REVERT: B 80 ARG cc_start: 0.8775 (OUTLIER) cc_final: 0.7888 (ttp-170) REVERT: B 192 MET cc_start: 0.8830 (mmp) cc_final: 0.8618 (mmp) REVERT: C 80 ARG cc_start: 0.8690 (OUTLIER) cc_final: 0.8457 (ttt180) REVERT: C 349 LYS cc_start: 0.8457 (OUTLIER) cc_final: 0.8018 (ttpt) REVERT: C 365 GLU cc_start: 0.6996 (OUTLIER) cc_final: 0.6762 (mt-10) REVERT: C 388 LEU cc_start: 0.6778 (OUTLIER) cc_final: 0.6479 (tp) REVERT: H 138 ARG cc_start: 0.8474 (OUTLIER) cc_final: 0.8194 (tpt-90) outliers start: 53 outliers final: 28 residues processed: 308 average time/residue: 1.8624 time to fit residues: 629.3200 Evaluate side-chains 305 residues out of total 1782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 267 time to evaluate : 2.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 83 GLN Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 186 ARG Chi-restraints excluded: chain D residue 213 THR Chi-restraints excluded: chain D residue 259 ASN Chi-restraints excluded: chain D residue 328 SER Chi-restraints excluded: chain D residue 346 LEU Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 160 LYS Chi-restraints excluded: chain E residue 186 ARG Chi-restraints excluded: chain E residue 306 ASN Chi-restraints excluded: chain E residue 310 TYR Chi-restraints excluded: chain E residue 460 GLU Chi-restraints excluded: chain E residue 523 VAL Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 35 MET Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 80 ARG Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 173 ASP Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain C residue 80 ARG Chi-restraints excluded: chain C residue 173 ASP Chi-restraints excluded: chain C residue 349 LYS Chi-restraints excluded: chain C residue 365 GLU Chi-restraints excluded: chain C residue 388 LEU Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 41 THR Chi-restraints excluded: chain G residue 89 SER Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain H residue 138 ARG Chi-restraints excluded: chain H residue 165 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 169 optimal weight: 2.9990 chunk 115 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 chunk 151 optimal weight: 4.9990 chunk 83 optimal weight: 7.9990 chunk 173 optimal weight: 0.3980 chunk 140 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 103 optimal weight: 5.9990 chunk 182 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 90 ASN D 442 ASN ** E 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 337 GLN B 301 ASN ** C 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 379 GLN G 158 GLN H 34 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.1101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 17861 Z= 0.128 Angle : 0.407 5.010 24231 Z= 0.230 Chirality : 0.036 0.133 2461 Planarity : 0.003 0.035 3153 Dihedral : 5.512 55.169 2364 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 16.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.69 % Allowed : 14.25 % Favored : 83.05 % 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: 1.76 (0.19), residues: 2101 helix: 1.55 (0.14), residues: 1338 sheet: 1.74 (0.84), residues: 44 loop : 0.57 (0.25), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 43 HIS 0.004 0.001 HIS E 343 PHE 0.010 0.001 PHE C 288 TYR 0.015 0.001 TYR E 156 ARG 0.003 0.000 ARG E 320 *********************** 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 318 residues out of total 1782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 270 time to evaluate : 2.356 Fit side-chains REVERT: D 186 ARG cc_start: 0.8797 (OUTLIER) cc_final: 0.7600 (tmt90) REVERT: D 403 ILE cc_start: 0.8462 (OUTLIER) cc_final: 0.8225 (tp) REVERT: E 206 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8510 (mp) REVERT: E 460 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.7958 (mt-10) REVERT: B 34 LYS cc_start: 0.8373 (OUTLIER) cc_final: 0.8117 (mttp) REVERT: B 35 MET cc_start: 0.8575 (OUTLIER) cc_final: 0.8136 (tmt) REVERT: B 68 ASP cc_start: 0.8789 (OUTLIER) cc_final: 0.7749 (m-30) REVERT: B 80 ARG cc_start: 0.8760 (OUTLIER) cc_final: 0.7508 (ttp-170) REVERT: C 15 GLU cc_start: 0.7195 (OUTLIER) cc_final: 0.6902 (tt0) REVERT: C 80 ARG cc_start: 0.8619 (OUTLIER) cc_final: 0.8345 (ttt180) REVERT: C 349 LYS cc_start: 0.8451 (OUTLIER) cc_final: 0.8089 (ttpt) REVERT: C 365 GLU cc_start: 0.6970 (OUTLIER) cc_final: 0.6747 (mt-10) REVERT: G 157 LYS cc_start: 0.8246 (OUTLIER) cc_final: 0.8039 (mtmt) REVERT: H 138 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.8206 (tpt-90) outliers start: 48 outliers final: 26 residues processed: 301 average time/residue: 1.8818 time to fit residues: 621.6822 Evaluate side-chains 309 residues out of total 1782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 269 time to evaluate : 2.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 61 LYS Chi-restraints excluded: chain D residue 83 GLN Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 186 ARG Chi-restraints excluded: chain D residue 213 THR Chi-restraints excluded: chain D residue 259 ASN Chi-restraints excluded: chain D residue 346 LEU Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 160 LYS Chi-restraints excluded: chain E residue 186 ARG Chi-restraints excluded: chain E residue 206 LEU Chi-restraints excluded: chain E residue 306 ASN Chi-restraints excluded: chain E residue 310 TYR Chi-restraints excluded: chain E residue 460 GLU Chi-restraints excluded: chain E residue 523 VAL Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 35 MET Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 80 ARG Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 173 ASP Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain C residue 15 GLU Chi-restraints excluded: chain C residue 80 ARG Chi-restraints excluded: chain C residue 173 ASP Chi-restraints excluded: chain C residue 349 LYS Chi-restraints excluded: chain C residue 365 GLU Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 41 THR Chi-restraints excluded: chain G residue 89 SER Chi-restraints excluded: chain G residue 157 LYS Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 41 THR Chi-restraints excluded: chain H residue 138 ARG Chi-restraints excluded: chain H residue 165 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 68 optimal weight: 5.9990 chunk 182 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 119 optimal weight: 0.9990 chunk 50 optimal weight: 7.9990 chunk 203 optimal weight: 7.9990 chunk 168 optimal weight: 3.9990 chunk 94 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 90 ASN D 155 ASN ** E 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 337 GLN B 301 ASN ** C 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 379 GLN G 158 GLN H 34 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.0840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 17861 Z= 0.258 Angle : 0.496 7.256 24231 Z= 0.278 Chirality : 0.042 0.148 2461 Planarity : 0.004 0.041 3153 Dihedral : 5.667 56.474 2361 Min Nonbonded Distance : 1.759 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.86 % Allowed : 14.14 % Favored : 83.00 % 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: 1.25 (0.14), residues: 1338 sheet: 1.76 (0.85), residues: 44 loop : 0.47 (0.25), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 276 HIS 0.007 0.001 HIS D 382 PHE 0.018 0.002 PHE D 275 TYR 0.019 0.002 TYR D 115 ARG 0.007 0.001 ARG B 261 *********************** 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 319 residues out of total 1782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 268 time to evaluate : 2.501 Fit side-chains REVERT: D 186 ARG cc_start: 0.8847 (OUTLIER) cc_final: 0.8170 (tmt90) REVERT: D 474 GLU cc_start: 0.8019 (tt0) cc_final: 0.7768 (tt0) REVERT: E 206 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8514 (mp) REVERT: E 460 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.7919 (mt-10) REVERT: B 34 LYS cc_start: 0.8385 (OUTLIER) cc_final: 0.8149 (mttp) REVERT: B 35 MET cc_start: 0.8598 (OUTLIER) cc_final: 0.8076 (tmt) REVERT: B 80 ARG cc_start: 0.8790 (OUTLIER) cc_final: 0.7901 (ttp-170) REVERT: C 80 ARG cc_start: 0.8711 (OUTLIER) cc_final: 0.8483 (ttt180) REVERT: C 349 LYS cc_start: 0.8455 (OUTLIER) cc_final: 0.8012 (ttpt) REVERT: C 365 GLU cc_start: 0.6987 (OUTLIER) cc_final: 0.6754 (mt-10) REVERT: G 127 TYR cc_start: 0.8740 (m-80) cc_final: 0.8524 (m-80) REVERT: H 138 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.8195 (tpt-90) outliers start: 51 outliers final: 30 residues processed: 304 average time/residue: 1.8245 time to fit residues: 608.6487 Evaluate side-chains 307 residues out of total 1782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 267 time to evaluate : 2.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 83 GLN Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 186 ARG Chi-restraints excluded: chain D residue 213 THR Chi-restraints excluded: chain D residue 259 ASN Chi-restraints excluded: chain D residue 346 LEU Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain E residue 160 LYS Chi-restraints excluded: chain E residue 186 ARG Chi-restraints excluded: chain E residue 206 LEU Chi-restraints excluded: chain E residue 306 ASN Chi-restraints excluded: chain E residue 310 TYR Chi-restraints excluded: chain E residue 381 ASP Chi-restraints excluded: chain E residue 460 GLU Chi-restraints excluded: chain E residue 523 VAL Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 35 MET Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 80 ARG Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 173 ASP Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain C residue 80 ARG Chi-restraints excluded: chain C residue 173 ASP Chi-restraints excluded: chain C residue 349 LYS Chi-restraints excluded: chain C residue 365 GLU Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 41 THR Chi-restraints excluded: chain G residue 89 SER Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain H residue 138 ARG Chi-restraints excluded: chain H residue 165 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 195 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 115 optimal weight: 4.9990 chunk 148 optimal weight: 7.9990 chunk 114 optimal weight: 0.8980 chunk 171 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 202 optimal weight: 7.9990 chunk 126 optimal weight: 6.9990 chunk 123 optimal weight: 3.9990 chunk 93 optimal weight: 6.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 90 ASN ** E 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 337 GLN B 301 ASN C 165 GLN C 379 GLN G 158 GLN H 34 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.0722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 17861 Z= 0.343 Angle : 0.557 8.740 24231 Z= 0.311 Chirality : 0.045 0.161 2461 Planarity : 0.005 0.048 3153 Dihedral : 5.897 58.306 2361 Min Nonbonded Distance : 1.726 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.25 % Allowed : 13.75 % Favored : 83.00 % 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: 1.08 (0.18), residues: 2101 helix: 0.97 (0.14), residues: 1338 sheet: 1.73 (0.87), residues: 44 loop : 0.41 (0.25), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 276 HIS 0.005 0.002 HIS B 106 PHE 0.020 0.003 PHE D 275 TYR 0.022 0.003 TYR D 115 ARG 0.010 0.001 ARG B 261 *********************** 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 326 residues out of total 1782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 268 time to evaluate : 2.219 Fit side-chains REVERT: D 186 ARG cc_start: 0.8907 (OUTLIER) cc_final: 0.8220 (tmt90) REVERT: D 474 GLU cc_start: 0.8075 (tt0) cc_final: 0.7813 (tt0) REVERT: E 206 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8550 (mp) REVERT: E 460 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.7956 (mt-10) REVERT: B 34 LYS cc_start: 0.8406 (OUTLIER) cc_final: 0.8155 (mttp) REVERT: B 35 MET cc_start: 0.8617 (OUTLIER) cc_final: 0.8106 (tmt) REVERT: B 80 ARG cc_start: 0.8792 (OUTLIER) cc_final: 0.7862 (ttp-170) REVERT: C 80 ARG cc_start: 0.8735 (OUTLIER) cc_final: 0.8488 (ttt180) REVERT: C 349 LYS cc_start: 0.8453 (OUTLIER) cc_final: 0.8023 (ttpt) REVERT: C 365 GLU cc_start: 0.6990 (OUTLIER) cc_final: 0.6764 (mt-10) REVERT: G 75 VAL cc_start: 0.8877 (t) cc_final: 0.8634 (p) REVERT: G 127 TYR cc_start: 0.8795 (m-80) cc_final: 0.8586 (m-80) REVERT: H 138 ARG cc_start: 0.8517 (OUTLIER) cc_final: 0.8223 (tpt-90) outliers start: 58 outliers final: 34 residues processed: 310 average time/residue: 1.8823 time to fit residues: 647.0643 Evaluate side-chains 307 residues out of total 1782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 263 time to evaluate : 2.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 83 GLN Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 186 ARG Chi-restraints excluded: chain D residue 213 THR Chi-restraints excluded: chain D residue 259 ASN Chi-restraints excluded: chain D residue 346 LEU Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain D residue 440 GLU Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 160 LYS Chi-restraints excluded: chain E residue 186 ARG Chi-restraints excluded: chain E residue 206 LEU Chi-restraints excluded: chain E residue 306 ASN Chi-restraints excluded: chain E residue 310 TYR Chi-restraints excluded: chain E residue 435 THR Chi-restraints excluded: chain E residue 460 GLU Chi-restraints excluded: chain E residue 523 VAL Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 35 MET Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 80 ARG Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 173 ASP Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain C residue 80 ARG Chi-restraints excluded: chain C residue 173 ASP Chi-restraints excluded: chain C residue 349 LYS Chi-restraints excluded: chain C residue 365 GLU Chi-restraints excluded: chain C residue 382 LYS Chi-restraints excluded: chain C residue 388 LEU Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 41 THR Chi-restraints excluded: chain G residue 89 SER Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain H residue 138 ARG Chi-restraints excluded: chain H residue 165 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 125 optimal weight: 0.9990 chunk 80 optimal weight: 6.9990 chunk 120 optimal weight: 6.9990 chunk 60 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 128 optimal weight: 0.8980 chunk 137 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 159 optimal weight: 3.9990 chunk 184 optimal weight: 4.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 90 ASN ** E 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 337 GLN B 301 ASN ** C 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 379 GLN G 158 GLN H 34 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.0895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 17861 Z= 0.199 Angle : 0.463 6.283 24231 Z= 0.261 Chirality : 0.039 0.146 2461 Planarity : 0.004 0.037 3153 Dihedral : 5.671 56.661 2361 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.86 % Allowed : 14.31 % Favored : 82.83 % 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: 1.35 (0.19), residues: 2101 helix: 1.20 (0.14), residues: 1338 sheet: 1.77 (0.85), residues: 44 loop : 0.45 (0.25), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 43 HIS 0.005 0.001 HIS D 382 PHE 0.015 0.002 PHE D 275 TYR 0.017 0.002 TYR D 115 ARG 0.005 0.000 ARG B 261 *********************** 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 317 residues out of total 1782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 266 time to evaluate : 2.279 Fit side-chains REVERT: D 186 ARG cc_start: 0.8862 (OUTLIER) cc_final: 0.7984 (tmt90) REVERT: D 295 LYS cc_start: 0.8922 (OUTLIER) cc_final: 0.8675 (tmtm) REVERT: D 474 GLU cc_start: 0.7998 (tt0) cc_final: 0.7746 (tt0) REVERT: E 206 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8526 (mp) REVERT: E 460 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.7916 (mt-10) REVERT: B 34 LYS cc_start: 0.8385 (OUTLIER) cc_final: 0.8136 (mttp) REVERT: B 35 MET cc_start: 0.8596 (OUTLIER) cc_final: 0.8069 (tmt) REVERT: B 80 ARG cc_start: 0.8799 (OUTLIER) cc_final: 0.7912 (ttp-170) REVERT: C 80 ARG cc_start: 0.8704 (OUTLIER) cc_final: 0.8460 (ttt180) REVERT: C 349 LYS cc_start: 0.8444 (OUTLIER) cc_final: 0.8001 (ttpt) REVERT: C 365 GLU cc_start: 0.6985 (OUTLIER) cc_final: 0.6756 (mt-10) REVERT: G 127 TYR cc_start: 0.8775 (m-80) cc_final: 0.8504 (m-80) REVERT: H 138 ARG cc_start: 0.8481 (OUTLIER) cc_final: 0.8202 (tpt-90) outliers start: 51 outliers final: 31 residues processed: 302 average time/residue: 1.8866 time to fit residues: 625.1636 Evaluate side-chains 308 residues out of total 1782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 266 time to evaluate : 2.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 83 GLN Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 186 ARG Chi-restraints excluded: chain D residue 213 THR Chi-restraints excluded: chain D residue 259 ASN Chi-restraints excluded: chain D residue 295 LYS Chi-restraints excluded: chain D residue 346 LEU Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain D residue 440 GLU Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 160 LYS Chi-restraints excluded: chain E residue 186 ARG Chi-restraints excluded: chain E residue 206 LEU Chi-restraints excluded: chain E residue 306 ASN Chi-restraints excluded: chain E residue 310 TYR Chi-restraints excluded: chain E residue 451 GLN Chi-restraints excluded: chain E residue 460 GLU Chi-restraints excluded: chain E residue 523 VAL Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 35 MET Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 80 ARG Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 173 ASP Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain C residue 80 ARG Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 173 ASP Chi-restraints excluded: chain C residue 349 LYS Chi-restraints excluded: chain C residue 365 GLU Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 41 THR Chi-restraints excluded: chain G residue 89 SER Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain H residue 138 ARG Chi-restraints excluded: chain H residue 165 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 193 optimal weight: 5.9990 chunk 176 optimal weight: 2.9990 chunk 188 optimal weight: 0.9980 chunk 113 optimal weight: 6.9990 chunk 82 optimal weight: 2.9990 chunk 148 optimal weight: 0.1980 chunk 57 optimal weight: 5.9990 chunk 170 optimal weight: 0.9990 chunk 178 optimal weight: 3.9990 chunk 187 optimal weight: 4.9990 chunk 123 optimal weight: 6.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 90 ASN ** D 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 337 GLN B 301 ASN ** C 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 379 GLN G 158 GLN H 34 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.0893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 17861 Z= 0.207 Angle : 0.468 6.317 24231 Z= 0.263 Chirality : 0.040 0.148 2461 Planarity : 0.004 0.038 3153 Dihedral : 5.657 56.659 2361 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 15.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.97 % Allowed : 14.20 % Favored : 82.83 % 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: 1.38 (0.19), residues: 2101 helix: 1.24 (0.14), residues: 1338 sheet: 1.79 (0.85), residues: 44 loop : 0.46 (0.25), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 43 HIS 0.005 0.001 HIS D 382 PHE 0.016 0.002 PHE D 275 TYR 0.017 0.002 TYR D 115 ARG 0.005 0.000 ARG B 261 *********************** 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 321 residues out of total 1782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 268 time to evaluate : 2.374 Fit side-chains REVERT: D 186 ARG cc_start: 0.8826 (OUTLIER) cc_final: 0.7871 (tmt90) REVERT: D 295 LYS cc_start: 0.8923 (OUTLIER) cc_final: 0.8675 (tmtm) REVERT: E 206 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8531 (mp) REVERT: E 460 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.7922 (mt-10) REVERT: B 34 LYS cc_start: 0.8384 (OUTLIER) cc_final: 0.8137 (mttp) REVERT: B 35 MET cc_start: 0.8597 (OUTLIER) cc_final: 0.8072 (tmt) REVERT: B 80 ARG cc_start: 0.8779 (OUTLIER) cc_final: 0.7884 (ttp-170) REVERT: C 80 ARG cc_start: 0.8705 (OUTLIER) cc_final: 0.8417 (ttt180) REVERT: C 349 LYS cc_start: 0.8444 (OUTLIER) cc_final: 0.8010 (ttpt) REVERT: C 365 GLU cc_start: 0.6987 (OUTLIER) cc_final: 0.6759 (mt-10) REVERT: G 127 TYR cc_start: 0.8796 (m-80) cc_final: 0.8580 (m-80) REVERT: H 138 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.8213 (tpt-90) outliers start: 53 outliers final: 37 residues processed: 304 average time/residue: 1.8110 time to fit residues: 605.0354 Evaluate side-chains 313 residues out of total 1782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 265 time to evaluate : 2.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 61 LYS Chi-restraints excluded: chain D residue 83 GLN Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 186 ARG Chi-restraints excluded: chain D residue 213 THR Chi-restraints excluded: chain D residue 259 ASN Chi-restraints excluded: chain D residue 295 LYS Chi-restraints excluded: chain D residue 346 LEU Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain D residue 440 GLU Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 160 LYS Chi-restraints excluded: chain E residue 186 ARG Chi-restraints excluded: chain E residue 206 LEU Chi-restraints excluded: chain E residue 306 ASN Chi-restraints excluded: chain E residue 310 TYR Chi-restraints excluded: chain E residue 451 GLN Chi-restraints excluded: chain E residue 460 GLU Chi-restraints excluded: chain E residue 523 VAL Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 35 MET Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 80 ARG Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 173 ASP Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain C residue 80 ARG Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 173 ASP Chi-restraints excluded: chain C residue 349 LYS Chi-restraints excluded: chain C residue 365 GLU Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 41 THR Chi-restraints excluded: chain G residue 89 SER Chi-restraints excluded: chain G residue 123 MET Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 48 GLU Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain H residue 138 ARG Chi-restraints excluded: chain H residue 165 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 199 optimal weight: 4.9990 chunk 121 optimal weight: 6.9990 chunk 94 optimal weight: 0.0970 chunk 138 optimal weight: 2.9990 chunk 209 optimal weight: 4.9990 chunk 192 optimal weight: 4.9990 chunk 166 optimal weight: 2.9990 chunk 17 optimal weight: 0.0980 chunk 128 optimal weight: 0.6980 chunk 102 optimal weight: 0.8980 chunk 132 optimal weight: 0.7980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 90 ASN ** D 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 442 ASN ** E 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 337 GLN B 301 ASN ** C 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 379 GLN G 158 GLN H 34 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.1234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 17861 Z= 0.111 Angle : 0.394 4.986 24231 Z= 0.222 Chirality : 0.036 0.149 2461 Planarity : 0.003 0.035 3153 Dihedral : 5.251 55.227 2361 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 17.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.36 % Allowed : 14.93 % Favored : 82.72 % 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: 1.81 (0.19), residues: 2101 helix: 1.60 (0.14), residues: 1345 sheet: 1.91 (0.84), residues: 44 loop : 0.56 (0.25), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 43 HIS 0.004 0.001 HIS E 343 PHE 0.008 0.001 PHE C 154 TYR 0.015 0.001 TYR E 156 ARG 0.004 0.000 ARG E 320 ********************** 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 318 residues out of total 1782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 276 time to evaluate : 2.296 Fit side-chains revert: symmetry clash REVERT: D 186 ARG cc_start: 0.8805 (OUTLIER) cc_final: 0.7266 (tmt90) REVERT: D 259 ASN cc_start: 0.7788 (OUTLIER) cc_final: 0.7563 (t0) REVERT: D 403 ILE cc_start: 0.8356 (OUTLIER) cc_final: 0.8118 (tp) REVERT: E 460 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7983 (mt-10) REVERT: B 34 LYS cc_start: 0.8392 (OUTLIER) cc_final: 0.8147 (mttp) REVERT: B 68 ASP cc_start: 0.8758 (OUTLIER) cc_final: 0.7729 (m-30) REVERT: B 80 ARG cc_start: 0.8757 (OUTLIER) cc_final: 0.7505 (ttp-170) REVERT: H 138 ARG cc_start: 0.8459 (OUTLIER) cc_final: 0.8225 (tpt-90) outliers start: 42 outliers final: 28 residues processed: 302 average time/residue: 1.8659 time to fit residues: 619.9272 Evaluate side-chains 310 residues out of total 1782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 274 time to evaluate : 2.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 83 GLN Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 186 ARG Chi-restraints excluded: chain D residue 213 THR Chi-restraints excluded: chain D residue 259 ASN Chi-restraints excluded: chain D residue 346 LEU Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 160 LYS Chi-restraints excluded: chain E residue 186 ARG Chi-restraints excluded: chain E residue 306 ASN Chi-restraints excluded: chain E residue 310 TYR Chi-restraints excluded: chain E residue 451 GLN Chi-restraints excluded: chain E residue 460 GLU Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 80 ARG Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 173 ASP Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain C residue 173 ASP Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 41 THR Chi-restraints excluded: chain G residue 89 SER Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 48 GLU Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain H residue 138 ARG Chi-restraints excluded: chain H residue 165 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 6.9990 chunk 51 optimal weight: 0.9980 chunk 153 optimal weight: 0.1980 chunk 24 optimal weight: 7.9990 chunk 46 optimal weight: 5.9990 chunk 166 optimal weight: 0.0670 chunk 69 optimal weight: 7.9990 chunk 171 optimal weight: 0.5980 chunk 21 optimal weight: 3.9990 chunk 30 optimal weight: 0.3980 chunk 146 optimal weight: 1.9990 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 90 ASN ** E 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 337 GLN B 301 ASN ** C 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 379 GLN G 144 ASN G 158 GLN H 34 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.123750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.110516 restraints weight = 22836.626| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 0.76 r_work: 0.3000 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 17861 Z= 0.105 Angle : 0.378 5.079 24231 Z= 0.212 Chirality : 0.035 0.131 2461 Planarity : 0.003 0.036 3153 Dihedral : 4.944 54.120 2361 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 19.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.80 % Allowed : 15.49 % Favored : 82.72 % 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: 2.10 (0.19), residues: 2101 helix: 1.85 (0.14), residues: 1347 sheet: 1.97 (0.84), residues: 44 loop : 0.60 (0.25), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 43 HIS 0.003 0.001 HIS E 343 PHE 0.008 0.001 PHE D 39 TYR 0.018 0.001 TYR E 156 ARG 0.004 0.000 ARG E 320 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9091.99 seconds wall clock time: 160 minutes 8.75 seconds (9608.75 seconds total)