Starting phenix.real_space_refine on Mon Aug 25 17:01:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zar_39885/08_2025/8zar_39885.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zar_39885/08_2025/8zar_39885.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zar_39885/08_2025/8zar_39885.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zar_39885/08_2025/8zar_39885.map" model { file = "/net/cci-nas-00/data/ceres_data/8zar_39885/08_2025/8zar_39885.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zar_39885/08_2025/8zar_39885.cif" } resolution = 3.59 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.023 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: 4 Type Number sf(0) Gaussians S 86 5.16 5 C 18696 2.51 5 N 5279 2.21 5 O 5808 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29869 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2638 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 14, 'TRANS': 329} Chain: "B" Number of atoms: 2672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2672 Classifications: {'peptide': 348} Link IDs: {'PTRANS': 14, 'TRANS': 333} Chain: "C" Number of atoms: 2686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2686 Classifications: {'peptide': 349} Link IDs: {'PTRANS': 14, 'TRANS': 334} Chain: "D" Number of atoms: 2877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2877 Classifications: {'peptide': 373} Link IDs: {'PTRANS': 14, 'TRANS': 358} Chain: "E" Number of atoms: 2638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2638 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 14, 'TRANS': 329} Chain: "F" Number of atoms: 2638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2638 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 14, 'TRANS': 329} Chain: "J" Number of atoms: 3805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 3805 Classifications: {'peptide': 494} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 470} Chain: "G" Number of atoms: 3305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3305 Classifications: {'peptide': 428} Link IDs: {'PTRANS': 10, 'TRANS': 417} Chain: "H" Number of atoms: 3305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3305 Classifications: {'peptide': 428} Link IDs: {'PTRANS': 10, 'TRANS': 417} Chain: "I" Number of atoms: 3305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3305 Classifications: {'peptide': 428} Link IDs: {'PTRANS': 10, 'TRANS': 417} Time building chain proxies: 7.26, per 1000 atoms: 0.24 Number of scatterers: 29869 At special positions: 0 Unit cell: (110.24, 110.24, 334.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 86 16.00 O 5808 8.00 N 5279 7.00 C 18696 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.73 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 1.7 microseconds 7720 Ramachandran restraints generated. 3860 Oldfield, 0 Emsley, 3860 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7344 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 25 sheets defined 57.4% alpha, 11.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.19 Creating SS restraints... Processing helix chain 'A' and resid 94 through 152 removed outlier: 3.823A pdb=" N LYS A 123 " --> pdb=" O MET A 119 " (cutoff:3.500A) Proline residue: A 148 - end of helix Processing helix chain 'A' and resid 156 through 186 removed outlier: 3.705A pdb=" N LEU A 160 " --> pdb=" O GLY A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 195 Processing helix chain 'A' and resid 196 through 215 Processing helix chain 'A' and resid 279 through 283 removed outlier: 4.091A pdb=" N ASP A 282 " --> pdb=" O TYR A 279 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL A 283 " --> pdb=" O GLY A 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 279 through 283' Processing helix chain 'A' and resid 326 through 331 removed outlier: 3.507A pdb=" N LEU A 330 " --> pdb=" O ASP A 326 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU A 331 " --> pdb=" O GLN A 327 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 326 through 331' Processing helix chain 'A' and resid 374 through 388 Processing helix chain 'B' and resid 44 through 48 Processing helix chain 'B' and resid 95 through 152 removed outlier: 3.783A pdb=" N LYS B 123 " --> pdb=" O MET B 119 " (cutoff:3.500A) Proline residue: B 148 - end of helix removed outlier: 3.533A pdb=" N ASN B 151 " --> pdb=" O VAL B 147 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA B 152 " --> pdb=" O PRO B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 186 Processing helix chain 'B' and resid 192 through 195 Processing helix chain 'B' and resid 196 through 215 Processing helix chain 'B' and resid 261 through 263 No H-bonds generated for 'chain 'B' and resid 261 through 263' Processing helix chain 'B' and resid 326 through 333 removed outlier: 3.708A pdb=" N GLN B 332 " --> pdb=" O LYS B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 388 Processing helix chain 'C' and resid 43 through 48 Processing helix chain 'C' and resid 94 through 152 removed outlier: 3.810A pdb=" N GLN C 99 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA C 100 " --> pdb=" O ASP C 96 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N HIS C 116 " --> pdb=" O VAL C 112 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN C 117 " --> pdb=" O ARG C 113 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU C 118 " --> pdb=" O GLN C 114 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LYS C 123 " --> pdb=" O MET C 119 " (cutoff:3.500A) Proline residue: C 148 - end of helix removed outlier: 3.572A pdb=" N ASN C 151 " --> pdb=" O VAL C 147 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA C 152 " --> pdb=" O PRO C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 186 removed outlier: 3.667A pdb=" N LEU C 160 " --> pdb=" O GLY C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 195 Processing helix chain 'C' and resid 196 through 215 removed outlier: 3.815A pdb=" N GLU C 205 " --> pdb=" O GLN C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 264 removed outlier: 4.359A pdb=" N ALA C 264 " --> pdb=" O GLU C 260 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 260 through 264' Processing helix chain 'C' and resid 279 through 283 removed outlier: 3.564A pdb=" N ASP C 282 " --> pdb=" O TYR C 279 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N VAL C 283 " --> pdb=" O GLY C 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 279 through 283' Processing helix chain 'C' and resid 326 through 331 removed outlier: 3.866A pdb=" N LEU C 330 " --> pdb=" O ASP C 326 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU C 331 " --> pdb=" O GLN C 327 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 326 through 331' Processing helix chain 'C' and resid 374 through 389 Processing helix chain 'D' and resid 19 through 48 removed outlier: 3.589A pdb=" N THR D 28 " --> pdb=" O LEU D 24 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE D 31 " --> pdb=" O LEU D 27 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE D 40 " --> pdb=" O VAL D 36 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TYR D 41 " --> pdb=" O ALA D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 152 removed outlier: 4.132A pdb=" N LYS D 123 " --> pdb=" O MET D 119 " (cutoff:3.500A) Proline residue: D 148 - end of helix removed outlier: 3.555A pdb=" N ASN D 151 " --> pdb=" O VAL D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 183 removed outlier: 3.757A pdb=" N LEU D 160 " --> pdb=" O GLY D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 195 Processing helix chain 'D' and resid 196 through 215 removed outlier: 3.669A pdb=" N ALA D 202 " --> pdb=" O ALA D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 262 through 266 removed outlier: 4.231A pdb=" N ASN D 265 " --> pdb=" O GLN D 262 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N MET D 266 " --> pdb=" O ILE D 263 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 262 through 266' Processing helix chain 'D' and resid 327 through 333 removed outlier: 3.630A pdb=" N GLU D 331 " --> pdb=" O GLN D 327 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLN D 332 " --> pdb=" O LYS D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 388 Processing helix chain 'E' and resid 94 through 152 removed outlier: 3.759A pdb=" N LYS E 123 " --> pdb=" O MET E 119 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR E 143 " --> pdb=" O ALA E 139 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG E 145 " --> pdb=" O SER E 141 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ARG E 146 " --> pdb=" O ASP E 142 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL E 147 " --> pdb=" O TYR E 143 " (cutoff:3.500A) Proline residue: E 148 - end of helix removed outlier: 3.557A pdb=" N ALA E 152 " --> pdb=" O PRO E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 156 through 186 Processing helix chain 'E' and resid 196 through 215 Processing helix chain 'E' and resid 262 through 266 removed outlier: 4.118A pdb=" N ASN E 265 " --> pdb=" O GLN E 262 " (cutoff:3.500A) Processing helix chain 'E' and resid 326 through 333 removed outlier: 3.891A pdb=" N GLN E 332 " --> pdb=" O LYS E 328 " (cutoff:3.500A) Processing helix chain 'E' and resid 374 through 389 Processing helix chain 'F' and resid 94 through 151 removed outlier: 4.317A pdb=" N SER F 122 " --> pdb=" O LEU F 118 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N LYS F 123 " --> pdb=" O MET F 119 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLN F 124 " --> pdb=" O ILE F 120 " (cutoff:3.500A) Proline residue: F 148 - end of helix removed outlier: 3.903A pdb=" N ASN F 151 " --> pdb=" O VAL F 147 " (cutoff:3.500A) Processing helix chain 'F' and resid 156 through 186 removed outlier: 3.567A pdb=" N LEU F 160 " --> pdb=" O GLY F 156 " (cutoff:3.500A) Processing helix chain 'F' and resid 192 through 195 Processing helix chain 'F' and resid 196 through 215 removed outlier: 3.521A pdb=" N ALA F 202 " --> pdb=" O ALA F 198 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU F 205 " --> pdb=" O GLN F 201 " (cutoff:3.500A) Processing helix chain 'F' and resid 262 through 266 removed outlier: 4.484A pdb=" N ASN F 265 " --> pdb=" O GLN F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 326 through 331 removed outlier: 3.594A pdb=" N LEU F 330 " --> pdb=" O ASP F 326 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLU F 331 " --> pdb=" O GLN F 327 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 326 through 331' Processing helix chain 'F' and resid 374 through 387 Processing helix chain 'J' and resid 11 through 44 removed outlier: 4.083A pdb=" N GLN J 26 " --> pdb=" O ALA J 22 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL J 27 " --> pdb=" O THR J 23 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA J 33 " --> pdb=" O ASP J 29 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ASN J 34 " --> pdb=" O SER J 30 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL J 35 " --> pdb=" O THR J 31 " (cutoff:3.500A) Proline residue: J 38 - end of helix Processing helix chain 'J' and resid 47 through 52 Processing helix chain 'J' and resid 52 through 66 removed outlier: 4.271A pdb=" N PHE J 58 " --> pdb=" O VAL J 54 " (cutoff:3.500A) Processing helix chain 'J' and resid 68 through 76 removed outlier: 3.519A pdb=" N LEU J 72 " --> pdb=" O LEU J 68 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG J 75 " --> pdb=" O TRP J 71 " (cutoff:3.500A) Processing helix chain 'J' and resid 77 through 98 Processing helix chain 'J' and resid 101 through 117 removed outlier: 3.753A pdb=" N GLY J 117 " --> pdb=" O GLY J 113 " (cutoff:3.500A) Processing helix chain 'J' and resid 119 through 131 Processing helix chain 'J' and resid 132 through 134 No H-bonds generated for 'chain 'J' and resid 132 through 134' Processing helix chain 'J' and resid 135 through 165 removed outlier: 3.722A pdb=" N THR J 146 " --> pdb=" O LEU J 142 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL J 147 " --> pdb=" O TRP J 143 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA J 150 " --> pdb=" O THR J 146 " (cutoff:3.500A) Proline residue: J 151 - end of helix Proline residue: J 155 - end of helix Processing helix chain 'J' and resid 173 through 189 removed outlier: 3.693A pdb=" N ILE J 177 " --> pdb=" O ILE J 173 " (cutoff:3.500A) Processing helix chain 'J' and resid 202 through 223 removed outlier: 3.834A pdb=" N LEU J 206 " --> pdb=" O ASP J 202 " (cutoff:3.500A) Processing helix chain 'J' and resid 227 through 230 Processing helix chain 'J' and resid 231 through 253 removed outlier: 3.525A pdb=" N LEU J 253 " --> pdb=" O ILE J 249 " (cutoff:3.500A) Processing helix chain 'J' and resid 261 through 266 removed outlier: 4.031A pdb=" N LEU J 264 " --> pdb=" O ASP J 261 " (cutoff:3.500A) Processing helix chain 'J' and resid 267 through 289 removed outlier: 3.661A pdb=" N VAL J 289 " --> pdb=" O PHE J 285 " (cutoff:3.500A) Processing helix chain 'J' and resid 289 through 299 removed outlier: 4.230A pdb=" N GLN J 293 " --> pdb=" O VAL J 289 " (cutoff:3.500A) Processing helix chain 'J' and resid 302 through 309 Processing helix chain 'J' and resid 310 through 314 removed outlier: 3.504A pdb=" N VAL J 313 " --> pdb=" O SER J 310 " (cutoff:3.500A) Processing helix chain 'J' and resid 316 through 327 Proline residue: J 322 - end of helix Processing helix chain 'J' and resid 328 through 332 removed outlier: 3.734A pdb=" N LEU J 331 " --> pdb=" O ALA J 328 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ASP J 332 " --> pdb=" O HIS J 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 328 through 332' Processing helix chain 'J' and resid 333 through 353 Processing helix chain 'J' and resid 360 through 364 Processing helix chain 'J' and resid 365 through 387 removed outlier: 4.273A pdb=" N PHE J 373 " --> pdb=" O PHE J 369 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA J 374 " --> pdb=" O ILE J 370 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE J 378 " --> pdb=" O ALA J 374 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N PHE J 379 " --> pdb=" O VAL J 375 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N MET J 380 " --> pdb=" O ALA J 376 " (cutoff:3.500A) Proline residue: J 381 - end of helix Processing helix chain 'J' and resid 391 through 393 No H-bonds generated for 'chain 'J' and resid 391 through 393' Processing helix chain 'J' and resid 394 through 434 removed outlier: 3.681A pdb=" N THR J 419 " --> pdb=" O SER J 415 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLU J 434 " --> pdb=" O ALA J 430 " (cutoff:3.500A) Processing helix chain 'J' and resid 443 through 453 removed outlier: 3.593A pdb=" N TYR J 447 " --> pdb=" O ALA J 443 " (cutoff:3.500A) Processing helix chain 'J' and resid 456 through 492 removed outlier: 3.669A pdb=" N VAL J 490 " --> pdb=" O GLY J 486 " (cutoff:3.500A) Processing helix chain 'J' and resid 493 through 498 removed outlier: 3.743A pdb=" N ALA J 498 " --> pdb=" O VAL J 495 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 14 removed outlier: 3.660A pdb=" N GLN G 9 " --> pdb=" O GLN G 5 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU G 12 " --> pdb=" O GLN G 8 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 36 removed outlier: 3.957A pdb=" N ILE G 31 " --> pdb=" O ALA G 27 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ASN G 32 " --> pdb=" O PHE G 28 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLU G 33 " --> pdb=" O GLU G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 78 through 147 removed outlier: 3.707A pdb=" N LEU G 117 " --> pdb=" O TYR G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 150 through 186 removed outlier: 3.771A pdb=" N VAL G 154 " --> pdb=" O ALA G 150 " (cutoff:3.500A) Processing helix chain 'G' and resid 197 through 201 removed outlier: 3.526A pdb=" N PHE G 201 " --> pdb=" O VAL G 198 " (cutoff:3.500A) Processing helix chain 'G' and resid 208 through 220 removed outlier: 3.509A pdb=" N LEU G 212 " --> pdb=" O PRO G 208 " (cutoff:3.500A) Processing helix chain 'G' and resid 220 through 241 Processing helix chain 'G' and resid 242 through 245 Processing helix chain 'G' and resid 293 through 295 No H-bonds generated for 'chain 'G' and resid 293 through 295' Processing helix chain 'G' and resid 296 through 365 removed outlier: 4.086A pdb=" N LYS G 303 " --> pdb=" O ASN G 299 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER G 353 " --> pdb=" O VAL G 349 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER G 354 " --> pdb=" O SER G 350 " (cutoff:3.500A) Processing helix chain 'G' and resid 368 through 405 removed outlier: 3.690A pdb=" N VAL G 372 " --> pdb=" O THR G 368 " (cutoff:3.500A) Processing helix chain 'G' and resid 412 through 417 removed outlier: 3.840A pdb=" N ASN G 417 " --> pdb=" O LEU G 413 " (cutoff:3.500A) Processing helix chain 'H' and resid 2 through 14 removed outlier: 3.992A pdb=" N LEU H 12 " --> pdb=" O GLN H 8 " (cutoff:3.500A) Processing helix chain 'H' and resid 14 through 36 removed outlier: 3.862A pdb=" N ILE H 31 " --> pdb=" O ALA H 27 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ASN H 32 " --> pdb=" O PHE H 28 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N GLU H 33 " --> pdb=" O GLU H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 39 No H-bonds generated for 'chain 'H' and resid 37 through 39' Processing helix chain 'H' and resid 77 through 147 removed outlier: 4.459A pdb=" N TRP H 81 " --> pdb=" O ASP H 77 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG H 82 " --> pdb=" O MET H 78 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA H 83 " --> pdb=" O SER H 79 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL H 116 " --> pdb=" O ALA H 112 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU H 117 " --> pdb=" O TYR H 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 150 through 187 removed outlier: 3.834A pdb=" N VAL H 154 " --> pdb=" O ALA H 150 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE H 185 " --> pdb=" O GLN H 181 " (cutoff:3.500A) Processing helix chain 'H' and resid 198 through 201 removed outlier: 3.746A pdb=" N PHE H 201 " --> pdb=" O VAL H 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 198 through 201' Processing helix chain 'H' and resid 208 through 220 Processing helix chain 'H' and resid 220 through 242 Processing helix chain 'H' and resid 295 through 365 removed outlier: 4.289A pdb=" N ASN H 299 " --> pdb=" O GLY H 295 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLN H 301 " --> pdb=" O MET H 297 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N VAL H 302 " --> pdb=" O VAL H 298 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS H 303 " --> pdb=" O ASN H 299 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ASN H 335 " --> pdb=" O PHE H 331 " (cutoff:3.500A) Processing helix chain 'H' and resid 368 through 405 removed outlier: 3.745A pdb=" N VAL H 372 " --> pdb=" O THR H 368 " (cutoff:3.500A) Processing helix chain 'H' and resid 408 through 417 removed outlier: 3.676A pdb=" N ALA H 414 " --> pdb=" O GLN H 410 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LEU H 415 " --> pdb=" O ASP H 411 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ASN H 416 " --> pdb=" O LEU H 412 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASN H 417 " --> pdb=" O LEU H 413 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 14 removed outlier: 3.639A pdb=" N LEU I 12 " --> pdb=" O GLN I 8 " (cutoff:3.500A) Processing helix chain 'I' and resid 14 through 36 removed outlier: 3.595A pdb=" N ARG I 18 " --> pdb=" O ASN I 14 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ILE I 31 " --> pdb=" O ALA I 27 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ASN I 32 " --> pdb=" O PHE I 28 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLU I 33 " --> pdb=" O GLU I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 37 through 39 No H-bonds generated for 'chain 'I' and resid 37 through 39' Processing helix chain 'I' and resid 77 through 147 removed outlier: 4.288A pdb=" N TRP I 81 " --> pdb=" O ASP I 77 " (cutoff:3.500A) Processing helix chain 'I' and resid 150 through 187 removed outlier: 3.787A pdb=" N VAL I 154 " --> pdb=" O ALA I 150 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE I 185 " --> pdb=" O GLN I 181 " (cutoff:3.500A) Processing helix chain 'I' and resid 198 through 201 removed outlier: 3.753A pdb=" N PHE I 201 " --> pdb=" O VAL I 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 198 through 201' Processing helix chain 'I' and resid 208 through 217 removed outlier: 3.546A pdb=" N LEU I 212 " --> pdb=" O PRO I 208 " (cutoff:3.500A) Processing helix chain 'I' and resid 221 through 242 Processing helix chain 'I' and resid 243 through 245 No H-bonds generated for 'chain 'I' and resid 243 through 245' Processing helix chain 'I' and resid 298 through 365 removed outlier: 3.835A pdb=" N LYS I 303 " --> pdb=" O ASN I 299 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN I 304 " --> pdb=" O SER I 300 " (cutoff:3.500A) Processing helix chain 'I' and resid 369 through 405 Processing helix chain 'I' and resid 408 through 417 removed outlier: 3.907A pdb=" N LEU I 412 " --> pdb=" O ASN I 408 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA I 414 " --> pdb=" O GLN I 410 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LEU I 415 " --> pdb=" O ASP I 411 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASN I 417 " --> pdb=" O LEU I 413 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 49 through 52 Processing sheet with id=AA2, first strand: chain 'A' and resid 56 through 58 removed outlier: 5.268A pdb=" N LEU A 292 " --> pdb=" O PRO A 320 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ARG A 322 " --> pdb=" O VAL A 290 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 62 through 64 removed outlier: 4.101A pdb=" N MET A 244 " --> pdb=" O ILE A 64 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 217 through 219 removed outlier: 3.891A pdb=" N VAL A 90 " --> pdb=" O ILE A 218 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N LEU A 89 " --> pdb=" O VAL A 75 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N VAL A 75 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N THR A 91 " --> pdb=" O THR A 73 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 49 through 52 removed outlier: 5.935A pdb=" N VAL B 289 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N GLU B 324 " --> pdb=" O VAL B 289 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLY B 291 " --> pdb=" O ARG B 322 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL B 254 " --> pdb=" O ILE B 323 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 62 through 64 removed outlier: 3.989A pdb=" N MET B 244 " --> pdb=" O ILE B 64 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 217 through 219 removed outlier: 3.939A pdb=" N VAL B 90 " --> pdb=" O ILE B 218 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N LEU B 89 " --> pdb=" O VAL B 75 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N VAL B 75 " --> pdb=" O LEU B 89 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N THR B 91 " --> pdb=" O THR B 73 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 258 through 259 Processing sheet with id=AA9, first strand: chain 'C' and resid 49 through 58 removed outlier: 9.854A pdb=" N THR C 52 " --> pdb=" O LYS C 259 " (cutoff:3.500A) removed outlier: 9.327A pdb=" N LYS C 259 " --> pdb=" O THR C 52 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N ASP C 54 " --> pdb=" O ASN C 257 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ASN C 257 " --> pdb=" O ASP C 54 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N LEU C 292 " --> pdb=" O PRO C 320 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ARG C 322 " --> pdb=" O VAL C 290 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N THR C 341 " --> pdb=" O ASP C 54 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N ASP C 54 " --> pdb=" O THR C 341 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 62 through 64 removed outlier: 4.099A pdb=" N MET C 244 " --> pdb=" O ILE C 64 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 217 through 219 removed outlier: 6.835A pdb=" N ILE C 218 " --> pdb=" O LEU C 89 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N LEU C 89 " --> pdb=" O VAL C 75 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N VAL C 75 " --> pdb=" O LEU C 89 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N THR C 91 " --> pdb=" O THR C 73 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 365 through 366 removed outlier: 3.662A pdb=" N ALA C 365 " --> pdb=" O VAL D 75 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N THR D 91 " --> pdb=" O THR D 73 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N VAL D 75 " --> pdb=" O LEU D 89 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N LEU D 89 " --> pdb=" O VAL D 75 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL D 90 " --> pdb=" O ILE D 218 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 50 through 58 removed outlier: 9.783A pdb=" N THR D 52 " --> pdb=" O LYS D 259 " (cutoff:3.500A) removed outlier: 9.347A pdb=" N LYS D 259 " --> pdb=" O THR D 52 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N ASP D 54 " --> pdb=" O ASN D 257 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N LEU D 292 " --> pdb=" O PRO D 320 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ARG D 322 " --> pdb=" O VAL D 290 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N THR D 341 " --> pdb=" O ASP D 54 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N ASP D 54 " --> pdb=" O THR D 341 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 62 through 63 removed outlier: 6.603A pdb=" N ALA D 245 " --> pdb=" O SER D 227 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 49 through 58 removed outlier: 9.687A pdb=" N THR E 52 " --> pdb=" O LYS E 259 " (cutoff:3.500A) removed outlier: 9.372A pdb=" N LYS E 259 " --> pdb=" O THR E 52 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N ASP E 54 " --> pdb=" O ASN E 257 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N LEU E 292 " --> pdb=" O PRO E 320 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ARG E 322 " --> pdb=" O VAL E 290 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N THR E 341 " --> pdb=" O ASP E 54 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N ASP E 54 " --> pdb=" O THR E 341 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 62 through 64 removed outlier: 4.161A pdb=" N MET E 244 " --> pdb=" O ILE E 64 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 217 through 219 removed outlier: 6.908A pdb=" N ILE E 218 " --> pdb=" O LEU E 89 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS E 74 " --> pdb=" O THR E 91 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY E 70 " --> pdb=" O ILE E 237 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 49 through 58 removed outlier: 9.512A pdb=" N THR F 52 " --> pdb=" O LYS F 259 " (cutoff:3.500A) removed outlier: 9.085A pdb=" N LYS F 259 " --> pdb=" O THR F 52 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N ASP F 54 " --> pdb=" O ASN F 257 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE F 258 " --> pdb=" O LEU F 319 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLY F 291 " --> pdb=" O ARG F 322 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N GLU F 324 " --> pdb=" O VAL F 289 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N VAL F 289 " --> pdb=" O GLU F 324 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N VAL F 283 " --> pdb=" O THR F 276 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N THR F 276 " --> pdb=" O VAL F 283 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N THR F 341 " --> pdb=" O ASP F 54 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N ASP F 54 " --> pdb=" O THR F 341 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 62 through 63 Processing sheet with id=AC2, first strand: chain 'F' and resid 217 through 219 removed outlier: 6.775A pdb=" N ILE F 218 " --> pdb=" O LEU F 89 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N LEU F 89 " --> pdb=" O VAL F 75 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N VAL F 75 " --> pdb=" O LEU F 89 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N THR F 91 " --> pdb=" O THR F 73 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 41 through 44 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 41 through 44 current: chain 'G' and resid 247 through 256 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 280 through 281 current: chain 'H' and resid 66 through 76 removed outlier: 4.092A pdb=" N THR H 254 " --> pdb=" O LEU H 69 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LEU H 248 " --> pdb=" O ILE H 75 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY H 255 " --> pdb=" O GLN H 281 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLN H 281 " --> pdb=" O GLY H 255 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER H 257 " --> pdb=" O MET H 279 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N MET H 279 " --> pdb=" O SER H 257 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 279 through 281 current: chain 'I' and resid 63 through 76 removed outlier: 4.202A pdb=" N THR I 65 " --> pdb=" O ASP I 258 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASP I 258 " --> pdb=" O THR I 65 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA I 67 " --> pdb=" O ILE I 256 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LEU I 248 " --> pdb=" O ILE I 75 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N MET I 279 " --> pdb=" O SER I 257 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N SER I 277 " --> pdb=" O THR I 259 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 192 through 194 Processing sheet with id=AC5, first strand: chain 'H' and resid 61 through 62 removed outlier: 4.263A pdb=" N ASN H 61 " --> pdb=" O SER H 262 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER H 262 " --> pdb=" O ASN H 61 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'H' and resid 192 through 196 removed outlier: 3.626A pdb=" N LYS H 421 " --> pdb=" O ALA H 195 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 192 through 196 1888 hydrogen bonds defined for protein. 5523 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: 6.31 Time building geometry restraints manager: 3.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 5224 1.32 - 1.44: 7405 1.44 - 1.57: 17521 1.57 - 1.69: 0 1.69 - 1.81: 165 Bond restraints: 30315 Sorted by residual: bond pdb=" C ILE I 151 " pdb=" O ILE I 151 " ideal model delta sigma weight residual 1.237 1.198 0.040 1.23e-02 6.61e+03 1.04e+01 bond pdb=" N HIS D 48 " pdb=" CA HIS D 48 " ideal model delta sigma weight residual 1.456 1.497 -0.042 1.32e-02 5.74e+03 9.96e+00 bond pdb=" N ILE F 120 " pdb=" CA ILE F 120 " ideal model delta sigma weight residual 1.460 1.499 -0.039 1.26e-02 6.30e+03 9.66e+00 bond pdb=" N ILE B 155 " pdb=" CA ILE B 155 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.30e+00 bond pdb=" C ARG D 20 " pdb=" O ARG D 20 " ideal model delta sigma weight residual 1.236 1.201 0.035 1.15e-02 7.56e+03 9.23e+00 ... (remaining 30310 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 39818 1.61 - 3.22: 1136 3.22 - 4.82: 272 4.82 - 6.43: 19 6.43 - 8.04: 1 Bond angle restraints: 41246 Sorted by residual: angle pdb=" N ARG D 20 " pdb=" CA ARG D 20 " pdb=" C ARG D 20 " ideal model delta sigma weight residual 111.11 103.07 8.04 1.20e+00 6.94e-01 4.49e+01 angle pdb=" CA ARG D 20 " pdb=" C ARG D 20 " pdb=" O ARG D 20 " ideal model delta sigma weight residual 120.90 115.09 5.81 1.07e+00 8.73e-01 2.95e+01 angle pdb=" CA ILE I 151 " pdb=" C ILE I 151 " pdb=" O ILE I 151 " ideal model delta sigma weight residual 120.57 115.11 5.46 1.07e+00 8.73e-01 2.60e+01 angle pdb=" N ASN B 144 " pdb=" CA ASN B 144 " pdb=" C ASN B 144 " ideal model delta sigma weight residual 111.75 105.33 6.42 1.28e+00 6.10e-01 2.52e+01 angle pdb=" CA ASN B 153 " pdb=" C ASN B 153 " pdb=" O ASN B 153 " ideal model delta sigma weight residual 122.63 116.70 5.93 1.29e+00 6.01e-01 2.11e+01 ... (remaining 41241 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 17474 17.78 - 35.55: 741 35.55 - 53.33: 192 53.33 - 71.11: 66 71.11 - 88.89: 25 Dihedral angle restraints: 18498 sinusoidal: 7170 harmonic: 11328 Sorted by residual: dihedral pdb=" CD ARG C 145 " pdb=" NE ARG C 145 " pdb=" CZ ARG C 145 " pdb=" NH1 ARG C 145 " ideal model delta sinusoidal sigma weight residual 0.00 88.78 -88.78 1 1.00e+01 1.00e-02 9.39e+01 dihedral pdb=" CD ARG D 22 " pdb=" NE ARG D 22 " pdb=" CZ ARG D 22 " pdb=" NH1 ARG D 22 " ideal model delta sinusoidal sigma weight residual 0.00 83.40 -83.40 1 1.00e+01 1.00e-02 8.50e+01 dihedral pdb=" CD ARG B 145 " pdb=" NE ARG B 145 " pdb=" CZ ARG B 145 " pdb=" NH1 ARG B 145 " ideal model delta sinusoidal sigma weight residual 0.00 -80.40 80.40 1 1.00e+01 1.00e-02 8.00e+01 ... (remaining 18495 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 4052 0.054 - 0.108: 622 0.108 - 0.162: 165 0.162 - 0.217: 46 0.217 - 0.271: 4 Chirality restraints: 4889 Sorted by residual: chirality pdb=" CA ILE I 292 " pdb=" N ILE I 292 " pdb=" C ILE I 292 " pdb=" CB ILE I 292 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" CB VAL H 146 " pdb=" CA VAL H 146 " pdb=" CG1 VAL H 146 " pdb=" CG2 VAL H 146 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CG LEU D 24 " pdb=" CB LEU D 24 " pdb=" CD1 LEU D 24 " pdb=" CD2 LEU D 24 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.46e+00 ... (remaining 4886 not shown) Planarity restraints: 5392 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 145 " -1.096 9.50e-02 1.11e+02 4.91e-01 1.45e+02 pdb=" NE ARG C 145 " 0.066 2.00e-02 2.50e+03 pdb=" CZ ARG C 145 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG C 145 " -0.014 2.00e-02 2.50e+03 pdb=" NH2 ARG C 145 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 22 " 1.091 9.50e-02 1.11e+02 4.89e-01 1.44e+02 pdb=" NE ARG D 22 " -0.065 2.00e-02 2.50e+03 pdb=" CZ ARG D 22 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG D 22 " 0.012 2.00e-02 2.50e+03 pdb=" NH2 ARG D 22 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 145 " 1.082 9.50e-02 1.11e+02 4.85e-01 1.42e+02 pdb=" NE ARG B 145 " -0.065 2.00e-02 2.50e+03 pdb=" CZ ARG B 145 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG B 145 " 0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG B 145 " 0.019 2.00e-02 2.50e+03 ... (remaining 5389 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.26: 9 2.26 - 2.92: 13290 2.92 - 3.58: 43699 3.58 - 4.24: 65897 4.24 - 4.90: 112983 Nonbonded interactions: 235878 Sorted by model distance: nonbonded pdb=" OE1 GLU C 158 " pdb=" CD2 LEU H 148 " model vdw 1.606 3.460 nonbonded pdb=" O LEU D 154 " pdb=" OG1 THR H 368 " model vdw 1.781 3.040 nonbonded pdb=" O PHE I 76 " pdb=" OG1 THR I 247 " model vdw 2.119 3.040 nonbonded pdb=" OD2 ASP H 77 " pdb=" OG SER H 79 " model vdw 2.176 3.040 nonbonded pdb=" CD GLU C 158 " pdb=" CD2 LEU H 148 " model vdw 2.204 3.690 ... (remaining 235873 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 47 through 390) selection = (chain 'C' and resid 47 through 390) selection = (chain 'D' and resid 47 through 390) selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 28.940 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7018 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 30315 Z= 0.280 Angle : 0.641 8.038 41246 Z= 0.441 Chirality : 0.046 0.271 4889 Planarity : 0.024 0.491 5392 Dihedral : 12.060 88.886 11154 Min Nonbonded Distance : 1.606 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.15 % Allowed : 5.51 % Favored : 94.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.30 (0.14), residues: 3860 helix: 2.69 (0.11), residues: 1974 sheet: -0.90 (0.23), residues: 501 loop : -1.24 (0.16), residues: 1385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 229 TYR 0.014 0.001 TYR I 7 PHE 0.011 0.001 PHE J 247 TRP 0.010 0.001 TRP J 482 HIS 0.004 0.001 HIS C 48 Details of bonding type rmsd covalent geometry : bond 0.00429 (30315) covalent geometry : angle 0.64107 (41246) hydrogen bonds : bond 0.17669 ( 1888) hydrogen bonds : angle 6.09732 ( 5523) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7720 Ramachandran restraints generated. 3860 Oldfield, 0 Emsley, 3860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7720 Ramachandran restraints generated. 3860 Oldfield, 0 Emsley, 3860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1325 residues out of total 3232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 1320 time to evaluate : 1.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.7104 (t0) cc_final: 0.6595 (t0) REVERT: A 56 TYR cc_start: 0.6733 (m-80) cc_final: 0.6286 (m-80) REVERT: A 128 ASN cc_start: 0.7287 (t0) cc_final: 0.7021 (t0) REVERT: A 173 GLN cc_start: 0.7293 (mm-40) cc_final: 0.6969 (mm-40) REVERT: A 184 ASN cc_start: 0.7408 (t0) cc_final: 0.7171 (t0) REVERT: A 187 MET cc_start: 0.8025 (mmm) cc_final: 0.7771 (mmm) REVERT: A 205 GLU cc_start: 0.7527 (tp30) cc_final: 0.7318 (tp30) REVERT: A 216 THR cc_start: 0.8350 (m) cc_final: 0.8064 (t) REVERT: A 225 TYR cc_start: 0.7999 (m-80) cc_final: 0.7205 (m-80) REVERT: A 247 VAL cc_start: 0.8929 (t) cc_final: 0.8574 (m) REVERT: A 259 LYS cc_start: 0.7908 (mtmm) cc_final: 0.7521 (mtmm) REVERT: A 284 LYS cc_start: 0.7786 (mtpp) cc_final: 0.7258 (mtpp) REVERT: A 294 MET cc_start: 0.5498 (mmm) cc_final: 0.5170 (mmm) REVERT: A 340 SER cc_start: 0.7663 (t) cc_final: 0.7374 (p) REVERT: B 50 GLU cc_start: 0.7405 (mm-30) cc_final: 0.7164 (mm-30) REVERT: B 66 SER cc_start: 0.7861 (t) cc_final: 0.7631 (p) REVERT: B 84 LYS cc_start: 0.7702 (mttp) cc_final: 0.7409 (mttp) REVERT: B 133 LYS cc_start: 0.7386 (mtpp) cc_final: 0.7135 (mtpp) REVERT: B 141 SER cc_start: 0.6752 (t) cc_final: 0.6218 (p) REVERT: B 142 ASP cc_start: 0.5687 (t0) cc_final: 0.4317 (t0) REVERT: B 143 TYR cc_start: 0.7742 (t80) cc_final: 0.7464 (t80) REVERT: B 145 ARG cc_start: 0.7670 (mtm-85) cc_final: 0.7358 (mtt-85) REVERT: B 161 GLN cc_start: 0.7939 (tp40) cc_final: 0.7606 (tp-100) REVERT: B 165 ASP cc_start: 0.7086 (m-30) cc_final: 0.6876 (m-30) REVERT: B 187 MET cc_start: 0.7447 (mmm) cc_final: 0.7244 (mtm) REVERT: B 195 ASP cc_start: 0.7266 (m-30) cc_final: 0.6759 (m-30) REVERT: B 207 ARG cc_start: 0.7624 (mtt90) cc_final: 0.7396 (mtt-85) REVERT: B 258 PHE cc_start: 0.7604 (m-80) cc_final: 0.7293 (m-80) REVERT: B 300 PHE cc_start: 0.7742 (m-10) cc_final: 0.7513 (m-10) REVERT: B 332 GLN cc_start: 0.7141 (tm-30) cc_final: 0.6469 (tm-30) REVERT: B 333 TYR cc_start: 0.7787 (m-80) cc_final: 0.7457 (m-80) REVERT: B 368 THR cc_start: 0.7199 (t) cc_final: 0.6870 (t) REVERT: B 386 LYS cc_start: 0.7717 (tttt) cc_final: 0.7427 (tttt) REVERT: C 56 TYR cc_start: 0.7286 (m-80) cc_final: 0.6773 (m-80) REVERT: C 106 THR cc_start: 0.7963 (p) cc_final: 0.7678 (m) REVERT: C 130 GLU cc_start: 0.7568 (tp30) cc_final: 0.7290 (tp30) REVERT: C 154 LEU cc_start: 0.7229 (mp) cc_final: 0.6726 (mt) REVERT: C 185 GLN cc_start: 0.6965 (tp40) cc_final: 0.6688 (tm-30) REVERT: C 195 ASP cc_start: 0.7821 (m-30) cc_final: 0.7620 (m-30) REVERT: C 200 GLN cc_start: 0.7349 (mt0) cc_final: 0.7087 (mt0) REVERT: C 266 MET cc_start: 0.7311 (mtm) cc_final: 0.7070 (mtp) REVERT: D 64 ILE cc_start: 0.8446 (mm) cc_final: 0.8197 (mm) REVERT: D 138 LYS cc_start: 0.7322 (tttt) cc_final: 0.6665 (tttt) REVERT: D 184 ASN cc_start: 0.7514 (t0) cc_final: 0.7310 (t0) REVERT: D 187 MET cc_start: 0.7377 (mmm) cc_final: 0.6769 (tpp) REVERT: D 218 ILE cc_start: 0.7914 (mt) cc_final: 0.7663 (mt) REVERT: D 219 ILE cc_start: 0.8209 (mm) cc_final: 0.7863 (mm) REVERT: D 225 TYR cc_start: 0.8325 (m-80) cc_final: 0.8045 (m-80) REVERT: D 237 ILE cc_start: 0.8509 (mm) cc_final: 0.8028 (tt) REVERT: D 259 LYS cc_start: 0.7767 (mttt) cc_final: 0.6716 (mmtp) REVERT: D 265 ASN cc_start: 0.6933 (m-40) cc_final: 0.6602 (m110) REVERT: D 288 LYS cc_start: 0.8346 (ptpt) cc_final: 0.7823 (mtmm) REVERT: D 304 PRO cc_start: 0.7330 (Cg_endo) cc_final: 0.7112 (Cg_exo) REVERT: D 313 ILE cc_start: 0.7605 (mp) cc_final: 0.7391 (mp) REVERT: D 353 GLN cc_start: 0.6792 (pt0) cc_final: 0.5957 (pt0) REVERT: D 357 ASN cc_start: 0.7853 (p0) cc_final: 0.7580 (p0) REVERT: D 372 ILE cc_start: 0.8634 (mp) cc_final: 0.8432 (mm) REVERT: D 378 ASN cc_start: 0.7956 (m-40) cc_final: 0.7671 (m110) REVERT: D 384 ILE cc_start: 0.8259 (mt) cc_final: 0.7935 (mm) REVERT: E 53 ASP cc_start: 0.6811 (t70) cc_final: 0.5936 (t70) REVERT: E 93 ASP cc_start: 0.8214 (t0) cc_final: 0.7864 (t70) REVERT: E 103 LYS cc_start: 0.7259 (tttm) cc_final: 0.7030 (tttm) REVERT: E 133 LYS cc_start: 0.7921 (ttmm) cc_final: 0.7663 (mtpp) REVERT: E 192 LYS cc_start: 0.7603 (mmmm) cc_final: 0.6637 (mmmm) REVERT: E 200 GLN cc_start: 0.7650 (mm-40) cc_final: 0.7280 (mp10) REVERT: E 201 GLN cc_start: 0.8306 (tt0) cc_final: 0.8026 (tt0) REVERT: E 211 LEU cc_start: 0.8684 (mt) cc_final: 0.8475 (mt) REVERT: E 225 TYR cc_start: 0.8582 (m-80) cc_final: 0.7388 (m-80) REVERT: E 229 ARG cc_start: 0.7991 (ttp80) cc_final: 0.7488 (ptm-80) REVERT: E 283 VAL cc_start: 0.8472 (t) cc_final: 0.8237 (m) REVERT: E 294 MET cc_start: 0.6658 (mmm) cc_final: 0.6173 (mmp) REVERT: F 138 LYS cc_start: 0.7312 (ttpt) cc_final: 0.7010 (ttpp) REVERT: F 141 SER cc_start: 0.8106 (m) cc_final: 0.7489 (p) REVERT: F 154 LEU cc_start: 0.6562 (mt) cc_final: 0.6247 (mp) REVERT: F 196 GLN cc_start: 0.8219 (mm-40) cc_final: 0.7670 (mm-40) REVERT: F 206 VAL cc_start: 0.8300 (t) cc_final: 0.7824 (p) REVERT: F 217 ARG cc_start: 0.7602 (mtt180) cc_final: 0.6825 (ptp-110) REVERT: F 244 MET cc_start: 0.7508 (ptm) cc_final: 0.7302 (ptp) REVERT: F 251 ASN cc_start: 0.7497 (m110) cc_final: 0.7286 (m-40) REVERT: F 273 THR cc_start: 0.8284 (m) cc_final: 0.7992 (t) REVERT: F 274 ILE cc_start: 0.8091 (mp) cc_final: 0.7873 (mm) REVERT: F 283 VAL cc_start: 0.7154 (p) cc_final: 0.6880 (m) REVERT: F 294 MET cc_start: 0.6057 (mtp) cc_final: 0.5802 (mtp) REVERT: F 373 SER cc_start: 0.8504 (t) cc_final: 0.8054 (p) REVERT: F 383 ASP cc_start: 0.7343 (m-30) cc_final: 0.7060 (m-30) REVERT: J 28 LEU cc_start: 0.7824 (tp) cc_final: 0.7498 (tt) REVERT: J 44 LEU cc_start: 0.7350 (mt) cc_final: 0.7116 (mt) REVERT: J 161 ILE cc_start: 0.7747 (mm) cc_final: 0.7500 (mm) REVERT: J 184 MET cc_start: 0.7470 (mtm) cc_final: 0.7104 (mtm) REVERT: J 219 MET cc_start: 0.7122 (tmt) cc_final: 0.6860 (tmt) REVERT: J 220 LEU cc_start: 0.7571 (mt) cc_final: 0.7205 (mm) REVERT: J 299 TYR cc_start: 0.7536 (m-80) cc_final: 0.7235 (m-80) REVERT: J 301 TYR cc_start: 0.7618 (m-80) cc_final: 0.7202 (m-80) REVERT: J 327 PHE cc_start: 0.6177 (t80) cc_final: 0.5748 (t80) REVERT: J 357 PRO cc_start: 0.8179 (Cg_exo) cc_final: 0.7701 (Cg_endo) REVERT: J 382 LEU cc_start: 0.7236 (tp) cc_final: 0.6934 (tt) REVERT: J 411 SER cc_start: 0.7821 (m) cc_final: 0.7487 (p) REVERT: J 421 TRP cc_start: 0.7097 (t60) cc_final: 0.6833 (t60) REVERT: J 447 TYR cc_start: 0.8329 (m-80) cc_final: 0.7847 (m-80) REVERT: J 458 GLN cc_start: 0.7542 (tt0) cc_final: 0.7299 (tt0) REVERT: J 487 ILE cc_start: 0.8106 (mt) cc_final: 0.7812 (mm) REVERT: G 19 LYS cc_start: 0.6677 (tttm) cc_final: 0.6298 (tttm) REVERT: G 23 ASP cc_start: 0.6497 (m-30) cc_final: 0.6127 (m-30) REVERT: G 29 GLU cc_start: 0.5714 (tp30) cc_final: 0.5472 (tp30) REVERT: G 47 ASP cc_start: 0.5784 (p0) cc_final: 0.5426 (p0) REVERT: G 95 ASP cc_start: 0.7130 (t70) cc_final: 0.6795 (t0) REVERT: G 103 GLN cc_start: 0.7101 (mt0) cc_final: 0.6814 (mm-40) REVERT: G 127 GLN cc_start: 0.7548 (tm-30) cc_final: 0.7227 (tm-30) REVERT: G 181 GLN cc_start: 0.8055 (mm-40) cc_final: 0.7763 (tp40) REVERT: G 186 THR cc_start: 0.7328 (p) cc_final: 0.5965 (p) REVERT: G 215 GLU cc_start: 0.6430 (tm-30) cc_final: 0.5687 (tm-30) REVERT: G 221 LEU cc_start: 0.7333 (mt) cc_final: 0.6828 (mm) REVERT: G 242 ASP cc_start: 0.5771 (t0) cc_final: 0.5447 (t0) REVERT: G 303 LYS cc_start: 0.7743 (mtpp) cc_final: 0.7187 (mtpp) REVERT: G 317 GLU cc_start: 0.7170 (tp30) cc_final: 0.6740 (tp30) REVERT: G 321 ARG cc_start: 0.7320 (mtt180) cc_final: 0.6984 (mtt180) REVERT: G 368 THR cc_start: 0.7859 (t) cc_final: 0.7503 (m) REVERT: G 374 ASP cc_start: 0.7509 (t70) cc_final: 0.7020 (t0) REVERT: G 391 TYR cc_start: 0.7772 (m-10) cc_final: 0.7516 (m-80) REVERT: G 401 LYS cc_start: 0.8095 (tptm) cc_final: 0.7881 (tppp) REVERT: H 7 TYR cc_start: 0.7509 (t80) cc_final: 0.7253 (t80) REVERT: H 29 GLU cc_start: 0.6751 (tp30) cc_final: 0.6484 (tp30) REVERT: H 223 LEU cc_start: 0.8179 (mt) cc_final: 0.7875 (mt) REVERT: H 237 ILE cc_start: 0.8208 (mt) cc_final: 0.7248 (mt) REVERT: H 248 LEU cc_start: 0.7170 (mt) cc_final: 0.6811 (mt) REVERT: H 302 VAL cc_start: 0.7725 (t) cc_final: 0.7146 (m) REVERT: H 337 SER cc_start: 0.8275 (m) cc_final: 0.7990 (p) REVERT: H 356 ASP cc_start: 0.7145 (t0) cc_final: 0.6884 (t0) REVERT: H 374 ASP cc_start: 0.6769 (t0) cc_final: 0.6504 (t0) REVERT: H 412 LEU cc_start: 0.7265 (tp) cc_final: 0.7003 (tt) REVERT: I 8 GLN cc_start: 0.7726 (mm-40) cc_final: 0.7267 (mm-40) REVERT: I 29 GLU cc_start: 0.6321 (tp30) cc_final: 0.6060 (tp30) REVERT: I 42 LEU cc_start: 0.6720 (tt) cc_final: 0.5445 (tt) REVERT: I 130 LYS cc_start: 0.8395 (ttpt) cc_final: 0.8130 (ttpt) REVERT: I 145 ASN cc_start: 0.7731 (t0) cc_final: 0.7494 (t0) REVERT: I 158 ARG cc_start: 0.7577 (mtt180) cc_final: 0.7356 (mtt180) REVERT: I 168 GLU cc_start: 0.7155 (tt0) cc_final: 0.6389 (tt0) REVERT: I 212 LEU cc_start: 0.8543 (tp) cc_final: 0.8212 (tt) REVERT: I 215 GLU cc_start: 0.7189 (tp30) cc_final: 0.6906 (tp30) REVERT: I 223 LEU cc_start: 0.8331 (pp) cc_final: 0.6966 (mt) REVERT: I 224 LEU cc_start: 0.8137 (tp) cc_final: 0.7610 (mp) REVERT: I 225 GLN cc_start: 0.6867 (tm-30) cc_final: 0.6565 (tm-30) REVERT: I 232 LEU cc_start: 0.8146 (pp) cc_final: 0.7756 (pp) REVERT: I 235 GLU cc_start: 0.6956 (tp30) cc_final: 0.6709 (tp30) REVERT: I 394 LEU cc_start: 0.8494 (mt) cc_final: 0.8185 (mm) REVERT: I 395 ILE cc_start: 0.8591 (mm) cc_final: 0.8160 (mm) REVERT: I 398 LEU cc_start: 0.8311 (tp) cc_final: 0.8070 (tp) outliers start: 5 outliers final: 0 residues processed: 1325 average time/residue: 0.2267 time to fit residues: 460.5721 Evaluate side-chains 1089 residues out of total 3232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1089 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 0.1980 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 4.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN A 180 GLN A 200 GLN A 311 ASN B 162 HIS B 171 GLN B 180 GLN B 265 ASN C 61 GLN C 124 GLN C 179 GLN C 232 GLN D 182 ASN D 306 GLN E 117 GLN E 124 GLN E 201 GLN E 236 GLN E 257 ASN F 162 HIS ** F 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 346 ASN G 8 GLN ** G 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 173 ASN G 241 GLN G 299 ASN G 315 GLN H 8 GLN H 14 ASN H 103 GLN H 155 GLN H 173 ASN ** H 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 230 GLN H 244 HIS I 87 GLN I 184 GLN I 220 ASN ** I 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 320 HIS I 325 GLN I 332 ASN I 335 ASN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.117262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.099200 restraints weight = 59714.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.102228 restraints weight = 26316.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.104104 restraints weight = 14196.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.105278 restraints weight = 8892.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.106068 restraints weight = 6322.892| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.3846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 30315 Z= 0.247 Angle : 0.716 10.023 41246 Z= 0.380 Chirality : 0.047 0.295 4889 Planarity : 0.006 0.088 5392 Dihedral : 4.309 23.056 4179 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.56 % Allowed : 15.13 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.59 (0.14), residues: 3860 helix: 2.78 (0.11), residues: 2025 sheet: -0.69 (0.23), residues: 505 loop : -1.03 (0.16), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG J 424 TYR 0.040 0.002 TYR G 307 PHE 0.023 0.002 PHE I 331 TRP 0.034 0.002 TRP E 312 HIS 0.006 0.001 HIS J 428 Details of bonding type rmsd covalent geometry : bond 0.00515 (30315) covalent geometry : angle 0.71646 (41246) hydrogen bonds : bond 0.07794 ( 1888) hydrogen bonds : angle 4.75419 ( 5523) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7720 Ramachandran restraints generated. 3860 Oldfield, 0 Emsley, 3860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7720 Ramachandran restraints generated. 3860 Oldfield, 0 Emsley, 3860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1395 residues out of total 3232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 1280 time to evaluate : 1.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 PHE cc_start: 0.6957 (m-80) cc_final: 0.6587 (m-80) REVERT: A 50 GLU cc_start: 0.6722 (mm-30) cc_final: 0.6419 (mm-30) REVERT: A 53 ASP cc_start: 0.6945 (t0) cc_final: 0.6420 (t0) REVERT: A 56 TYR cc_start: 0.7672 (m-80) cc_final: 0.6997 (m-80) REVERT: A 79 ASN cc_start: 0.7787 (t0) cc_final: 0.7568 (t0) REVERT: A 122 SER cc_start: 0.8114 (m) cc_final: 0.7669 (t) REVERT: A 128 ASN cc_start: 0.8397 (t0) cc_final: 0.7953 (t0) REVERT: A 130 GLU cc_start: 0.7406 (mm-30) cc_final: 0.6738 (mm-30) REVERT: A 133 LYS cc_start: 0.8347 (mtpt) cc_final: 0.8119 (mtpp) REVERT: A 138 LYS cc_start: 0.8028 (mttt) cc_final: 0.7510 (tttm) REVERT: A 146 ARG cc_start: 0.7729 (ttm-80) cc_final: 0.7321 (mtt90) REVERT: A 151 ASN cc_start: 0.7586 (m-40) cc_final: 0.7346 (m-40) REVERT: A 154 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8446 (mp) REVERT: A 158 GLU cc_start: 0.7875 (tt0) cc_final: 0.7438 (tt0) REVERT: A 173 GLN cc_start: 0.7701 (mm-40) cc_final: 0.7269 (mm-40) REVERT: A 205 GLU cc_start: 0.7065 (tp30) cc_final: 0.6733 (tp30) REVERT: A 225 TYR cc_start: 0.8185 (m-80) cc_final: 0.7148 (m-80) REVERT: A 247 VAL cc_start: 0.8743 (t) cc_final: 0.8385 (m) REVERT: A 259 LYS cc_start: 0.8151 (mtmm) cc_final: 0.7723 (mtmm) REVERT: A 284 LYS cc_start: 0.7440 (mtpp) cc_final: 0.7170 (mtpp) REVERT: A 293 ASP cc_start: 0.7381 (t0) cc_final: 0.6926 (t0) REVERT: A 306 GLN cc_start: 0.6488 (tp-100) cc_final: 0.6226 (tp-100) REVERT: A 332 GLN cc_start: 0.7514 (mm-40) cc_final: 0.7262 (mp10) REVERT: B 49 PHE cc_start: 0.7393 (m-10) cc_final: 0.6778 (m-10) REVERT: B 84 LYS cc_start: 0.7463 (mttp) cc_final: 0.7130 (mttp) REVERT: B 101 PHE cc_start: 0.7604 (t80) cc_final: 0.7259 (t80) REVERT: B 117 GLN cc_start: 0.7462 (OUTLIER) cc_final: 0.6991 (tt0) REVERT: B 133 LYS cc_start: 0.7766 (mtpp) cc_final: 0.7546 (mtpp) REVERT: B 142 ASP cc_start: 0.6740 (t0) cc_final: 0.5721 (t0) REVERT: B 143 TYR cc_start: 0.8507 (t80) cc_final: 0.8179 (t80) REVERT: B 145 ARG cc_start: 0.8174 (mtt-85) cc_final: 0.7129 (mtt-85) REVERT: B 146 ARG cc_start: 0.7455 (mtt-85) cc_final: 0.6900 (mtt-85) REVERT: B 157 ARG cc_start: 0.7086 (mtp-110) cc_final: 0.6697 (mtm110) REVERT: B 158 GLU cc_start: 0.7445 (tt0) cc_final: 0.7216 (tt0) REVERT: B 161 GLN cc_start: 0.8144 (tp40) cc_final: 0.7743 (tp40) REVERT: B 164 ARG cc_start: 0.7460 (ttm-80) cc_final: 0.7020 (ttm-80) REVERT: B 171 GLN cc_start: 0.7877 (tp40) cc_final: 0.7662 (tp-100) REVERT: B 195 ASP cc_start: 0.6682 (m-30) cc_final: 0.6272 (m-30) REVERT: B 207 ARG cc_start: 0.7340 (mtt90) cc_final: 0.7137 (mtt-85) REVERT: B 244 MET cc_start: 0.8001 (ptp) cc_final: 0.7769 (ptp) REVERT: B 265 ASN cc_start: 0.7831 (m-40) cc_final: 0.7611 (m-40) REVERT: B 284 LYS cc_start: 0.8264 (mtpt) cc_final: 0.7921 (mtpt) REVERT: B 328 LYS cc_start: 0.7806 (mmpt) cc_final: 0.7263 (mmpt) REVERT: B 330 LEU cc_start: 0.8051 (tt) cc_final: 0.7710 (tp) REVERT: B 368 THR cc_start: 0.7364 (t) cc_final: 0.7114 (p) REVERT: B 371 GLU cc_start: 0.6964 (mt-10) cc_final: 0.6729 (mt-10) REVERT: B 386 LYS cc_start: 0.8072 (tttt) cc_final: 0.7727 (tttt) REVERT: C 83 VAL cc_start: 0.7322 (m) cc_final: 0.7043 (p) REVERT: C 130 GLU cc_start: 0.7695 (tp30) cc_final: 0.7454 (tp30) REVERT: C 142 ASP cc_start: 0.7225 (t70) cc_final: 0.6012 (t0) REVERT: C 154 LEU cc_start: 0.8196 (mp) cc_final: 0.7990 (mt) REVERT: C 158 GLU cc_start: 0.7490 (tt0) cc_final: 0.7257 (tt0) REVERT: C 161 GLN cc_start: 0.7707 (tp40) cc_final: 0.6599 (tp40) REVERT: C 164 ARG cc_start: 0.7027 (ttp80) cc_final: 0.6377 (ttp80) REVERT: C 195 ASP cc_start: 0.7524 (m-30) cc_final: 0.7073 (m-30) REVERT: C 200 GLN cc_start: 0.7064 (mt0) cc_final: 0.6606 (mt0) REVERT: C 231 VAL cc_start: 0.8169 (t) cc_final: 0.7712 (p) REVERT: C 257 ASN cc_start: 0.7863 (m-40) cc_final: 0.7661 (m110) REVERT: C 288 LYS cc_start: 0.7645 (mtmm) cc_final: 0.7362 (mtmm) REVERT: C 302 LEU cc_start: 0.8647 (tp) cc_final: 0.8400 (tt) REVERT: C 312 TRP cc_start: 0.7977 (t60) cc_final: 0.7754 (t60) REVERT: C 328 LYS cc_start: 0.8252 (mttt) cc_final: 0.7984 (mttt) REVERT: C 332 GLN cc_start: 0.7060 (tp40) cc_final: 0.6767 (tp40) REVERT: C 379 LYS cc_start: 0.7656 (ttmt) cc_final: 0.7410 (ttmt) REVERT: D 50 GLU cc_start: 0.6643 (tp30) cc_final: 0.6209 (tp30) REVERT: D 54 ASP cc_start: 0.6832 (t0) cc_final: 0.6263 (t0) REVERT: D 117 GLN cc_start: 0.7758 (tt0) cc_final: 0.7250 (tt0) REVERT: D 121 ASN cc_start: 0.7735 (m-40) cc_final: 0.7495 (m-40) REVERT: D 138 LYS cc_start: 0.8192 (tttt) cc_final: 0.7452 (tttt) REVERT: D 219 ILE cc_start: 0.8221 (mm) cc_final: 0.7942 (mm) REVERT: D 247 VAL cc_start: 0.8901 (t) cc_final: 0.8596 (m) REVERT: D 253 TRP cc_start: 0.8527 (p90) cc_final: 0.8170 (p90) REVERT: D 259 LYS cc_start: 0.8125 (mttt) cc_final: 0.7829 (mttm) REVERT: D 309 THR cc_start: 0.7674 (p) cc_final: 0.7316 (m) REVERT: D 311 ASN cc_start: 0.7297 (p0) cc_final: 0.7002 (p0) REVERT: D 314 LYS cc_start: 0.7515 (tttt) cc_final: 0.7230 (tttp) REVERT: D 327 GLN cc_start: 0.7833 (mm-40) cc_final: 0.7489 (mm-40) REVERT: D 331 GLU cc_start: 0.7004 (mp0) cc_final: 0.6385 (mp0) REVERT: D 345 VAL cc_start: 0.8475 (t) cc_final: 0.8156 (m) REVERT: D 353 GLN cc_start: 0.6791 (pt0) cc_final: 0.6224 (pt0) REVERT: D 357 ASN cc_start: 0.7811 (p0) cc_final: 0.7571 (p0) REVERT: D 366 VAL cc_start: 0.8696 (t) cc_final: 0.8487 (p) REVERT: D 378 ASN cc_start: 0.7951 (m-40) cc_final: 0.7179 (m-40) REVERT: D 382 ASP cc_start: 0.7136 (m-30) cc_final: 0.6771 (m-30) REVERT: E 53 ASP cc_start: 0.7057 (t70) cc_final: 0.6475 (t70) REVERT: E 65 MET cc_start: 0.7243 (mmm) cc_final: 0.6959 (mmm) REVERT: E 103 LYS cc_start: 0.7422 (tttm) cc_final: 0.7207 (tttm) REVERT: E 133 LYS cc_start: 0.8125 (ttmm) cc_final: 0.7816 (mttp) REVERT: E 154 LEU cc_start: 0.7154 (mt) cc_final: 0.6807 (mt) REVERT: E 160 LEU cc_start: 0.7874 (tp) cc_final: 0.7574 (tp) REVERT: E 161 GLN cc_start: 0.7864 (tt0) cc_final: 0.7094 (tm-30) REVERT: E 165 ASP cc_start: 0.7615 (m-30) cc_final: 0.6035 (m-30) REVERT: E 189 LEU cc_start: 0.8270 (mt) cc_final: 0.7963 (mt) REVERT: E 204 THR cc_start: 0.8645 (p) cc_final: 0.8415 (t) REVERT: E 210 TRP cc_start: 0.8385 (t60) cc_final: 0.7990 (t60) REVERT: E 229 ARG cc_start: 0.7866 (ttp80) cc_final: 0.7661 (ptm-80) REVERT: E 237 ILE cc_start: 0.8654 (pp) cc_final: 0.8450 (pt) REVERT: E 240 THR cc_start: 0.7884 (p) cc_final: 0.7534 (m) REVERT: E 251 ASN cc_start: 0.7120 (t0) cc_final: 0.6844 (t0) REVERT: E 260 GLU cc_start: 0.7329 (pt0) cc_final: 0.7055 (pt0) REVERT: E 294 MET cc_start: 0.6689 (mmm) cc_final: 0.6345 (mmp) REVERT: E 312 TRP cc_start: 0.8197 (t60) cc_final: 0.7561 (t60) REVERT: E 346 ASN cc_start: 0.7874 (m-40) cc_final: 0.7556 (m-40) REVERT: F 49 PHE cc_start: 0.7796 (m-80) cc_final: 0.7525 (m-80) REVERT: F 105 LYS cc_start: 0.7966 (mttt) cc_final: 0.7751 (mtmt) REVERT: F 138 LYS cc_start: 0.8237 (ttpt) cc_final: 0.7972 (ttpp) REVERT: F 141 SER cc_start: 0.8370 (m) cc_final: 0.8152 (t) REVERT: F 153 ASN cc_start: 0.7165 (m-40) cc_final: 0.6812 (m110) REVERT: F 158 GLU cc_start: 0.7000 (tp30) cc_final: 0.6523 (tp30) REVERT: F 167 VAL cc_start: 0.8258 (t) cc_final: 0.8056 (p) REVERT: F 175 ASP cc_start: 0.7315 (m-30) cc_final: 0.7071 (m-30) REVERT: F 192 LYS cc_start: 0.8051 (mttp) cc_final: 0.7659 (mttp) REVERT: F 196 GLN cc_start: 0.8082 (mm-40) cc_final: 0.7695 (mm-40) REVERT: F 200 GLN cc_start: 0.7119 (mp10) cc_final: 0.6818 (mp10) REVERT: F 214 GLU cc_start: 0.7439 (tp30) cc_final: 0.6587 (mp0) REVERT: F 217 ARG cc_start: 0.6881 (mtt180) cc_final: 0.6613 (ttm110) REVERT: F 222 MET cc_start: 0.6932 (ptp) cc_final: 0.6704 (ptp) REVERT: F 273 THR cc_start: 0.8210 (m) cc_final: 0.7975 (t) REVERT: F 274 ILE cc_start: 0.8041 (mp) cc_final: 0.7817 (mt) REVERT: F 288 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.7954 (mtmt) REVERT: F 314 LYS cc_start: 0.8055 (ttmm) cc_final: 0.7669 (tppt) REVERT: F 364 VAL cc_start: 0.7954 (t) cc_final: 0.7662 (p) REVERT: F 379 LYS cc_start: 0.7515 (tptm) cc_final: 0.6853 (tptm) REVERT: F 383 ASP cc_start: 0.6986 (m-30) cc_final: 0.6444 (m-30) REVERT: J 21 LEU cc_start: 0.8161 (mt) cc_final: 0.7917 (mm) REVERT: J 40 ILE cc_start: 0.8254 (mt) cc_final: 0.7939 (pt) REVERT: J 82 PHE cc_start: 0.8123 (t80) cc_final: 0.7839 (t80) REVERT: J 87 ILE cc_start: 0.8529 (tt) cc_final: 0.8185 (pt) REVERT: J 109 ARG cc_start: 0.8088 (mmm160) cc_final: 0.7568 (ttt90) REVERT: J 122 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7594 (mp) REVERT: J 123 SER cc_start: 0.7187 (t) cc_final: 0.6704 (m) REVERT: J 184 MET cc_start: 0.7629 (mtm) cc_final: 0.7201 (mtm) REVERT: J 219 MET cc_start: 0.7225 (tmt) cc_final: 0.6945 (tmt) REVERT: J 251 TRP cc_start: 0.6010 (t-100) cc_final: 0.5788 (t-100) REVERT: J 271 THR cc_start: 0.8171 (m) cc_final: 0.7898 (p) REVERT: J 301 TYR cc_start: 0.8386 (m-80) cc_final: 0.8171 (m-80) REVERT: J 308 LEU cc_start: 0.8026 (mt) cc_final: 0.7640 (mt) REVERT: J 319 ILE cc_start: 0.7878 (mt) cc_final: 0.7672 (pt) REVERT: J 333 MET cc_start: 0.7168 (mtm) cc_final: 0.6450 (mtm) REVERT: J 339 PHE cc_start: 0.7906 (t80) cc_final: 0.7587 (t80) REVERT: J 342 ILE cc_start: 0.8172 (mm) cc_final: 0.7935 (tp) REVERT: J 357 PRO cc_start: 0.8473 (Cg_exo) cc_final: 0.8160 (Cg_endo) REVERT: J 382 LEU cc_start: 0.7833 (tp) cc_final: 0.7626 (tt) REVERT: J 384 THR cc_start: 0.7693 (m) cc_final: 0.7392 (p) REVERT: J 403 ASN cc_start: 0.8326 (m-40) cc_final: 0.7803 (m-40) REVERT: J 424 ARG cc_start: 0.7360 (ttt-90) cc_final: 0.7075 (mmm160) REVERT: J 447 TYR cc_start: 0.8366 (m-80) cc_final: 0.8125 (m-80) REVERT: J 458 GLN cc_start: 0.7975 (tt0) cc_final: 0.7630 (tt0) REVERT: J 459 GLN cc_start: 0.7885 (mt0) cc_final: 0.7679 (mt0) REVERT: J 479 GLU cc_start: 0.7099 (mm-30) cc_final: 0.6774 (mt-10) REVERT: J 482 TRP cc_start: 0.7801 (t60) cc_final: 0.7540 (t60) REVERT: J 491 LEU cc_start: 0.8111 (mt) cc_final: 0.7708 (pp) REVERT: G 3 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8428 (tp) REVERT: G 5 GLN cc_start: 0.8206 (mt0) cc_final: 0.7794 (mt0) REVERT: G 7 TYR cc_start: 0.8579 (t80) cc_final: 0.8363 (t80) REVERT: G 9 GLN cc_start: 0.7020 (tm-30) cc_final: 0.6705 (tm-30) REVERT: G 11 ARG cc_start: 0.7905 (OUTLIER) cc_final: 0.7031 (ttp-110) REVERT: G 17 LEU cc_start: 0.8414 (mp) cc_final: 0.8075 (tt) REVERT: G 18 ARG cc_start: 0.7391 (OUTLIER) cc_final: 0.7110 (mtt-85) REVERT: G 29 GLU cc_start: 0.7465 (tp30) cc_final: 0.6279 (tp30) REVERT: G 30 LYS cc_start: 0.8673 (tttt) cc_final: 0.8381 (tttt) REVERT: G 32 ASN cc_start: 0.8022 (m-40) cc_final: 0.6792 (p0) REVERT: G 81 TRP cc_start: 0.7353 (m100) cc_final: 0.7084 (m100) REVERT: G 84 LEU cc_start: 0.9246 (mt) cc_final: 0.8933 (tp) REVERT: G 87 GLN cc_start: 0.8441 (tp40) cc_final: 0.8028 (tp40) REVERT: G 88 GLU cc_start: 0.8070 (pt0) cc_final: 0.7827 (pt0) REVERT: G 98 TYR cc_start: 0.8283 (t80) cc_final: 0.7884 (t80) REVERT: G 99 GLN cc_start: 0.7897 (tm-30) cc_final: 0.7162 (tm-30) REVERT: G 101 ASP cc_start: 0.7829 (t70) cc_final: 0.7616 (t0) REVERT: G 103 GLN cc_start: 0.8323 (mt0) cc_final: 0.7892 (mm-40) REVERT: G 104 THR cc_start: 0.8748 (m) cc_final: 0.8378 (p) REVERT: G 127 GLN cc_start: 0.8029 (tm-30) cc_final: 0.7757 (tm-30) REVERT: G 130 LYS cc_start: 0.8763 (tttt) cc_final: 0.8098 (ttpp) REVERT: G 138 ASP cc_start: 0.8159 (t0) cc_final: 0.7575 (t0) REVERT: G 158 ARG cc_start: 0.7483 (tpt170) cc_final: 0.7202 (tpt170) REVERT: G 168 GLU cc_start: 0.8253 (tt0) cc_final: 0.7938 (tt0) REVERT: G 169 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.7928 (mm) REVERT: G 181 GLN cc_start: 0.8566 (mm-40) cc_final: 0.7651 (tm-30) REVERT: G 185 ILE cc_start: 0.8394 (tp) cc_final: 0.8150 (tt) REVERT: G 215 GLU cc_start: 0.7436 (tm-30) cc_final: 0.6590 (tm-30) REVERT: G 217 GLU cc_start: 0.7994 (tm-30) cc_final: 0.7665 (mm-30) REVERT: G 225 GLN cc_start: 0.8314 (tm-30) cc_final: 0.8109 (tm-30) REVERT: G 230 GLN cc_start: 0.8536 (OUTLIER) cc_final: 0.8017 (pp30) REVERT: G 236 GLN cc_start: 0.8401 (mt0) cc_final: 0.7936 (mp10) REVERT: G 299 ASN cc_start: 0.8161 (m110) cc_final: 0.7681 (m-40) REVERT: G 303 LYS cc_start: 0.8614 (mtpp) cc_final: 0.8315 (mtpp) REVERT: G 307 TYR cc_start: 0.7851 (m-80) cc_final: 0.7597 (m-80) REVERT: G 314 GLU cc_start: 0.7930 (mm-30) cc_final: 0.7660 (mm-30) REVERT: G 317 GLU cc_start: 0.7936 (tp30) cc_final: 0.7018 (tp30) REVERT: G 321 ARG cc_start: 0.8466 (mtt180) cc_final: 0.7767 (mtt180) REVERT: G 344 TYR cc_start: 0.8147 (m-80) cc_final: 0.7943 (m-80) REVERT: G 385 GLU cc_start: 0.7621 (mm-30) cc_final: 0.7037 (mm-30) REVERT: G 397 GLN cc_start: 0.7778 (OUTLIER) cc_final: 0.7574 (mt0) REVERT: G 401 LYS cc_start: 0.8593 (tptm) cc_final: 0.8163 (tppp) REVERT: G 407 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.7996 (pp) REVERT: H 14 ASN cc_start: 0.7721 (t0) cc_final: 0.7170 (t0) REVERT: H 24 ARG cc_start: 0.8354 (ttp80) cc_final: 0.8118 (ttp80) REVERT: H 29 GLU cc_start: 0.7838 (tp30) cc_final: 0.6880 (tp30) REVERT: H 30 LYS cc_start: 0.8548 (ttpt) cc_final: 0.8081 (ttpt) REVERT: H 88 GLU cc_start: 0.8344 (mt-10) cc_final: 0.8091 (mt-10) REVERT: H 89 LYS cc_start: 0.8777 (mmmt) cc_final: 0.8320 (mmmt) REVERT: H 94 GLN cc_start: 0.7997 (tp40) cc_final: 0.7748 (tp40) REVERT: H 98 TYR cc_start: 0.8403 (t80) cc_final: 0.8200 (t80) REVERT: H 123 LEU cc_start: 0.8613 (tp) cc_final: 0.8096 (mt) REVERT: H 130 LYS cc_start: 0.8941 (ttpp) cc_final: 0.8329 (ttpp) REVERT: H 139 GLN cc_start: 0.8197 (tt0) cc_final: 0.7940 (tm-30) REVERT: H 168 GLU cc_start: 0.8181 (tt0) cc_final: 0.6841 (tt0) REVERT: H 169 LEU cc_start: 0.8780 (tt) cc_final: 0.8386 (tp) REVERT: H 179 VAL cc_start: 0.8840 (t) cc_final: 0.8582 (m) REVERT: H 180 GLU cc_start: 0.8414 (mm-30) cc_final: 0.8150 (mm-30) REVERT: H 181 GLN cc_start: 0.7966 (tm-30) cc_final: 0.7743 (tm-30) REVERT: H 184 GLN cc_start: 0.8276 (tt0) cc_final: 0.7693 (tm-30) REVERT: H 224 LEU cc_start: 0.8408 (mp) cc_final: 0.8083 (mm) REVERT: H 230 GLN cc_start: 0.7999 (tp40) cc_final: 0.7513 (tp40) REVERT: H 231 ASP cc_start: 0.7594 (t0) cc_final: 0.7264 (t0) REVERT: H 236 GLN cc_start: 0.7867 (tm-30) cc_final: 0.7487 (pp30) REVERT: H 237 ILE cc_start: 0.8799 (mt) cc_final: 0.8464 (mt) REVERT: H 238 ARG cc_start: 0.8212 (mtt180) cc_final: 0.7731 (mtt180) REVERT: H 245 LEU cc_start: 0.8374 (mt) cc_final: 0.7889 (mt) REVERT: H 301 GLN cc_start: 0.8470 (mt0) cc_final: 0.8158 (mp10) REVERT: H 302 VAL cc_start: 0.8231 (t) cc_final: 0.7888 (p) REVERT: H 314 GLU cc_start: 0.7787 (mm-30) cc_final: 0.7469 (mm-30) REVERT: H 317 GLU cc_start: 0.7543 (tp30) cc_final: 0.7199 (tp30) REVERT: H 320 HIS cc_start: 0.7406 (m90) cc_final: 0.7188 (m90) REVERT: H 321 ARG cc_start: 0.8279 (mtt180) cc_final: 0.7823 (mtt180) REVERT: H 337 SER cc_start: 0.8762 (m) cc_final: 0.8106 (p) REVERT: H 340 SER cc_start: 0.8835 (m) cc_final: 0.8314 (p) REVERT: H 356 ASP cc_start: 0.8200 (t0) cc_final: 0.7944 (t0) REVERT: H 374 ASP cc_start: 0.7925 (t0) cc_final: 0.7544 (t0) REVERT: H 412 LEU cc_start: 0.8465 (tp) cc_final: 0.8179 (tp) REVERT: H 421 LYS cc_start: 0.8689 (mttt) cc_final: 0.8470 (mttt) REVERT: I 8 GLN cc_start: 0.8252 (mm-40) cc_final: 0.7818 (mm-40) REVERT: I 28 PHE cc_start: 0.8308 (m-80) cc_final: 0.8056 (m-80) REVERT: I 29 GLU cc_start: 0.7596 (tp30) cc_final: 0.6778 (tp30) REVERT: I 31 ILE cc_start: 0.9071 (mt) cc_final: 0.8803 (mm) REVERT: I 42 LEU cc_start: 0.7557 (tt) cc_final: 0.6730 (tp) REVERT: I 99 GLN cc_start: 0.8323 (mt0) cc_final: 0.8074 (mt0) REVERT: I 103 GLN cc_start: 0.8470 (mt0) cc_final: 0.8115 (mm-40) REVERT: I 118 ASN cc_start: 0.8471 (t0) cc_final: 0.8188 (t0) REVERT: I 124 SER cc_start: 0.8507 (t) cc_final: 0.8292 (p) REVERT: I 143 ARG cc_start: 0.7514 (mtp85) cc_final: 0.7284 (mtp85) REVERT: I 158 ARG cc_start: 0.7707 (mtt180) cc_final: 0.7481 (mtt180) REVERT: I 162 ASP cc_start: 0.8740 (m-30) cc_final: 0.7916 (m-30) REVERT: I 212 LEU cc_start: 0.9158 (tp) cc_final: 0.8829 (tt) REVERT: I 213 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8765 (mt) REVERT: I 215 GLU cc_start: 0.8019 (tp30) cc_final: 0.7423 (tp30) REVERT: I 224 LEU cc_start: 0.8894 (tp) cc_final: 0.8651 (mt) REVERT: I 235 GLU cc_start: 0.7913 (tp30) cc_final: 0.7360 (tp30) REVERT: I 236 GLN cc_start: 0.8238 (mt0) cc_final: 0.8002 (mt0) REVERT: I 238 ARG cc_start: 0.8090 (mpt180) cc_final: 0.7655 (mpt180) REVERT: I 301 GLN cc_start: 0.8417 (tt0) cc_final: 0.8207 (mt0) REVERT: I 303 LYS cc_start: 0.8730 (mtpp) cc_final: 0.8314 (mtpp) REVERT: I 306 GLN cc_start: 0.8462 (pt0) cc_final: 0.8012 (mt0) REVERT: I 394 LEU cc_start: 0.8789 (mt) cc_final: 0.8570 (mm) REVERT: I 396 ASN cc_start: 0.8334 (m-40) cc_final: 0.7841 (m-40) outliers start: 115 outliers final: 58 residues processed: 1327 average time/residue: 0.2359 time to fit residues: 474.0777 Evaluate side-chains 1275 residues out of total 3232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 1205 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 288 LYS Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain B residue 117 GLN Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 344 SER Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain C residue 187 MET Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 340 SER Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain D residue 84 LYS Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 169 SER Chi-restraints excluded: chain D residue 337 ILE Chi-restraints excluded: chain D residue 379 LYS Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 214 GLU Chi-restraints excluded: chain E residue 273 THR Chi-restraints excluded: chain E residue 275 THR Chi-restraints excluded: chain E residue 284 LYS Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain E residue 344 SER Chi-restraints excluded: chain E residue 355 LEU Chi-restraints excluded: chain E residue 371 GLU Chi-restraints excluded: chain E residue 386 LYS Chi-restraints excluded: chain F residue 110 SER Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 162 HIS Chi-restraints excluded: chain F residue 194 GLU Chi-restraints excluded: chain F residue 237 ILE Chi-restraints excluded: chain F residue 288 LYS Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain F residue 380 LEU Chi-restraints excluded: chain F residue 386 LYS Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 39 THR Chi-restraints excluded: chain J residue 46 SER Chi-restraints excluded: chain J residue 122 LEU Chi-restraints excluded: chain J residue 408 LEU Chi-restraints excluded: chain G residue 3 LEU Chi-restraints excluded: chain G residue 11 ARG Chi-restraints excluded: chain G residue 18 ARG Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain G residue 183 ARG Chi-restraints excluded: chain G residue 230 GLN Chi-restraints excluded: chain G residue 232 LEU Chi-restraints excluded: chain G residue 397 GLN Chi-restraints excluded: chain G residue 407 LEU Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 221 LEU Chi-restraints excluded: chain H residue 310 VAL Chi-restraints excluded: chain H residue 353 SER Chi-restraints excluded: chain H residue 404 LEU Chi-restraints excluded: chain H residue 413 LEU Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 203 THR Chi-restraints excluded: chain I residue 213 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 267 optimal weight: 3.9990 chunk 341 optimal weight: 3.9990 chunk 344 optimal weight: 7.9990 chunk 329 optimal weight: 4.9990 chunk 182 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 342 optimal weight: 1.9990 chunk 110 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 ASN A 116 HIS A 124 GLN A 200 GLN B 114 GLN B 200 GLN B 349 ASN C 117 GLN D 388 ASN E 63 GLN ** E 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 311 ASN ** F 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 208 ASN F 251 ASN F 306 GLN ** F 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 346 ASN J 34 ASN J 444 GLN ** G 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 8 GLN H 136 GLN H 139 GLN H 155 GLN H 184 GLN H 294 GLN H 320 HIS H 396 ASN I 58 ASN I 127 GLN I 188 ASN I 320 HIS I 325 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.111264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.093276 restraints weight = 59431.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.096204 restraints weight = 26401.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.098042 restraints weight = 14340.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.099196 restraints weight = 9026.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.099978 restraints weight = 6450.848| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.5421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.101 30315 Z= 0.374 Angle : 0.756 11.065 41246 Z= 0.413 Chirality : 0.050 0.288 4889 Planarity : 0.006 0.076 5392 Dihedral : 4.853 24.476 4179 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 5.17 % Allowed : 18.19 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.00 (0.13), residues: 3860 helix: 2.20 (0.11), residues: 2027 sheet: -0.62 (0.23), residues: 496 loop : -1.29 (0.16), residues: 1337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG I 234 TYR 0.031 0.002 TYR G 293 PHE 0.030 0.003 PHE B 101 TRP 0.028 0.003 TRP J 482 HIS 0.020 0.002 HIS F 162 Details of bonding type rmsd covalent geometry : bond 0.00778 (30315) covalent geometry : angle 0.75568 (41246) hydrogen bonds : bond 0.08220 ( 1888) hydrogen bonds : angle 5.02864 ( 5523) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7720 Ramachandran restraints generated. 3860 Oldfield, 0 Emsley, 3860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7720 Ramachandran restraints generated. 3860 Oldfield, 0 Emsley, 3860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1491 residues out of total 3232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 1324 time to evaluate : 1.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.6866 (mm-30) cc_final: 0.6567 (mm-30) REVERT: A 54 ASP cc_start: 0.7755 (t0) cc_final: 0.6789 (t0) REVERT: A 57 VAL cc_start: 0.8522 (t) cc_final: 0.8246 (p) REVERT: A 79 ASN cc_start: 0.7756 (t0) cc_final: 0.7519 (t0) REVERT: A 133 LYS cc_start: 0.8316 (mtpt) cc_final: 0.8083 (mtpt) REVERT: A 138 LYS cc_start: 0.8239 (mttt) cc_final: 0.7640 (mttt) REVERT: A 143 TYR cc_start: 0.8318 (t80) cc_final: 0.7991 (t80) REVERT: A 146 ARG cc_start: 0.7999 (ttm-80) cc_final: 0.7566 (mtt90) REVERT: A 154 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8417 (mp) REVERT: A 158 GLU cc_start: 0.7863 (tt0) cc_final: 0.7372 (tt0) REVERT: A 161 GLN cc_start: 0.7332 (pt0) cc_final: 0.6463 (pt0) REVERT: A 165 ASP cc_start: 0.6764 (m-30) cc_final: 0.6545 (m-30) REVERT: A 173 GLN cc_start: 0.7900 (mm-40) cc_final: 0.7634 (mm110) REVERT: A 200 GLN cc_start: 0.7571 (mt0) cc_final: 0.7278 (mm-40) REVERT: A 247 VAL cc_start: 0.8804 (t) cc_final: 0.8449 (m) REVERT: A 259 LYS cc_start: 0.8232 (mtmm) cc_final: 0.7867 (mtmm) REVERT: A 284 LYS cc_start: 0.7415 (mtpp) cc_final: 0.7177 (mtpp) REVERT: A 306 GLN cc_start: 0.6904 (OUTLIER) cc_final: 0.6582 (tp-100) REVERT: A 347 THR cc_start: 0.7338 (OUTLIER) cc_final: 0.6763 (p) REVERT: A 371 GLU cc_start: 0.7368 (pm20) cc_final: 0.7057 (pm20) REVERT: A 379 LYS cc_start: 0.8001 (tttt) cc_final: 0.7761 (tttt) REVERT: A 381 ILE cc_start: 0.8605 (mt) cc_final: 0.8282 (mm) REVERT: B 50 GLU cc_start: 0.7584 (mm-30) cc_final: 0.7239 (mm-30) REVERT: B 75 VAL cc_start: 0.8510 (t) cc_final: 0.8283 (m) REVERT: B 93 ASP cc_start: 0.7939 (t0) cc_final: 0.7680 (t70) REVERT: B 98 ARG cc_start: 0.7344 (tpp80) cc_final: 0.7087 (ttm-80) REVERT: B 123 LYS cc_start: 0.7655 (mttp) cc_final: 0.7365 (mttp) REVERT: B 130 GLU cc_start: 0.7305 (mm-30) cc_final: 0.6946 (tm-30) REVERT: B 138 LYS cc_start: 0.8510 (ttpp) cc_final: 0.8212 (ttpp) REVERT: B 142 ASP cc_start: 0.7171 (t0) cc_final: 0.6645 (t0) REVERT: B 145 ARG cc_start: 0.7943 (mtt-85) cc_final: 0.7070 (mtt-85) REVERT: B 157 ARG cc_start: 0.6882 (mtp-110) cc_final: 0.6537 (mtm110) REVERT: B 158 GLU cc_start: 0.7297 (tt0) cc_final: 0.7087 (tt0) REVERT: B 160 LEU cc_start: 0.8909 (tp) cc_final: 0.8706 (tt) REVERT: B 161 GLN cc_start: 0.8200 (tp40) cc_final: 0.7648 (mm-40) REVERT: B 164 ARG cc_start: 0.7304 (ttm-80) cc_final: 0.7074 (ttm-80) REVERT: B 171 GLN cc_start: 0.8072 (tp40) cc_final: 0.7747 (tp-100) REVERT: B 179 GLN cc_start: 0.7662 (mm-40) cc_final: 0.7418 (mm-40) REVERT: B 187 MET cc_start: 0.6877 (OUTLIER) cc_final: 0.6475 (mtm) REVERT: B 194 GLU cc_start: 0.7401 (pp20) cc_final: 0.6961 (pp20) REVERT: B 195 ASP cc_start: 0.6492 (m-30) cc_final: 0.6156 (m-30) REVERT: B 207 ARG cc_start: 0.7453 (mtt90) cc_final: 0.7102 (mtt-85) REVERT: B 259 LYS cc_start: 0.7836 (mtmt) cc_final: 0.7520 (mtmt) REVERT: B 284 LYS cc_start: 0.8093 (mtpt) cc_final: 0.7784 (mtpt) REVERT: B 294 MET cc_start: 0.6961 (OUTLIER) cc_final: 0.6706 (mtp) REVERT: B 316 VAL cc_start: 0.8445 (OUTLIER) cc_final: 0.8087 (t) REVERT: B 317 GLN cc_start: 0.7737 (mm-40) cc_final: 0.7471 (mm-40) REVERT: B 327 GLN cc_start: 0.7285 (tm-30) cc_final: 0.6136 (tm-30) REVERT: B 328 LYS cc_start: 0.8240 (mmpt) cc_final: 0.7165 (mmpt) REVERT: B 330 LEU cc_start: 0.8226 (tt) cc_final: 0.7924 (tp) REVERT: B 358 LYS cc_start: 0.7950 (ttpp) cc_final: 0.7748 (ttpp) REVERT: B 371 GLU cc_start: 0.7070 (mt-10) cc_final: 0.6852 (mt-10) REVERT: B 379 LYS cc_start: 0.8275 (tttt) cc_final: 0.8016 (ttmt) REVERT: B 386 LYS cc_start: 0.8288 (tttt) cc_final: 0.7958 (tttt) REVERT: C 53 ASP cc_start: 0.6894 (t0) cc_final: 0.6632 (t0) REVERT: C 54 ASP cc_start: 0.7343 (t0) cc_final: 0.6870 (t0) REVERT: C 103 LYS cc_start: 0.7871 (tttt) cc_final: 0.7550 (tttt) REVERT: C 117 GLN cc_start: 0.7446 (mt0) cc_final: 0.6782 (mt0) REVERT: C 121 ASN cc_start: 0.7200 (m-40) cc_final: 0.6729 (m-40) REVERT: C 123 LYS cc_start: 0.7840 (mtmt) cc_final: 0.7618 (mtmt) REVERT: C 154 LEU cc_start: 0.8653 (mp) cc_final: 0.8399 (mt) REVERT: C 155 ILE cc_start: 0.8405 (tp) cc_final: 0.8183 (tp) REVERT: C 158 GLU cc_start: 0.7760 (tt0) cc_final: 0.7511 (tt0) REVERT: C 161 GLN cc_start: 0.7704 (tp40) cc_final: 0.6279 (tp40) REVERT: C 164 ARG cc_start: 0.6928 (ttp80) cc_final: 0.6231 (ttp80) REVERT: C 179 GLN cc_start: 0.8254 (mm-40) cc_final: 0.7998 (mm-40) REVERT: C 195 ASP cc_start: 0.7510 (m-30) cc_final: 0.6931 (m-30) REVERT: C 200 GLN cc_start: 0.7039 (mt0) cc_final: 0.6578 (mt0) REVERT: C 231 VAL cc_start: 0.8379 (OUTLIER) cc_final: 0.8054 (p) REVERT: C 257 ASN cc_start: 0.7875 (m-40) cc_final: 0.7256 (m110) REVERT: C 259 LYS cc_start: 0.7693 (mttm) cc_final: 0.6507 (mtmm) REVERT: C 296 THR cc_start: 0.7527 (p) cc_final: 0.7145 (t) REVERT: C 328 LYS cc_start: 0.8273 (mttt) cc_final: 0.8063 (mttt) REVERT: C 340 SER cc_start: 0.8516 (OUTLIER) cc_final: 0.8274 (p) REVERT: C 379 LYS cc_start: 0.7668 (ttmt) cc_final: 0.7457 (ttmt) REVERT: D 50 GLU cc_start: 0.6863 (OUTLIER) cc_final: 0.6362 (tp30) REVERT: D 54 ASP cc_start: 0.7025 (t0) cc_final: 0.6408 (t0) REVERT: D 73 THR cc_start: 0.8550 (m) cc_final: 0.8255 (m) REVERT: D 110 SER cc_start: 0.8578 (t) cc_final: 0.8354 (m) REVERT: D 117 GLN cc_start: 0.7984 (tt0) cc_final: 0.7438 (tt0) REVERT: D 121 ASN cc_start: 0.8005 (m-40) cc_final: 0.7578 (m-40) REVERT: D 123 LYS cc_start: 0.8213 (OUTLIER) cc_final: 0.7983 (mttm) REVERT: D 138 LYS cc_start: 0.8278 (tttt) cc_final: 0.7977 (tttt) REVERT: D 189 LEU cc_start: 0.7601 (tp) cc_final: 0.7376 (tt) REVERT: D 219 ILE cc_start: 0.8230 (mm) cc_final: 0.8014 (mm) REVERT: D 247 VAL cc_start: 0.8846 (t) cc_final: 0.8561 (m) REVERT: D 253 TRP cc_start: 0.8409 (p90) cc_final: 0.8082 (p90) REVERT: D 259 LYS cc_start: 0.8213 (mttt) cc_final: 0.7935 (mttm) REVERT: D 309 THR cc_start: 0.7800 (p) cc_final: 0.7440 (m) REVERT: D 314 LYS cc_start: 0.7355 (tttt) cc_final: 0.7117 (tttt) REVERT: D 315 VAL cc_start: 0.9035 (t) cc_final: 0.8651 (m) REVERT: D 323 ILE cc_start: 0.8166 (mp) cc_final: 0.7963 (mt) REVERT: D 324 GLU cc_start: 0.6720 (tm-30) cc_final: 0.6464 (tm-30) REVERT: D 331 GLU cc_start: 0.7037 (mp0) cc_final: 0.6637 (mp0) REVERT: D 332 GLN cc_start: 0.7420 (tp40) cc_final: 0.7015 (tp40) REVERT: D 345 VAL cc_start: 0.8524 (t) cc_final: 0.8140 (m) REVERT: D 378 ASN cc_start: 0.8008 (m-40) cc_final: 0.7243 (m-40) REVERT: D 382 ASP cc_start: 0.7269 (m-30) cc_final: 0.6892 (m-30) REVERT: E 53 ASP cc_start: 0.7083 (t70) cc_final: 0.5789 (t0) REVERT: E 85 GLU cc_start: 0.6952 (mm-30) cc_final: 0.6572 (tm-30) REVERT: E 138 LYS cc_start: 0.7825 (tttm) cc_final: 0.7224 (tttm) REVERT: E 142 ASP cc_start: 0.7428 (m-30) cc_final: 0.7037 (m-30) REVERT: E 153 ASN cc_start: 0.7681 (m-40) cc_final: 0.6836 (p0) REVERT: E 154 LEU cc_start: 0.8214 (mt) cc_final: 0.7741 (mt) REVERT: E 161 GLN cc_start: 0.7997 (tt0) cc_final: 0.7384 (tp-100) REVERT: E 164 ARG cc_start: 0.7429 (ttp80) cc_final: 0.7115 (ttp80) REVERT: E 165 ASP cc_start: 0.7590 (m-30) cc_final: 0.6987 (m-30) REVERT: E 181 TYR cc_start: 0.8231 (t80) cc_final: 0.7796 (t80) REVERT: E 189 LEU cc_start: 0.8172 (mt) cc_final: 0.7824 (mt) REVERT: E 196 GLN cc_start: 0.7856 (OUTLIER) cc_final: 0.7219 (mp10) REVERT: E 207 ARG cc_start: 0.8448 (ttm110) cc_final: 0.8158 (ttm110) REVERT: E 210 TRP cc_start: 0.8408 (t60) cc_final: 0.8142 (t60) REVERT: E 236 GLN cc_start: 0.7504 (mm-40) cc_final: 0.7296 (mm-40) REVERT: E 237 ILE cc_start: 0.8788 (pp) cc_final: 0.8573 (pt) REVERT: E 251 ASN cc_start: 0.7227 (t0) cc_final: 0.6858 (t0) REVERT: E 260 GLU cc_start: 0.7258 (pt0) cc_final: 0.7047 (pt0) REVERT: E 294 MET cc_start: 0.6778 (mmm) cc_final: 0.6341 (tpp) REVERT: E 346 ASN cc_start: 0.7914 (m-40) cc_final: 0.7690 (m-40) REVERT: F 49 PHE cc_start: 0.7780 (m-80) cc_final: 0.7353 (m-80) REVERT: F 105 LYS cc_start: 0.8182 (mttt) cc_final: 0.7870 (mtmm) REVERT: F 120 ILE cc_start: 0.8522 (OUTLIER) cc_final: 0.8256 (mp) REVERT: F 122 SER cc_start: 0.8410 (m) cc_final: 0.8115 (p) REVERT: F 133 LYS cc_start: 0.7943 (mttt) cc_final: 0.7734 (mttt) REVERT: F 138 LYS cc_start: 0.8422 (ttpt) cc_final: 0.8116 (tttp) REVERT: F 141 SER cc_start: 0.8578 (m) cc_final: 0.8276 (m) REVERT: F 145 ARG cc_start: 0.7288 (mtm-85) cc_final: 0.6968 (mtm-85) REVERT: F 158 GLU cc_start: 0.7090 (tp30) cc_final: 0.6482 (tp30) REVERT: F 161 GLN cc_start: 0.7493 (tp40) cc_final: 0.6521 (tp-100) REVERT: F 162 HIS cc_start: 0.7803 (OUTLIER) cc_final: 0.7039 (m-70) REVERT: F 178 ILE cc_start: 0.8142 (mt) cc_final: 0.7908 (mm) REVERT: F 192 LYS cc_start: 0.8099 (mttp) cc_final: 0.7750 (mttp) REVERT: F 200 GLN cc_start: 0.7276 (mp10) cc_final: 0.6668 (mp10) REVERT: F 214 GLU cc_start: 0.7558 (tp30) cc_final: 0.6791 (mp0) REVERT: F 217 ARG cc_start: 0.6934 (mtt180) cc_final: 0.6487 (ttm-80) REVERT: F 228 ARG cc_start: 0.7018 (mtt180) cc_final: 0.6748 (mtm-85) REVERT: F 288 LYS cc_start: 0.8337 (OUTLIER) cc_final: 0.7829 (mtmt) REVERT: F 317 GLN cc_start: 0.7325 (mm-40) cc_final: 0.7106 (mp10) REVERT: F 364 VAL cc_start: 0.7817 (t) cc_final: 0.7578 (p) REVERT: F 373 SER cc_start: 0.8423 (t) cc_final: 0.7957 (p) REVERT: F 379 LYS cc_start: 0.7703 (tptm) cc_final: 0.7189 (tptm) REVERT: F 383 ASP cc_start: 0.7129 (m-30) cc_final: 0.6752 (m-30) REVERT: J 21 LEU cc_start: 0.8272 (mt) cc_final: 0.7959 (mm) REVERT: J 40 ILE cc_start: 0.8237 (mt) cc_final: 0.7915 (pt) REVERT: J 66 ILE cc_start: 0.8572 (mt) cc_final: 0.8251 (mm) REVERT: J 87 ILE cc_start: 0.8680 (tt) cc_final: 0.8422 (pt) REVERT: J 104 MET cc_start: 0.7160 (ttp) cc_final: 0.6937 (ttp) REVERT: J 109 ARG cc_start: 0.8223 (mmm160) cc_final: 0.7995 (ttt90) REVERT: J 114 ILE cc_start: 0.8291 (mm) cc_final: 0.8066 (mm) REVERT: J 119 LEU cc_start: 0.7704 (mm) cc_final: 0.7482 (mm) REVERT: J 120 ILE cc_start: 0.7991 (mm) cc_final: 0.7730 (mt) REVERT: J 122 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.7766 (mp) REVERT: J 130 ASN cc_start: 0.6872 (m-40) cc_final: 0.6592 (m-40) REVERT: J 131 TYR cc_start: 0.7265 (OUTLIER) cc_final: 0.6987 (t80) REVERT: J 145 MET cc_start: 0.6738 (tmm) cc_final: 0.6170 (tmm) REVERT: J 161 ILE cc_start: 0.8308 (mm) cc_final: 0.7958 (mp) REVERT: J 171 PHE cc_start: 0.8176 (m-80) cc_final: 0.7966 (m-80) REVERT: J 184 MET cc_start: 0.7591 (mtm) cc_final: 0.7380 (mtm) REVERT: J 216 LEU cc_start: 0.8561 (tp) cc_final: 0.8191 (tt) REVERT: J 217 GLN cc_start: 0.7835 (tp40) cc_final: 0.7573 (tp40) REVERT: J 219 MET cc_start: 0.7388 (tmt) cc_final: 0.7073 (tmt) REVERT: J 235 ILE cc_start: 0.8098 (mt) cc_final: 0.7874 (mm) REVERT: J 251 TRP cc_start: 0.6889 (t-100) cc_final: 0.6347 (t-100) REVERT: J 270 PHE cc_start: 0.8571 (t80) cc_final: 0.8194 (t80) REVERT: J 271 THR cc_start: 0.8363 (m) cc_final: 0.8115 (p) REVERT: J 297 GLU cc_start: 0.7421 (tt0) cc_final: 0.7132 (tt0) REVERT: J 308 LEU cc_start: 0.8027 (mt) cc_final: 0.7626 (mt) REVERT: J 327 PHE cc_start: 0.6708 (t80) cc_final: 0.5962 (t80) REVERT: J 333 MET cc_start: 0.7459 (mtm) cc_final: 0.6952 (mtm) REVERT: J 334 ARG cc_start: 0.7853 (mtm180) cc_final: 0.7627 (mtm180) REVERT: J 339 PHE cc_start: 0.8043 (t80) cc_final: 0.7803 (t80) REVERT: J 342 ILE cc_start: 0.8381 (mm) cc_final: 0.8145 (tp) REVERT: J 357 PRO cc_start: 0.8558 (Cg_exo) cc_final: 0.8281 (Cg_endo) REVERT: J 384 THR cc_start: 0.8295 (m) cc_final: 0.7945 (p) REVERT: J 390 LEU cc_start: 0.8464 (tp) cc_final: 0.8109 (tp) REVERT: J 394 ARG cc_start: 0.7429 (mtm180) cc_final: 0.7039 (mtm110) REVERT: J 402 SER cc_start: 0.8072 (t) cc_final: 0.7769 (m) REVERT: J 403 ASN cc_start: 0.8449 (m-40) cc_final: 0.7819 (m-40) REVERT: J 406 ARG cc_start: 0.7415 (ttp80) cc_final: 0.7189 (ttp80) REVERT: J 408 LEU cc_start: 0.7611 (OUTLIER) cc_final: 0.7342 (tt) REVERT: J 421 TRP cc_start: 0.8194 (t60) cc_final: 0.7849 (t60) REVERT: J 447 TYR cc_start: 0.8497 (m-80) cc_final: 0.8274 (m-80) REVERT: J 458 GLN cc_start: 0.8298 (tt0) cc_final: 0.7954 (tt0) REVERT: J 459 GLN cc_start: 0.8078 (mt0) cc_final: 0.7598 (mt0) REVERT: J 466 GLN cc_start: 0.7824 (OUTLIER) cc_final: 0.7324 (mp10) REVERT: J 467 GLN cc_start: 0.8130 (mm-40) cc_final: 0.7895 (mm110) REVERT: J 471 GLN cc_start: 0.7861 (mm-40) cc_final: 0.7333 (mm-40) REVERT: J 479 GLU cc_start: 0.7076 (mm-30) cc_final: 0.6619 (mt-10) REVERT: J 491 LEU cc_start: 0.7994 (mt) cc_final: 0.7630 (pp) REVERT: G 3 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8544 (tp) REVERT: G 5 GLN cc_start: 0.8347 (mt0) cc_final: 0.7762 (mt0) REVERT: G 9 GLN cc_start: 0.6870 (tm-30) cc_final: 0.6521 (tm-30) REVERT: G 17 LEU cc_start: 0.8657 (mp) cc_final: 0.8352 (tt) REVERT: G 24 ARG cc_start: 0.7846 (tpt170) cc_final: 0.7243 (tpt170) REVERT: G 28 PHE cc_start: 0.7375 (t80) cc_final: 0.7141 (t80) REVERT: G 29 GLU cc_start: 0.7797 (tp30) cc_final: 0.6797 (tp30) REVERT: G 30 LYS cc_start: 0.8854 (tttt) cc_final: 0.8432 (tttt) REVERT: G 32 ASN cc_start: 0.8126 (m-40) cc_final: 0.6793 (p0) REVERT: G 42 LEU cc_start: 0.8447 (mp) cc_final: 0.8196 (mm) REVERT: G 70 GLN cc_start: 0.6984 (pm20) cc_final: 0.6736 (mp10) REVERT: G 76 PHE cc_start: 0.7320 (t80) cc_final: 0.7118 (t80) REVERT: G 77 ASP cc_start: 0.8685 (t0) cc_final: 0.5206 (p0) REVERT: G 81 TRP cc_start: 0.7377 (m100) cc_final: 0.7123 (m100) REVERT: G 87 GLN cc_start: 0.8499 (tp40) cc_final: 0.8120 (tp40) REVERT: G 88 GLU cc_start: 0.8126 (pt0) cc_final: 0.7925 (pt0) REVERT: G 99 GLN cc_start: 0.7702 (tm-30) cc_final: 0.7154 (tm-30) REVERT: G 101 ASP cc_start: 0.7840 (t70) cc_final: 0.7183 (t0) REVERT: G 103 GLN cc_start: 0.8361 (mt0) cc_final: 0.7908 (mm-40) REVERT: G 104 THR cc_start: 0.8761 (m) cc_final: 0.8528 (p) REVERT: G 130 LYS cc_start: 0.8789 (tttt) cc_final: 0.8274 (ttpp) REVERT: G 156 ASN cc_start: 0.8115 (t0) cc_final: 0.7797 (t0) REVERT: G 169 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8235 (mm) REVERT: G 181 GLN cc_start: 0.8553 (mm-40) cc_final: 0.7776 (tm-30) REVERT: G 185 ILE cc_start: 0.8486 (tp) cc_final: 0.8226 (tt) REVERT: G 215 GLU cc_start: 0.7594 (tm-30) cc_final: 0.6740 (tm-30) REVERT: G 217 GLU cc_start: 0.8035 (tm-30) cc_final: 0.7690 (mm-30) REVERT: G 225 GLN cc_start: 0.8387 (tm-30) cc_final: 0.8166 (tm-30) REVERT: G 230 GLN cc_start: 0.8529 (pt0) cc_final: 0.8136 (pp30) REVERT: G 232 LEU cc_start: 0.9254 (tt) cc_final: 0.8594 (tt) REVERT: G 236 GLN cc_start: 0.8337 (mt0) cc_final: 0.7967 (mm110) REVERT: G 279 MET cc_start: 0.4210 (tpt) cc_final: 0.3792 (tpt) REVERT: G 299 ASN cc_start: 0.8167 (m110) cc_final: 0.7788 (m-40) REVERT: G 303 LYS cc_start: 0.8747 (mtpp) cc_final: 0.8364 (mtpp) REVERT: G 315 GLN cc_start: 0.8670 (tp40) cc_final: 0.8161 (tp-100) REVERT: G 317 GLU cc_start: 0.7997 (tp30) cc_final: 0.7124 (tp30) REVERT: G 321 ARG cc_start: 0.8488 (mtt180) cc_final: 0.7975 (mtt180) REVERT: G 385 GLU cc_start: 0.7588 (mm-30) cc_final: 0.7010 (mm-30) REVERT: G 401 LYS cc_start: 0.8549 (tptm) cc_final: 0.8150 (tppp) REVERT: G 411 ASP cc_start: 0.5302 (t0) cc_final: 0.4436 (t0) REVERT: H 14 ASN cc_start: 0.8171 (t0) cc_final: 0.7660 (t0) REVERT: H 17 LEU cc_start: 0.8978 (mm) cc_final: 0.8623 (mm) REVERT: H 24 ARG cc_start: 0.8430 (ttp80) cc_final: 0.8159 (ttp80) REVERT: H 29 GLU cc_start: 0.7880 (tp30) cc_final: 0.7224 (tp30) REVERT: H 30 LYS cc_start: 0.8600 (ttpt) cc_final: 0.8018 (ttpt) REVERT: H 33 GLU cc_start: 0.7619 (pp20) cc_final: 0.7278 (pp20) REVERT: H 78 MET cc_start: 0.7052 (mtt) cc_final: 0.5605 (mtt) REVERT: H 88 GLU cc_start: 0.8431 (mt-10) cc_final: 0.8136 (mt-10) REVERT: H 89 LYS cc_start: 0.8818 (mmmt) cc_final: 0.8424 (mmmt) REVERT: H 135 ARG cc_start: 0.8087 (ttm-80) cc_final: 0.7444 (mmm160) REVERT: H 136 GLN cc_start: 0.8364 (tp40) cc_final: 0.7946 (tp40) REVERT: H 142 GLN cc_start: 0.8051 (mm-40) cc_final: 0.7799 (mm-40) REVERT: H 179 VAL cc_start: 0.8959 (t) cc_final: 0.8633 (p) REVERT: H 180 GLU cc_start: 0.8552 (mm-30) cc_final: 0.8051 (tm-30) REVERT: H 184 GLN cc_start: 0.8397 (tt0) cc_final: 0.7820 (tm-30) REVERT: H 218 LYS cc_start: 0.8791 (mmtt) cc_final: 0.8480 (mmtt) REVERT: H 224 LEU cc_start: 0.8689 (mp) cc_final: 0.8253 (mm) REVERT: H 230 GLN cc_start: 0.8064 (tp40) cc_final: 0.7452 (tp40) REVERT: H 231 ASP cc_start: 0.7777 (t0) cc_final: 0.7479 (t0) REVERT: H 236 GLN cc_start: 0.7836 (tm-30) cc_final: 0.7522 (tm-30) REVERT: H 237 ILE cc_start: 0.8811 (mt) cc_final: 0.8323 (mt) REVERT: H 241 GLN cc_start: 0.8057 (mt0) cc_final: 0.7709 (mt0) REVERT: H 288 PHE cc_start: 0.7669 (t80) cc_final: 0.7284 (t80) REVERT: H 302 VAL cc_start: 0.8438 (t) cc_final: 0.8136 (p) REVERT: H 314 GLU cc_start: 0.7735 (mm-30) cc_final: 0.7354 (mm-30) REVERT: H 317 GLU cc_start: 0.7711 (tp30) cc_final: 0.7319 (tp30) REVERT: H 321 ARG cc_start: 0.8377 (mtt180) cc_final: 0.7752 (mtt90) REVERT: H 340 SER cc_start: 0.8802 (m) cc_final: 0.8261 (p) REVERT: H 341 ILE cc_start: 0.8875 (OUTLIER) cc_final: 0.8641 (tt) REVERT: H 371 ASP cc_start: 0.7857 (m-30) cc_final: 0.7614 (m-30) REVERT: H 374 ASP cc_start: 0.7902 (t0) cc_final: 0.7380 (t0) REVERT: H 390 ARG cc_start: 0.8644 (mtt-85) cc_final: 0.8351 (ttm170) REVERT: H 392 ASN cc_start: 0.8396 (m-40) cc_final: 0.8006 (t0) REVERT: H 396 ASN cc_start: 0.8160 (m-40) cc_final: 0.7742 (m110) REVERT: H 412 LEU cc_start: 0.8579 (tp) cc_final: 0.8352 (tp) REVERT: I 8 GLN cc_start: 0.8453 (mm-40) cc_final: 0.8016 (mm-40) REVERT: I 11 ARG cc_start: 0.8049 (ttp80) cc_final: 0.7067 (ttp80) REVERT: I 19 LYS cc_start: 0.8631 (tttt) cc_final: 0.8411 (tptt) REVERT: I 25 ASP cc_start: 0.8261 (t0) cc_final: 0.7788 (t0) REVERT: I 28 PHE cc_start: 0.8312 (m-80) cc_final: 0.7946 (m-80) REVERT: I 35 ARG cc_start: 0.7698 (mtp-110) cc_final: 0.7466 (mtp-110) REVERT: I 42 LEU cc_start: 0.7605 (tt) cc_final: 0.7252 (tp) REVERT: I 76 PHE cc_start: 0.7596 (t80) cc_final: 0.7069 (t80) REVERT: I 95 ASP cc_start: 0.8234 (t0) cc_final: 0.7459 (t0) REVERT: I 99 GLN cc_start: 0.8319 (mt0) cc_final: 0.7893 (mt0) REVERT: I 103 GLN cc_start: 0.8525 (mt0) cc_final: 0.8282 (mm-40) REVERT: I 118 ASN cc_start: 0.8554 (t0) cc_final: 0.8057 (t0) REVERT: I 124 SER cc_start: 0.8663 (t) cc_final: 0.8434 (p) REVERT: I 138 ASP cc_start: 0.8455 (t0) cc_final: 0.8252 (t0) REVERT: I 215 GLU cc_start: 0.8108 (tp30) cc_final: 0.7523 (tp30) REVERT: I 217 GLU cc_start: 0.7525 (mm-30) cc_final: 0.7301 (mm-30) REVERT: I 224 LEU cc_start: 0.8905 (tp) cc_final: 0.8658 (mm) REVERT: I 225 GLN cc_start: 0.8004 (tm-30) cc_final: 0.7394 (tm-30) REVERT: I 235 GLU cc_start: 0.7901 (tp30) cc_final: 0.7544 (tp30) REVERT: I 236 GLN cc_start: 0.8328 (mt0) cc_final: 0.8021 (mt0) REVERT: I 238 ARG cc_start: 0.8192 (mpt180) cc_final: 0.7795 (mpt180) REVERT: I 241 GLN cc_start: 0.8130 (mp10) cc_final: 0.7640 (mm-40) REVERT: I 259 THR cc_start: 0.3560 (OUTLIER) cc_final: 0.3350 (m) REVERT: I 301 GLN cc_start: 0.8463 (tt0) cc_final: 0.7920 (mt0) REVERT: I 306 GLN cc_start: 0.8448 (pt0) cc_final: 0.8211 (pp30) REVERT: I 325 GLN cc_start: 0.8346 (OUTLIER) cc_final: 0.7962 (pp30) REVERT: I 396 ASN cc_start: 0.8344 (m-40) cc_final: 0.7862 (m-40) REVERT: I 401 LYS cc_start: 0.8904 (mmmt) cc_final: 0.8661 (mmmm) outliers start: 167 outliers final: 92 residues processed: 1400 average time/residue: 0.2266 time to fit residues: 481.4045 Evaluate side-chains 1351 residues out of total 3232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 1236 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 194 GLU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 288 LYS Chi-restraints excluded: chain A residue 306 GLN Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 294 MET Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 344 SER Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 187 MET Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 340 SER Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain D residue 84 LYS Chi-restraints excluded: chain D residue 123 LYS Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 169 SER Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 288 LYS Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 337 ILE Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 379 LYS Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 196 GLN Chi-restraints excluded: chain E residue 214 GLU Chi-restraints excluded: chain E residue 227 SER Chi-restraints excluded: chain E residue 273 THR Chi-restraints excluded: chain E residue 275 THR Chi-restraints excluded: chain E residue 284 LYS Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain E residue 344 SER Chi-restraints excluded: chain E residue 371 GLU Chi-restraints excluded: chain E residue 373 SER Chi-restraints excluded: chain E residue 386 LYS Chi-restraints excluded: chain F residue 110 SER Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 162 HIS Chi-restraints excluded: chain F residue 179 GLN Chi-restraints excluded: chain F residue 237 ILE Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 288 LYS Chi-restraints excluded: chain F residue 372 ILE Chi-restraints excluded: chain F residue 380 LEU Chi-restraints excluded: chain F residue 381 ILE Chi-restraints excluded: chain F residue 386 LYS Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 39 THR Chi-restraints excluded: chain J residue 48 LEU Chi-restraints excluded: chain J residue 122 LEU Chi-restraints excluded: chain J residue 131 TYR Chi-restraints excluded: chain J residue 166 HIS Chi-restraints excluded: chain J residue 293 GLN Chi-restraints excluded: chain J residue 371 GLN Chi-restraints excluded: chain J residue 408 LEU Chi-restraints excluded: chain J residue 466 GLN Chi-restraints excluded: chain J residue 494 LEU Chi-restraints excluded: chain G residue 3 LEU Chi-restraints excluded: chain G residue 11 ARG Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain G residue 177 ASN Chi-restraints excluded: chain G residue 203 THR Chi-restraints excluded: chain G residue 234 ARG Chi-restraints excluded: chain G residue 237 ILE Chi-restraints excluded: chain G residue 245 LEU Chi-restraints excluded: chain G residue 272 THR Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 143 ARG Chi-restraints excluded: chain H residue 221 LEU Chi-restraints excluded: chain H residue 286 LEU Chi-restraints excluded: chain H residue 310 VAL Chi-restraints excluded: chain H residue 315 GLN Chi-restraints excluded: chain H residue 341 ILE Chi-restraints excluded: chain H residue 353 SER Chi-restraints excluded: chain H residue 404 LEU Chi-restraints excluded: chain H residue 413 LEU Chi-restraints excluded: chain I residue 58 ASN Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 203 THR Chi-restraints excluded: chain I residue 259 THR Chi-restraints excluded: chain I residue 272 THR Chi-restraints excluded: chain I residue 325 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 268 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 230 optimal weight: 1.9990 chunk 272 optimal weight: 2.9990 chunk 360 optimal weight: 7.9990 chunk 344 optimal weight: 8.9990 chunk 231 optimal weight: 1.9990 chunk 264 optimal weight: 5.9990 chunk 130 optimal weight: 0.8980 chunk 137 optimal weight: 0.8980 chunk 296 optimal weight: 0.5980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN A 144 ASN A 200 GLN A 201 GLN B 173 GLN C 251 ASN ** D 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 306 GLN D 353 GLN E 185 GLN E 236 GLN F 67 GLN F 116 HIS ** F 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 208 ASN F 251 ASN F 306 GLN F 307 ASN F 327 GLN F 346 ASN J 34 ASN J 269 ASN J 449 GLN J 478 ASN G 14 ASN G 142 GLN ** G 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 94 GLN ** H 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 173 ASN ** H 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 320 HIS I 325 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.112080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.093955 restraints weight = 58351.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.096904 restraints weight = 25900.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.098734 restraints weight = 14112.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.099952 restraints weight = 8939.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.100595 restraints weight = 6357.860| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.5851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 30315 Z= 0.232 Angle : 0.654 14.583 41246 Z= 0.348 Chirality : 0.045 0.210 4889 Planarity : 0.005 0.069 5392 Dihedral : 4.490 21.809 4179 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 4.89 % Allowed : 21.07 % Favored : 74.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.44 (0.14), residues: 3860 helix: 2.65 (0.11), residues: 2026 sheet: -0.58 (0.23), residues: 503 loop : -1.18 (0.16), residues: 1331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 18 TYR 0.024 0.002 TYR G 293 PHE 0.030 0.002 PHE J 265 TRP 0.034 0.002 TRP C 312 HIS 0.009 0.001 HIS F 162 Details of bonding type rmsd covalent geometry : bond 0.00481 (30315) covalent geometry : angle 0.65443 (41246) hydrogen bonds : bond 0.07253 ( 1888) hydrogen bonds : angle 4.63106 ( 5523) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7720 Ramachandran restraints generated. 3860 Oldfield, 0 Emsley, 3860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7720 Ramachandran restraints generated. 3860 Oldfield, 0 Emsley, 3860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1412 residues out of total 3232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 1254 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 PHE cc_start: 0.7149 (m-80) cc_final: 0.6540 (m-80) REVERT: A 50 GLU cc_start: 0.6939 (mm-30) cc_final: 0.6638 (mm-30) REVERT: A 54 ASP cc_start: 0.7716 (t0) cc_final: 0.7148 (t0) REVERT: A 56 TYR cc_start: 0.7504 (m-80) cc_final: 0.6753 (m-80) REVERT: A 57 VAL cc_start: 0.8543 (t) cc_final: 0.8211 (p) REVERT: A 79 ASN cc_start: 0.7768 (t0) cc_final: 0.7566 (t0) REVERT: A 130 GLU cc_start: 0.7552 (mm-30) cc_final: 0.7108 (mm-30) REVERT: A 138 LYS cc_start: 0.8227 (mttt) cc_final: 0.7925 (tttp) REVERT: A 143 TYR cc_start: 0.8227 (t80) cc_final: 0.7955 (t80) REVERT: A 146 ARG cc_start: 0.7821 (ttm-80) cc_final: 0.7583 (mtt90) REVERT: A 154 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8386 (mp) REVERT: A 161 GLN cc_start: 0.7321 (pt0) cc_final: 0.6312 (pt0) REVERT: A 171 GLN cc_start: 0.8087 (tp40) cc_final: 0.7411 (tp40) REVERT: A 173 GLN cc_start: 0.7874 (mm-40) cc_final: 0.7589 (mm110) REVERT: A 175 ASP cc_start: 0.6889 (m-30) cc_final: 0.6360 (m-30) REVERT: A 201 GLN cc_start: 0.6958 (mm-40) cc_final: 0.6757 (mm110) REVERT: A 228 ARG cc_start: 0.7651 (mtm-85) cc_final: 0.7179 (mtm-85) REVERT: A 237 ILE cc_start: 0.8076 (mm) cc_final: 0.7746 (pt) REVERT: A 247 VAL cc_start: 0.8713 (t) cc_final: 0.8424 (m) REVERT: A 259 LYS cc_start: 0.8191 (mtmm) cc_final: 0.7821 (mtmm) REVERT: A 274 ILE cc_start: 0.7834 (mt) cc_final: 0.7598 (mm) REVERT: A 284 LYS cc_start: 0.7422 (mtpp) cc_final: 0.7112 (mtpp) REVERT: A 306 GLN cc_start: 0.6864 (tp-100) cc_final: 0.6459 (tp-100) REVERT: A 351 ASP cc_start: 0.7211 (m-30) cc_final: 0.6576 (m-30) REVERT: A 379 LYS cc_start: 0.7977 (tttt) cc_final: 0.7733 (tttt) REVERT: A 381 ILE cc_start: 0.8527 (mt) cc_final: 0.8167 (mm) REVERT: B 50 GLU cc_start: 0.7653 (mm-30) cc_final: 0.7273 (mm-30) REVERT: B 66 SER cc_start: 0.7872 (t) cc_final: 0.7602 (p) REVERT: B 93 ASP cc_start: 0.7929 (t0) cc_final: 0.7667 (t70) REVERT: B 98 ARG cc_start: 0.7308 (tpp80) cc_final: 0.7029 (ttm-80) REVERT: B 123 LYS cc_start: 0.7609 (mttp) cc_final: 0.7145 (mttp) REVERT: B 130 GLU cc_start: 0.7260 (mm-30) cc_final: 0.6940 (tm-30) REVERT: B 138 LYS cc_start: 0.8565 (ttpp) cc_final: 0.8363 (ttpp) REVERT: B 145 ARG cc_start: 0.7872 (mtt-85) cc_final: 0.6920 (mtt-85) REVERT: B 159 GLU cc_start: 0.7738 (tp30) cc_final: 0.7478 (tp30) REVERT: B 160 LEU cc_start: 0.8937 (tp) cc_final: 0.8681 (tt) REVERT: B 171 GLN cc_start: 0.8094 (tp40) cc_final: 0.7738 (tp40) REVERT: B 179 GLN cc_start: 0.7712 (mm-40) cc_final: 0.7048 (mm-40) REVERT: B 194 GLU cc_start: 0.7460 (pp20) cc_final: 0.6971 (pp20) REVERT: B 195 ASP cc_start: 0.6474 (m-30) cc_final: 0.6193 (m-30) REVERT: B 207 ARG cc_start: 0.7400 (mtt90) cc_final: 0.7186 (mtt-85) REVERT: B 259 LYS cc_start: 0.7863 (mtmt) cc_final: 0.7520 (mtmt) REVERT: B 284 LYS cc_start: 0.8001 (mtpt) cc_final: 0.7742 (mtpt) REVERT: B 293 ASP cc_start: 0.7217 (t0) cc_final: 0.6950 (t0) REVERT: B 294 MET cc_start: 0.7048 (OUTLIER) cc_final: 0.6611 (mtp) REVERT: B 316 VAL cc_start: 0.8457 (OUTLIER) cc_final: 0.8182 (t) REVERT: B 317 GLN cc_start: 0.7707 (mm-40) cc_final: 0.7411 (mm-40) REVERT: B 328 LYS cc_start: 0.8242 (mmpt) cc_final: 0.7752 (mmpt) REVERT: B 330 LEU cc_start: 0.8216 (tt) cc_final: 0.7873 (tp) REVERT: B 379 LYS cc_start: 0.8255 (tttt) cc_final: 0.8002 (ttmt) REVERT: B 386 LYS cc_start: 0.8159 (tttt) cc_final: 0.7776 (tttt) REVERT: C 53 ASP cc_start: 0.6871 (t0) cc_final: 0.6558 (t0) REVERT: C 54 ASP cc_start: 0.7376 (t0) cc_final: 0.7003 (t0) REVERT: C 103 LYS cc_start: 0.7976 (tttt) cc_final: 0.7646 (tttt) REVERT: C 121 ASN cc_start: 0.7214 (m-40) cc_final: 0.6713 (m-40) REVERT: C 123 LYS cc_start: 0.7858 (mtmt) cc_final: 0.7308 (mtmt) REVERT: C 138 LYS cc_start: 0.7822 (tttt) cc_final: 0.7372 (ttpp) REVERT: C 154 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8376 (mt) REVERT: C 158 GLU cc_start: 0.7762 (tt0) cc_final: 0.7390 (tt0) REVERT: C 164 ARG cc_start: 0.6903 (ttp80) cc_final: 0.6305 (ttp80) REVERT: C 179 GLN cc_start: 0.8220 (mm-40) cc_final: 0.7984 (mm-40) REVERT: C 195 ASP cc_start: 0.7536 (m-30) cc_final: 0.6976 (m-30) REVERT: C 200 GLN cc_start: 0.7001 (mt0) cc_final: 0.6514 (mt0) REVERT: C 231 VAL cc_start: 0.8319 (t) cc_final: 0.7965 (p) REVERT: C 257 ASN cc_start: 0.7892 (m-40) cc_final: 0.7320 (m110) REVERT: C 296 THR cc_start: 0.7542 (p) cc_final: 0.7103 (t) REVERT: C 340 SER cc_start: 0.8432 (OUTLIER) cc_final: 0.8159 (p) REVERT: D 50 GLU cc_start: 0.6809 (OUTLIER) cc_final: 0.6303 (tp30) REVERT: D 54 ASP cc_start: 0.6969 (t0) cc_final: 0.5993 (t0) REVERT: D 61 GLN cc_start: 0.8029 (OUTLIER) cc_final: 0.7744 (pm20) REVERT: D 73 THR cc_start: 0.8588 (OUTLIER) cc_final: 0.8284 (m) REVERT: D 110 SER cc_start: 0.8551 (t) cc_final: 0.8333 (m) REVERT: D 117 GLN cc_start: 0.7967 (tt0) cc_final: 0.7238 (tt0) REVERT: D 121 ASN cc_start: 0.7972 (m-40) cc_final: 0.7556 (m-40) REVERT: D 138 LYS cc_start: 0.8227 (tttt) cc_final: 0.7879 (tttt) REVERT: D 145 ARG cc_start: 0.7979 (mtm-85) cc_final: 0.7739 (mtt90) REVERT: D 147 VAL cc_start: 0.8911 (t) cc_final: 0.8693 (t) REVERT: D 157 ARG cc_start: 0.7315 (mtm110) cc_final: 0.6856 (mtm110) REVERT: D 189 LEU cc_start: 0.7581 (tp) cc_final: 0.7343 (tt) REVERT: D 219 ILE cc_start: 0.8160 (mm) cc_final: 0.7913 (mm) REVERT: D 247 VAL cc_start: 0.8885 (t) cc_final: 0.8572 (m) REVERT: D 257 ASN cc_start: 0.8031 (m-40) cc_final: 0.7021 (m110) REVERT: D 294 MET cc_start: 0.7791 (mmm) cc_final: 0.7519 (mmm) REVERT: D 309 THR cc_start: 0.7810 (p) cc_final: 0.7307 (m) REVERT: D 311 ASN cc_start: 0.7523 (p0) cc_final: 0.7310 (p0) REVERT: D 323 ILE cc_start: 0.8162 (mp) cc_final: 0.7922 (mt) REVERT: D 324 GLU cc_start: 0.6753 (tm-30) cc_final: 0.6476 (tm-30) REVERT: D 331 GLU cc_start: 0.7046 (mp0) cc_final: 0.6574 (mp0) REVERT: D 332 GLN cc_start: 0.7371 (tp40) cc_final: 0.6982 (tp40) REVERT: D 345 VAL cc_start: 0.8510 (t) cc_final: 0.8061 (m) REVERT: D 378 ASN cc_start: 0.7882 (m-40) cc_final: 0.7060 (m-40) REVERT: D 382 ASP cc_start: 0.7232 (m-30) cc_final: 0.6843 (m-30) REVERT: E 53 ASP cc_start: 0.7008 (t70) cc_final: 0.5591 (t0) REVERT: E 85 GLU cc_start: 0.6894 (mm-30) cc_final: 0.6456 (tm-30) REVERT: E 126 GLN cc_start: 0.8087 (tm-30) cc_final: 0.7607 (tm-30) REVERT: E 142 ASP cc_start: 0.7365 (m-30) cc_final: 0.7042 (m-30) REVERT: E 153 ASN cc_start: 0.7653 (m-40) cc_final: 0.6866 (p0) REVERT: E 154 LEU cc_start: 0.8145 (mt) cc_final: 0.7745 (mt) REVERT: E 161 GLN cc_start: 0.7849 (tt0) cc_final: 0.6853 (tp-100) REVERT: E 164 ARG cc_start: 0.7367 (ttp80) cc_final: 0.6895 (ttp80) REVERT: E 165 ASP cc_start: 0.7451 (m-30) cc_final: 0.6909 (m-30) REVERT: E 189 LEU cc_start: 0.8168 (mt) cc_final: 0.7861 (mt) REVERT: E 196 GLN cc_start: 0.7860 (OUTLIER) cc_final: 0.7199 (mp10) REVERT: E 200 GLN cc_start: 0.7382 (mm-40) cc_final: 0.7174 (mt0) REVERT: E 204 THR cc_start: 0.8602 (p) cc_final: 0.8379 (t) REVERT: E 207 ARG cc_start: 0.8399 (ttm110) cc_final: 0.8008 (ttm110) REVERT: E 229 ARG cc_start: 0.7993 (ptm-80) cc_final: 0.7714 (ttp80) REVERT: E 237 ILE cc_start: 0.8747 (pp) cc_final: 0.8522 (pt) REVERT: E 251 ASN cc_start: 0.7196 (t0) cc_final: 0.6858 (t0) REVERT: E 283 VAL cc_start: 0.8481 (t) cc_final: 0.8106 (m) REVERT: E 294 MET cc_start: 0.6716 (mmm) cc_final: 0.6432 (mmm) REVERT: E 312 TRP cc_start: 0.8324 (t60) cc_final: 0.8060 (t60) REVERT: E 346 ASN cc_start: 0.7892 (m-40) cc_final: 0.7652 (m-40) REVERT: F 105 LYS cc_start: 0.8083 (mttt) cc_final: 0.7812 (mtmm) REVERT: F 119 MET cc_start: 0.7844 (mtt) cc_final: 0.7491 (mtt) REVERT: F 120 ILE cc_start: 0.8418 (OUTLIER) cc_final: 0.8194 (mp) REVERT: F 124 GLN cc_start: 0.7611 (mt0) cc_final: 0.7243 (mt0) REVERT: F 138 LYS cc_start: 0.8506 (ttpt) cc_final: 0.8225 (ttpp) REVERT: F 140 GLN cc_start: 0.7945 (mt0) cc_final: 0.7735 (mt0) REVERT: F 141 SER cc_start: 0.8414 (m) cc_final: 0.8108 (t) REVERT: F 143 TYR cc_start: 0.7889 (t80) cc_final: 0.7619 (t80) REVERT: F 145 ARG cc_start: 0.7408 (mtm-85) cc_final: 0.7031 (ttm170) REVERT: F 158 GLU cc_start: 0.7149 (tp30) cc_final: 0.6538 (tp30) REVERT: F 164 ARG cc_start: 0.7609 (ttm-80) cc_final: 0.7203 (ttm-80) REVERT: F 178 ILE cc_start: 0.8075 (mt) cc_final: 0.7845 (mm) REVERT: F 192 LYS cc_start: 0.8087 (mttp) cc_final: 0.7747 (mttp) REVERT: F 200 GLN cc_start: 0.7189 (mp10) cc_final: 0.6625 (mp10) REVERT: F 205 GLU cc_start: 0.7505 (mm-30) cc_final: 0.7232 (mt-10) REVERT: F 214 GLU cc_start: 0.7562 (tp30) cc_final: 0.6838 (mp0) REVERT: F 217 ARG cc_start: 0.6861 (mtt180) cc_final: 0.6643 (ttm110) REVERT: F 288 LYS cc_start: 0.8319 (OUTLIER) cc_final: 0.7839 (mtmt) REVERT: F 317 GLN cc_start: 0.7328 (mm-40) cc_final: 0.7069 (mp10) REVERT: F 379 LYS cc_start: 0.7665 (tptm) cc_final: 0.7147 (tptm) REVERT: F 383 ASP cc_start: 0.7133 (m-30) cc_final: 0.6775 (m-30) REVERT: J 21 LEU cc_start: 0.8206 (mt) cc_final: 0.7932 (mm) REVERT: J 40 ILE cc_start: 0.8272 (mt) cc_final: 0.7938 (pt) REVERT: J 66 ILE cc_start: 0.8593 (mt) cc_final: 0.8260 (mm) REVERT: J 87 ILE cc_start: 0.8666 (tt) cc_final: 0.8388 (pt) REVERT: J 114 ILE cc_start: 0.8255 (mm) cc_final: 0.7965 (mm) REVERT: J 124 GLN cc_start: 0.7819 (tt0) cc_final: 0.7386 (tt0) REVERT: J 145 MET cc_start: 0.6709 (tmm) cc_final: 0.6108 (tmm) REVERT: J 161 ILE cc_start: 0.8326 (mm) cc_final: 0.7971 (mp) REVERT: J 184 MET cc_start: 0.7604 (mtm) cc_final: 0.7389 (mtm) REVERT: J 213 ILE cc_start: 0.8287 (OUTLIER) cc_final: 0.7983 (mt) REVERT: J 217 GLN cc_start: 0.7829 (tp40) cc_final: 0.7563 (tp40) REVERT: J 233 GLU cc_start: 0.7760 (mp0) cc_final: 0.7340 (mp0) REVERT: J 247 PHE cc_start: 0.7590 (t80) cc_final: 0.7265 (m-80) REVERT: J 251 TRP cc_start: 0.6878 (t-100) cc_final: 0.6453 (t-100) REVERT: J 268 ARG cc_start: 0.7803 (ttt180) cc_final: 0.7550 (ttt180) REVERT: J 271 THR cc_start: 0.8329 (m) cc_final: 0.8087 (p) REVERT: J 297 GLU cc_start: 0.7379 (tt0) cc_final: 0.7129 (tt0) REVERT: J 308 LEU cc_start: 0.8039 (mt) cc_final: 0.7616 (mt) REVERT: J 327 PHE cc_start: 0.6771 (t80) cc_final: 0.6009 (t80) REVERT: J 333 MET cc_start: 0.7367 (mtm) cc_final: 0.7060 (mtm) REVERT: J 334 ARG cc_start: 0.7783 (mtm180) cc_final: 0.7424 (mtm180) REVERT: J 339 PHE cc_start: 0.7966 (t80) cc_final: 0.7469 (t80) REVERT: J 342 ILE cc_start: 0.8309 (mm) cc_final: 0.8069 (tt) REVERT: J 359 MET cc_start: 0.7172 (mtm) cc_final: 0.6819 (mtm) REVERT: J 384 THR cc_start: 0.8238 (m) cc_final: 0.7955 (p) REVERT: J 394 ARG cc_start: 0.7455 (mtm180) cc_final: 0.6888 (mtt90) REVERT: J 395 LEU cc_start: 0.7817 (mt) cc_final: 0.7424 (mt) REVERT: J 402 SER cc_start: 0.8114 (t) cc_final: 0.7833 (m) REVERT: J 403 ASN cc_start: 0.8379 (m-40) cc_final: 0.7649 (m110) REVERT: J 408 LEU cc_start: 0.7489 (OUTLIER) cc_final: 0.7183 (tt) REVERT: J 421 TRP cc_start: 0.8202 (t60) cc_final: 0.7712 (t60) REVERT: J 458 GLN cc_start: 0.8258 (tt0) cc_final: 0.7891 (tt0) REVERT: J 459 GLN cc_start: 0.8023 (mt0) cc_final: 0.7742 (mt0) REVERT: J 471 GLN cc_start: 0.7761 (mm-40) cc_final: 0.7206 (mm-40) REVERT: J 479 GLU cc_start: 0.7062 (mm-30) cc_final: 0.6618 (mt-10) REVERT: J 482 TRP cc_start: 0.7933 (t60) cc_final: 0.7694 (t60) REVERT: J 489 LEU cc_start: 0.8403 (mt) cc_final: 0.8157 (mt) REVERT: J 491 LEU cc_start: 0.7897 (mt) cc_final: 0.7477 (pp) REVERT: G 3 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8525 (tp) REVERT: G 5 GLN cc_start: 0.8372 (mt0) cc_final: 0.7811 (mt0) REVERT: G 9 GLN cc_start: 0.7006 (tm-30) cc_final: 0.6585 (tm-30) REVERT: G 17 LEU cc_start: 0.8625 (mp) cc_final: 0.8336 (tt) REVERT: G 19 LYS cc_start: 0.8300 (tttm) cc_final: 0.8038 (tttm) REVERT: G 29 GLU cc_start: 0.7773 (tp30) cc_final: 0.6714 (tp30) REVERT: G 30 LYS cc_start: 0.8601 (tttt) cc_final: 0.8267 (tttt) REVERT: G 32 ASN cc_start: 0.8133 (m-40) cc_final: 0.6874 (p0) REVERT: G 42 LEU cc_start: 0.8415 (mp) cc_final: 0.8172 (mm) REVERT: G 77 ASP cc_start: 0.8532 (t0) cc_final: 0.4963 (p0) REVERT: G 81 TRP cc_start: 0.7284 (m100) cc_final: 0.7078 (m100) REVERT: G 84 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8946 (tp) REVERT: G 87 GLN cc_start: 0.8494 (tp40) cc_final: 0.8049 (tp40) REVERT: G 88 GLU cc_start: 0.8074 (pt0) cc_final: 0.7852 (pt0) REVERT: G 99 GLN cc_start: 0.7679 (tm-30) cc_final: 0.7386 (tm-30) REVERT: G 101 ASP cc_start: 0.7716 (t70) cc_final: 0.7078 (t0) REVERT: G 104 THR cc_start: 0.8678 (m) cc_final: 0.8455 (p) REVERT: G 125 TYR cc_start: 0.8838 (t80) cc_final: 0.8622 (t80) REVERT: G 130 LYS cc_start: 0.8735 (tttt) cc_final: 0.8218 (ttpp) REVERT: G 136 GLN cc_start: 0.8465 (tp40) cc_final: 0.8152 (tp-100) REVERT: G 156 ASN cc_start: 0.8094 (t0) cc_final: 0.7731 (t0) REVERT: G 158 ARG cc_start: 0.7727 (tpm170) cc_final: 0.7170 (tpm170) REVERT: G 162 ASP cc_start: 0.8171 (m-30) cc_final: 0.7955 (m-30) REVERT: G 169 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8257 (mm) REVERT: G 181 GLN cc_start: 0.8467 (mm-40) cc_final: 0.7802 (tm-30) REVERT: G 215 GLU cc_start: 0.7575 (tm-30) cc_final: 0.6723 (tm-30) REVERT: G 217 GLU cc_start: 0.8023 (tm-30) cc_final: 0.7651 (mm-30) REVERT: G 225 GLN cc_start: 0.8357 (tm-30) cc_final: 0.8138 (tm-30) REVERT: G 230 GLN cc_start: 0.8570 (OUTLIER) cc_final: 0.7942 (pp30) REVERT: G 231 ASP cc_start: 0.8226 (m-30) cc_final: 0.7630 (m-30) REVERT: G 232 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.8642 (tt) REVERT: G 236 GLN cc_start: 0.8221 (mt0) cc_final: 0.7812 (mm-40) REVERT: G 237 ILE cc_start: 0.8871 (OUTLIER) cc_final: 0.8620 (tp) REVERT: G 299 ASN cc_start: 0.8290 (m110) cc_final: 0.7809 (m-40) REVERT: G 303 LYS cc_start: 0.8806 (mtpp) cc_final: 0.7763 (mtpp) REVERT: G 304 GLN cc_start: 0.8378 (pt0) cc_final: 0.7915 (pp30) REVERT: G 307 TYR cc_start: 0.7940 (m-80) cc_final: 0.7573 (m-80) REVERT: G 314 GLU cc_start: 0.7796 (mm-30) cc_final: 0.7369 (mm-30) REVERT: G 315 GLN cc_start: 0.8673 (tp40) cc_final: 0.8181 (tp-100) REVERT: G 317 GLU cc_start: 0.7956 (tp30) cc_final: 0.7141 (tp30) REVERT: G 321 ARG cc_start: 0.8467 (mtt180) cc_final: 0.7973 (mtt180) REVERT: G 344 TYR cc_start: 0.8235 (m-80) cc_final: 0.7606 (m-80) REVERT: G 401 LYS cc_start: 0.8543 (tptm) cc_final: 0.8192 (tppp) REVERT: G 411 ASP cc_start: 0.5391 (t0) cc_final: 0.4907 (t0) REVERT: H 9 GLN cc_start: 0.8641 (tp-100) cc_final: 0.8393 (tp-100) REVERT: H 14 ASN cc_start: 0.8090 (t0) cc_final: 0.7744 (t0) REVERT: H 25 ASP cc_start: 0.7862 (m-30) cc_final: 0.7554 (t0) REVERT: H 29 GLU cc_start: 0.7937 (tp30) cc_final: 0.7264 (tp30) REVERT: H 30 LYS cc_start: 0.8651 (ttpt) cc_final: 0.8080 (ttpt) REVERT: H 33 GLU cc_start: 0.7603 (pp20) cc_final: 0.7286 (pp20) REVERT: H 77 ASP cc_start: 0.7405 (t0) cc_final: 0.6795 (t0) REVERT: H 88 GLU cc_start: 0.8419 (mt-10) cc_final: 0.8147 (mt-10) REVERT: H 89 LYS cc_start: 0.8823 (mmmt) cc_final: 0.8417 (mmmt) REVERT: H 94 GLN cc_start: 0.8049 (OUTLIER) cc_final: 0.7772 (tt0) REVERT: H 135 ARG cc_start: 0.8084 (OUTLIER) cc_final: 0.7440 (mmm160) REVERT: H 136 GLN cc_start: 0.8308 (tp40) cc_final: 0.8076 (tp-100) REVERT: H 142 GLN cc_start: 0.8091 (mm-40) cc_final: 0.7658 (mm-40) REVERT: H 162 ASP cc_start: 0.8017 (m-30) cc_final: 0.7683 (m-30) REVERT: H 169 LEU cc_start: 0.8729 (tt) cc_final: 0.7777 (mt) REVERT: H 173 ASN cc_start: 0.8487 (m-40) cc_final: 0.8209 (m-40) REVERT: H 179 VAL cc_start: 0.8971 (t) cc_final: 0.8701 (p) REVERT: H 180 GLU cc_start: 0.8512 (mm-30) cc_final: 0.7994 (tm-30) REVERT: H 184 GLN cc_start: 0.8442 (tt0) cc_final: 0.7609 (tp-100) REVERT: H 218 LYS cc_start: 0.8756 (mmtt) cc_final: 0.8477 (mmtt) REVERT: H 224 LEU cc_start: 0.8657 (mp) cc_final: 0.8203 (mm) REVERT: H 230 GLN cc_start: 0.8205 (tp40) cc_final: 0.7530 (tp-100) REVERT: H 231 ASP cc_start: 0.7759 (t0) cc_final: 0.7465 (t0) REVERT: H 234 ARG cc_start: 0.8079 (mmm-85) cc_final: 0.7865 (mmm-85) REVERT: H 236 GLN cc_start: 0.7736 (tm-30) cc_final: 0.7311 (tm-30) REVERT: H 237 ILE cc_start: 0.8769 (mt) cc_final: 0.8298 (mt) REVERT: H 288 PHE cc_start: 0.7659 (t80) cc_final: 0.7255 (t80) REVERT: H 297 MET cc_start: 0.6511 (ttm) cc_final: 0.6173 (ttm) REVERT: H 301 GLN cc_start: 0.8483 (mt0) cc_final: 0.8072 (mp10) REVERT: H 303 LYS cc_start: 0.8418 (mttt) cc_final: 0.7895 (mttt) REVERT: H 314 GLU cc_start: 0.7636 (mm-30) cc_final: 0.7204 (mm-30) REVERT: H 317 GLU cc_start: 0.7729 (tp30) cc_final: 0.7217 (tp30) REVERT: H 321 ARG cc_start: 0.8307 (mtt180) cc_final: 0.7566 (mtt180) REVERT: H 331 PHE cc_start: 0.9069 (t80) cc_final: 0.8780 (t80) REVERT: H 340 SER cc_start: 0.8737 (m) cc_final: 0.8197 (p) REVERT: H 358 MET cc_start: 0.7885 (mmm) cc_final: 0.7599 (mmm) REVERT: H 367 ARG cc_start: 0.8003 (tpp80) cc_final: 0.7732 (mtm-85) REVERT: H 374 ASP cc_start: 0.7802 (t0) cc_final: 0.7481 (t0) REVERT: H 390 ARG cc_start: 0.8656 (mtt-85) cc_final: 0.8425 (ttm170) REVERT: H 392 ASN cc_start: 0.8417 (m-40) cc_final: 0.7889 (t0) REVERT: H 396 ASN cc_start: 0.8214 (m-40) cc_final: 0.7776 (m110) REVERT: H 397 GLN cc_start: 0.8119 (tt0) cc_final: 0.7355 (tm-30) REVERT: H 412 LEU cc_start: 0.8584 (tp) cc_final: 0.8356 (tp) REVERT: I 8 GLN cc_start: 0.8455 (mm-40) cc_final: 0.7835 (mm-40) REVERT: I 11 ARG cc_start: 0.7987 (ttp80) cc_final: 0.6968 (ttp80) REVERT: I 16 GLU cc_start: 0.7933 (mp0) cc_final: 0.7472 (mp0) REVERT: I 19 LYS cc_start: 0.8590 (tttt) cc_final: 0.8126 (tttt) REVERT: I 31 ILE cc_start: 0.9059 (mt) cc_final: 0.8799 (mm) REVERT: I 42 LEU cc_start: 0.7663 (tt) cc_final: 0.7386 (tp) REVERT: I 76 PHE cc_start: 0.7581 (t80) cc_final: 0.6877 (t80) REVERT: I 86 LEU cc_start: 0.9009 (mt) cc_final: 0.8767 (pp) REVERT: I 95 ASP cc_start: 0.8234 (t0) cc_final: 0.7326 (t0) REVERT: I 99 GLN cc_start: 0.8306 (mt0) cc_final: 0.7839 (mt0) REVERT: I 103 GLN cc_start: 0.8542 (mt0) cc_final: 0.8298 (mm-40) REVERT: I 124 SER cc_start: 0.8614 (t) cc_final: 0.8380 (p) REVERT: I 215 GLU cc_start: 0.8115 (tp30) cc_final: 0.7548 (tp30) REVERT: I 217 GLU cc_start: 0.7561 (mm-30) cc_final: 0.7257 (mm-30) REVERT: I 224 LEU cc_start: 0.8805 (tp) cc_final: 0.8186 (mm) REVERT: I 225 GLN cc_start: 0.8055 (tm-30) cc_final: 0.7390 (tm-30) REVERT: I 227 ARG cc_start: 0.7752 (mtm-85) cc_final: 0.7259 (mtm-85) REVERT: I 235 GLU cc_start: 0.7933 (tp30) cc_final: 0.7593 (tp30) REVERT: I 236 GLN cc_start: 0.8355 (mt0) cc_final: 0.8027 (mt0) REVERT: I 238 ARG cc_start: 0.8128 (mpt180) cc_final: 0.7728 (mpt180) REVERT: I 259 THR cc_start: 0.3527 (OUTLIER) cc_final: 0.3304 (m) REVERT: I 301 GLN cc_start: 0.8455 (tt0) cc_final: 0.8085 (mt0) REVERT: I 306 GLN cc_start: 0.8426 (pt0) cc_final: 0.7999 (pp30) REVERT: I 325 GLN cc_start: 0.8380 (OUTLIER) cc_final: 0.8158 (pp30) REVERT: I 356 ASP cc_start: 0.8272 (t0) cc_final: 0.8031 (t0) REVERT: I 384 GLN cc_start: 0.7829 (tm-30) cc_final: 0.7538 (tm-30) REVERT: I 396 ASN cc_start: 0.8348 (m-40) cc_final: 0.7800 (m-40) outliers start: 158 outliers final: 106 residues processed: 1321 average time/residue: 0.2091 time to fit residues: 417.1299 Evaluate side-chains 1345 residues out of total 3232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 1216 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 194 GLU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 133 LYS Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 294 MET Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 383 ASP Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 124 GLN Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 187 MET Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 340 SER Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain D residue 61 GLN Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 84 LYS Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 169 SER Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 288 LYS Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 337 ILE Chi-restraints excluded: chain D residue 353 GLN Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 379 LYS Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 65 MET Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 196 GLN Chi-restraints excluded: chain E residue 214 GLU Chi-restraints excluded: chain E residue 261 THR Chi-restraints excluded: chain E residue 273 THR Chi-restraints excluded: chain E residue 275 THR Chi-restraints excluded: chain E residue 284 LYS Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain E residue 309 THR Chi-restraints excluded: chain E residue 344 SER Chi-restraints excluded: chain E residue 371 GLU Chi-restraints excluded: chain E residue 373 SER Chi-restraints excluded: chain E residue 386 LYS Chi-restraints excluded: chain F residue 69 SER Chi-restraints excluded: chain F residue 110 SER Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 179 GLN Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 237 ILE Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 288 LYS Chi-restraints excluded: chain F residue 303 LEU Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain F residue 353 GLN Chi-restraints excluded: chain F residue 367 SER Chi-restraints excluded: chain F residue 372 ILE Chi-restraints excluded: chain F residue 380 LEU Chi-restraints excluded: chain F residue 386 LYS Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 48 LEU Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain J residue 122 LEU Chi-restraints excluded: chain J residue 166 HIS Chi-restraints excluded: chain J residue 213 ILE Chi-restraints excluded: chain J residue 293 GLN Chi-restraints excluded: chain J residue 371 GLN Chi-restraints excluded: chain J residue 408 LEU Chi-restraints excluded: chain J residue 455 MET Chi-restraints excluded: chain J residue 494 LEU Chi-restraints excluded: chain G residue 3 LEU Chi-restraints excluded: chain G residue 11 ARG Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain G residue 177 ASN Chi-restraints excluded: chain G residue 203 THR Chi-restraints excluded: chain G residue 230 GLN Chi-restraints excluded: chain G residue 232 LEU Chi-restraints excluded: chain G residue 237 ILE Chi-restraints excluded: chain G residue 244 HIS Chi-restraints excluded: chain G residue 245 LEU Chi-restraints excluded: chain G residue 318 SER Chi-restraints excluded: chain G residue 334 ILE Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 94 GLN Chi-restraints excluded: chain H residue 135 ARG Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 168 GLU Chi-restraints excluded: chain H residue 205 LYS Chi-restraints excluded: chain H residue 221 LEU Chi-restraints excluded: chain H residue 315 GLN Chi-restraints excluded: chain H residue 404 LEU Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 130 LYS Chi-restraints excluded: chain I residue 203 THR Chi-restraints excluded: chain I residue 259 THR Chi-restraints excluded: chain I residue 272 THR Chi-restraints excluded: chain I residue 292 ILE Chi-restraints excluded: chain I residue 325 GLN Chi-restraints excluded: chain I residue 374 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 173 optimal weight: 3.9990 chunk 129 optimal weight: 0.3980 chunk 118 optimal weight: 2.9990 chunk 232 optimal weight: 0.3980 chunk 349 optimal weight: 5.9990 chunk 330 optimal weight: 1.9990 chunk 137 optimal weight: 0.6980 chunk 354 optimal weight: 1.9990 chunk 237 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 370 optimal weight: 4.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 ASN B 162 HIS C 251 ASN ** D 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 196 GLN D 306 GLN D 353 GLN E 184 ASN F 251 ASN F 346 ASN J 34 ASN J 478 ASN G 220 ASN H 136 GLN H 139 GLN ** H 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 304 GLN I 9 GLN I 32 ASN I 118 ASN I 188 ASN I 320 HIS ** I 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.112710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.094683 restraints weight = 58568.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.097654 restraints weight = 25931.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.099527 restraints weight = 14066.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.100708 restraints weight = 8838.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.101515 restraints weight = 6304.600| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.6080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 30315 Z= 0.179 Angle : 0.618 11.696 41246 Z= 0.325 Chirality : 0.043 0.169 4889 Planarity : 0.005 0.064 5392 Dihedral : 4.286 21.077 4179 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 5.41 % Allowed : 21.94 % Favored : 72.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.66 (0.14), residues: 3860 helix: 2.89 (0.11), residues: 2010 sheet: -0.41 (0.22), residues: 516 loop : -1.17 (0.16), residues: 1334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG I 143 TYR 0.019 0.002 TYR I 161 PHE 0.019 0.001 PHE J 439 TRP 0.031 0.002 TRP C 312 HIS 0.005 0.001 HIS J 429 Details of bonding type rmsd covalent geometry : bond 0.00373 (30315) covalent geometry : angle 0.61810 (41246) hydrogen bonds : bond 0.06759 ( 1888) hydrogen bonds : angle 4.43060 ( 5523) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7720 Ramachandran restraints generated. 3860 Oldfield, 0 Emsley, 3860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7720 Ramachandran restraints generated. 3860 Oldfield, 0 Emsley, 3860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1423 residues out of total 3232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 1248 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.6943 (mm-30) cc_final: 0.6741 (mm-30) REVERT: A 54 ASP cc_start: 0.7665 (t0) cc_final: 0.7453 (t0) REVERT: A 56 TYR cc_start: 0.7309 (m-80) cc_final: 0.6470 (m-80) REVERT: A 79 ASN cc_start: 0.7740 (t0) cc_final: 0.7454 (t0) REVERT: A 130 GLU cc_start: 0.7514 (mm-30) cc_final: 0.7085 (mm-30) REVERT: A 138 LYS cc_start: 0.8200 (mttt) cc_final: 0.7933 (tttp) REVERT: A 143 TYR cc_start: 0.8201 (t80) cc_final: 0.7849 (t80) REVERT: A 146 ARG cc_start: 0.7782 (ttm-80) cc_final: 0.7522 (mtt90) REVERT: A 154 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8252 (mp) REVERT: A 161 GLN cc_start: 0.7508 (pt0) cc_final: 0.6919 (pt0) REVERT: A 171 GLN cc_start: 0.8079 (tp40) cc_final: 0.7279 (tp40) REVERT: A 173 GLN cc_start: 0.7877 (mm-40) cc_final: 0.7620 (mm110) REVERT: A 175 ASP cc_start: 0.6860 (m-30) cc_final: 0.6298 (m-30) REVERT: A 189 LEU cc_start: 0.8474 (mt) cc_final: 0.8252 (mp) REVERT: A 201 GLN cc_start: 0.7073 (mm-40) cc_final: 0.6789 (mm110) REVERT: A 228 ARG cc_start: 0.7578 (mtm-85) cc_final: 0.7103 (mtm-85) REVERT: A 237 ILE cc_start: 0.8052 (mm) cc_final: 0.7785 (pt) REVERT: A 259 LYS cc_start: 0.8164 (mtmm) cc_final: 0.7772 (mtmm) REVERT: A 284 LYS cc_start: 0.7436 (mtpp) cc_final: 0.7155 (mtpp) REVERT: A 306 GLN cc_start: 0.6905 (tp-100) cc_final: 0.6462 (tp-100) REVERT: A 347 THR cc_start: 0.7302 (OUTLIER) cc_final: 0.6840 (p) REVERT: A 379 LYS cc_start: 0.7942 (tttt) cc_final: 0.7704 (tttt) REVERT: A 381 ILE cc_start: 0.8534 (mt) cc_final: 0.8162 (mp) REVERT: B 50 GLU cc_start: 0.7556 (mm-30) cc_final: 0.7151 (mm-30) REVERT: B 66 SER cc_start: 0.7815 (t) cc_final: 0.7566 (p) REVERT: B 93 ASP cc_start: 0.7904 (t0) cc_final: 0.7605 (t70) REVERT: B 98 ARG cc_start: 0.7243 (tpp80) cc_final: 0.7020 (ttm-80) REVERT: B 123 LYS cc_start: 0.7493 (mttp) cc_final: 0.7105 (mttp) REVERT: B 130 GLU cc_start: 0.7251 (mm-30) cc_final: 0.6861 (tm-30) REVERT: B 145 ARG cc_start: 0.7918 (mtt-85) cc_final: 0.6899 (mtt-85) REVERT: B 158 GLU cc_start: 0.7055 (tt0) cc_final: 0.6557 (tm-30) REVERT: B 159 GLU cc_start: 0.7731 (tp30) cc_final: 0.7430 (tp30) REVERT: B 162 HIS cc_start: 0.7860 (m-70) cc_final: 0.7149 (m90) REVERT: B 171 GLN cc_start: 0.8094 (tp40) cc_final: 0.7731 (tp40) REVERT: B 184 ASN cc_start: 0.8022 (t0) cc_final: 0.7805 (t0) REVERT: B 194 GLU cc_start: 0.7483 (pp20) cc_final: 0.7274 (pp20) REVERT: B 207 ARG cc_start: 0.7376 (mtt90) cc_final: 0.7137 (mtt-85) REVERT: B 257 ASN cc_start: 0.7747 (m-40) cc_final: 0.7528 (t0) REVERT: B 259 LYS cc_start: 0.7880 (mtmt) cc_final: 0.7514 (mtmt) REVERT: B 284 LYS cc_start: 0.7827 (mtpt) cc_final: 0.7613 (mtpt) REVERT: B 293 ASP cc_start: 0.7203 (t0) cc_final: 0.6947 (t0) REVERT: B 294 MET cc_start: 0.7185 (OUTLIER) cc_final: 0.6751 (mtp) REVERT: B 300 PHE cc_start: 0.7932 (m-10) cc_final: 0.7716 (m-10) REVERT: B 328 LYS cc_start: 0.8214 (mmpt) cc_final: 0.7814 (mmpt) REVERT: B 329 GLN cc_start: 0.7070 (mt0) cc_final: 0.6721 (mp10) REVERT: B 330 LEU cc_start: 0.8259 (tt) cc_final: 0.7871 (tp) REVERT: B 332 GLN cc_start: 0.7547 (mm-40) cc_final: 0.6858 (tp40) REVERT: B 333 TYR cc_start: 0.7937 (m-10) cc_final: 0.7687 (m-10) REVERT: B 379 LYS cc_start: 0.8231 (tttt) cc_final: 0.7973 (ttmt) REVERT: B 386 LYS cc_start: 0.8033 (tttt) cc_final: 0.7647 (tttt) REVERT: C 53 ASP cc_start: 0.6830 (t0) cc_final: 0.6524 (t0) REVERT: C 54 ASP cc_start: 0.7329 (t0) cc_final: 0.7037 (t0) REVERT: C 103 LYS cc_start: 0.7973 (tttt) cc_final: 0.7607 (tttt) REVERT: C 117 GLN cc_start: 0.7347 (mt0) cc_final: 0.6519 (mt0) REVERT: C 121 ASN cc_start: 0.7289 (m-40) cc_final: 0.6942 (m-40) REVERT: C 133 LYS cc_start: 0.8285 (mtpt) cc_final: 0.7963 (mtpt) REVERT: C 154 LEU cc_start: 0.8607 (mp) cc_final: 0.8351 (mt) REVERT: C 158 GLU cc_start: 0.7712 (tt0) cc_final: 0.7433 (tt0) REVERT: C 161 GLN cc_start: 0.7569 (tp40) cc_final: 0.6033 (tp-100) REVERT: C 164 ARG cc_start: 0.6772 (ttp80) cc_final: 0.6115 (ttp80) REVERT: C 168 THR cc_start: 0.8321 (OUTLIER) cc_final: 0.8032 (p) REVERT: C 195 ASP cc_start: 0.7540 (m-30) cc_final: 0.6987 (m-30) REVERT: C 200 GLN cc_start: 0.6971 (mt0) cc_final: 0.6513 (mt0) REVERT: C 231 VAL cc_start: 0.8276 (OUTLIER) cc_final: 0.7948 (p) REVERT: C 257 ASN cc_start: 0.7929 (m-40) cc_final: 0.7412 (m110) REVERT: C 296 THR cc_start: 0.7537 (p) cc_final: 0.7129 (t) REVERT: C 329 GLN cc_start: 0.8055 (mm-40) cc_final: 0.7573 (mp10) REVERT: C 340 SER cc_start: 0.8354 (OUTLIER) cc_final: 0.8145 (p) REVERT: C 353 GLN cc_start: 0.5269 (tm-30) cc_final: 0.4980 (tm-30) REVERT: C 379 LYS cc_start: 0.7770 (ttmt) cc_final: 0.7499 (ttmt) REVERT: D 50 GLU cc_start: 0.6769 (OUTLIER) cc_final: 0.6372 (tp30) REVERT: D 54 ASP cc_start: 0.6962 (t0) cc_final: 0.6352 (t0) REVERT: D 73 THR cc_start: 0.8601 (OUTLIER) cc_final: 0.8304 (m) REVERT: D 110 SER cc_start: 0.8558 (t) cc_final: 0.8342 (m) REVERT: D 117 GLN cc_start: 0.7944 (tt0) cc_final: 0.7142 (tt0) REVERT: D 121 ASN cc_start: 0.7892 (m-40) cc_final: 0.7474 (m-40) REVERT: D 129 ILE cc_start: 0.8304 (mt) cc_final: 0.8028 (mm) REVERT: D 138 LYS cc_start: 0.8208 (tttt) cc_final: 0.7843 (tttt) REVERT: D 147 VAL cc_start: 0.8897 (t) cc_final: 0.8670 (t) REVERT: D 157 ARG cc_start: 0.7296 (mtm110) cc_final: 0.7003 (mtm110) REVERT: D 161 GLN cc_start: 0.7288 (mp10) cc_final: 0.7067 (mp10) REVERT: D 164 ARG cc_start: 0.7922 (ttp80) cc_final: 0.7322 (ttm-80) REVERT: D 187 MET cc_start: 0.7701 (mmm) cc_final: 0.6999 (mmt) REVERT: D 189 LEU cc_start: 0.7579 (tp) cc_final: 0.7363 (tt) REVERT: D 228 ARG cc_start: 0.6924 (mtp85) cc_final: 0.6529 (mtt90) REVERT: D 294 MET cc_start: 0.7718 (mmm) cc_final: 0.7453 (mmm) REVERT: D 309 THR cc_start: 0.7754 (p) cc_final: 0.7256 (m) REVERT: D 311 ASN cc_start: 0.7507 (p0) cc_final: 0.7290 (p0) REVERT: D 314 LYS cc_start: 0.6963 (tttt) cc_final: 0.6630 (tptt) REVERT: D 315 VAL cc_start: 0.8981 (t) cc_final: 0.8730 (m) REVERT: D 331 GLU cc_start: 0.7035 (mp0) cc_final: 0.6528 (mp0) REVERT: D 332 GLN cc_start: 0.7355 (tp40) cc_final: 0.6972 (tp40) REVERT: D 378 ASN cc_start: 0.7878 (m-40) cc_final: 0.7019 (m-40) REVERT: D 382 ASP cc_start: 0.7200 (m-30) cc_final: 0.6657 (m-30) REVERT: D 385 VAL cc_start: 0.8461 (t) cc_final: 0.8139 (p) REVERT: E 53 ASP cc_start: 0.7179 (t70) cc_final: 0.5821 (t0) REVERT: E 85 GLU cc_start: 0.6877 (OUTLIER) cc_final: 0.6475 (tm-30) REVERT: E 142 ASP cc_start: 0.7344 (m-30) cc_final: 0.6989 (m-30) REVERT: E 153 ASN cc_start: 0.7664 (m-40) cc_final: 0.6916 (p0) REVERT: E 154 LEU cc_start: 0.8114 (mt) cc_final: 0.7762 (mt) REVERT: E 157 ARG cc_start: 0.7247 (mtp180) cc_final: 0.7005 (mtp180) REVERT: E 161 GLN cc_start: 0.7647 (tt0) cc_final: 0.6578 (tp-100) REVERT: E 164 ARG cc_start: 0.7324 (ttp80) cc_final: 0.7029 (ttp80) REVERT: E 165 ASP cc_start: 0.7441 (m-30) cc_final: 0.6922 (m-30) REVERT: E 185 GLN cc_start: 0.7031 (tp-100) cc_final: 0.6766 (tp40) REVERT: E 189 LEU cc_start: 0.8161 (mt) cc_final: 0.7798 (mt) REVERT: E 192 LYS cc_start: 0.7637 (mmmm) cc_final: 0.7181 (mmmm) REVERT: E 196 GLN cc_start: 0.7821 (OUTLIER) cc_final: 0.7174 (mp10) REVERT: E 200 GLN cc_start: 0.7370 (mm-40) cc_final: 0.6993 (mt0) REVERT: E 204 THR cc_start: 0.8561 (p) cc_final: 0.8340 (t) REVERT: E 211 LEU cc_start: 0.8336 (mt) cc_final: 0.8018 (mm) REVERT: E 229 ARG cc_start: 0.8002 (ptm-80) cc_final: 0.7733 (ttp80) REVERT: E 251 ASN cc_start: 0.7209 (t0) cc_final: 0.6880 (t0) REVERT: E 283 VAL cc_start: 0.8485 (t) cc_final: 0.8039 (m) REVERT: E 294 MET cc_start: 0.6684 (mmm) cc_final: 0.6435 (mmm) REVERT: E 306 GLN cc_start: 0.7043 (mp10) cc_final: 0.6684 (mp10) REVERT: E 312 TRP cc_start: 0.8269 (t60) cc_final: 0.8032 (t60) REVERT: E 346 ASN cc_start: 0.7865 (m-40) cc_final: 0.7650 (m-40) REVERT: F 50 GLU cc_start: 0.7625 (mm-30) cc_final: 0.7162 (mm-30) REVERT: F 105 LYS cc_start: 0.8085 (mttt) cc_final: 0.7787 (mtmm) REVERT: F 114 GLN cc_start: 0.7864 (mt0) cc_final: 0.7582 (mm-40) REVERT: F 124 GLN cc_start: 0.7520 (mt0) cc_final: 0.7207 (mt0) REVERT: F 126 GLN cc_start: 0.7021 (tp40) cc_final: 0.6654 (tp40) REVERT: F 133 LYS cc_start: 0.7944 (OUTLIER) cc_final: 0.7547 (tttt) REVERT: F 138 LYS cc_start: 0.8538 (ttpt) cc_final: 0.8152 (tttp) REVERT: F 141 SER cc_start: 0.8356 (m) cc_final: 0.8094 (t) REVERT: F 143 TYR cc_start: 0.7877 (t80) cc_final: 0.7647 (t80) REVERT: F 145 ARG cc_start: 0.7386 (mtm-85) cc_final: 0.7014 (ttm170) REVERT: F 158 GLU cc_start: 0.7197 (tp30) cc_final: 0.6395 (tp30) REVERT: F 161 GLN cc_start: 0.7410 (tp40) cc_final: 0.6872 (tp40) REVERT: F 164 ARG cc_start: 0.7649 (ttm-80) cc_final: 0.7230 (ttm-80) REVERT: F 178 ILE cc_start: 0.8043 (mt) cc_final: 0.7824 (mm) REVERT: F 192 LYS cc_start: 0.8078 (mttp) cc_final: 0.7738 (mttp) REVERT: F 200 GLN cc_start: 0.7097 (mp10) cc_final: 0.6476 (mp10) REVERT: F 205 GLU cc_start: 0.7477 (mm-30) cc_final: 0.7246 (mt-10) REVERT: F 214 GLU cc_start: 0.7583 (tp30) cc_final: 0.6835 (mp0) REVERT: F 217 ARG cc_start: 0.6884 (mtt180) cc_final: 0.6530 (ptp-170) REVERT: F 259 LYS cc_start: 0.7604 (mmtp) cc_final: 0.7057 (mptp) REVERT: F 288 LYS cc_start: 0.8317 (OUTLIER) cc_final: 0.7849 (mtmt) REVERT: F 317 GLN cc_start: 0.7270 (mm-40) cc_final: 0.6936 (mp10) REVERT: F 372 ILE cc_start: 0.8645 (mp) cc_final: 0.8387 (mm) REVERT: F 379 LYS cc_start: 0.7707 (tptm) cc_final: 0.7183 (tptm) REVERT: F 383 ASP cc_start: 0.7125 (m-30) cc_final: 0.6789 (m-30) REVERT: J 21 LEU cc_start: 0.8208 (mt) cc_final: 0.7927 (mm) REVERT: J 66 ILE cc_start: 0.8592 (mt) cc_final: 0.8243 (mm) REVERT: J 87 ILE cc_start: 0.8649 (tt) cc_final: 0.8401 (pt) REVERT: J 114 ILE cc_start: 0.8274 (mm) cc_final: 0.7961 (mm) REVERT: J 122 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7592 (mp) REVERT: J 124 GLN cc_start: 0.7781 (tt0) cc_final: 0.7251 (tt0) REVERT: J 126 LEU cc_start: 0.8414 (mt) cc_final: 0.7793 (mm) REVERT: J 145 MET cc_start: 0.6683 (tmm) cc_final: 0.6075 (tmm) REVERT: J 161 ILE cc_start: 0.8371 (mm) cc_final: 0.8005 (mp) REVERT: J 184 MET cc_start: 0.7561 (mtm) cc_final: 0.7321 (mtm) REVERT: J 213 ILE cc_start: 0.8291 (OUTLIER) cc_final: 0.8015 (mt) REVERT: J 233 GLU cc_start: 0.7683 (mp0) cc_final: 0.7308 (mp0) REVERT: J 251 TRP cc_start: 0.6949 (t-100) cc_final: 0.6623 (t-100) REVERT: J 268 ARG cc_start: 0.7702 (ttt180) cc_final: 0.7464 (ttt180) REVERT: J 271 THR cc_start: 0.8319 (m) cc_final: 0.8077 (p) REVERT: J 297 GLU cc_start: 0.7371 (tt0) cc_final: 0.7077 (tt0) REVERT: J 308 LEU cc_start: 0.8022 (mt) cc_final: 0.7768 (mm) REVERT: J 327 PHE cc_start: 0.6755 (t80) cc_final: 0.6001 (t80) REVERT: J 333 MET cc_start: 0.7335 (mtm) cc_final: 0.6969 (mtm) REVERT: J 342 ILE cc_start: 0.8173 (mm) cc_final: 0.7914 (tt) REVERT: J 357 PRO cc_start: 0.8542 (Cg_exo) cc_final: 0.8323 (Cg_endo) REVERT: J 361 PHE cc_start: 0.7361 (t80) cc_final: 0.7058 (t80) REVERT: J 368 GLN cc_start: 0.7041 (OUTLIER) cc_final: 0.6758 (mt0) REVERT: J 382 LEU cc_start: 0.8244 (tp) cc_final: 0.8022 (mm) REVERT: J 384 THR cc_start: 0.8210 (m) cc_final: 0.7935 (p) REVERT: J 395 LEU cc_start: 0.7823 (mt) cc_final: 0.7440 (mt) REVERT: J 402 SER cc_start: 0.8095 (t) cc_final: 0.7829 (m) REVERT: J 403 ASN cc_start: 0.8329 (m-40) cc_final: 0.7738 (m110) REVERT: J 408 LEU cc_start: 0.7362 (OUTLIER) cc_final: 0.7037 (tt) REVERT: J 421 TRP cc_start: 0.8195 (t60) cc_final: 0.7719 (t60) REVERT: J 428 HIS cc_start: 0.8244 (m-70) cc_final: 0.7953 (m-70) REVERT: J 457 GLN cc_start: 0.7616 (mm-40) cc_final: 0.7243 (tp-100) REVERT: J 458 GLN cc_start: 0.8193 (tt0) cc_final: 0.7849 (tt0) REVERT: J 459 GLN cc_start: 0.7928 (mt0) cc_final: 0.7668 (mt0) REVERT: J 466 GLN cc_start: 0.7730 (OUTLIER) cc_final: 0.7258 (mp10) REVERT: J 471 GLN cc_start: 0.7743 (mm-40) cc_final: 0.7191 (mm-40) REVERT: J 489 LEU cc_start: 0.8401 (mt) cc_final: 0.8154 (mt) REVERT: J 491 LEU cc_start: 0.7824 (mt) cc_final: 0.7426 (pp) REVERT: G 3 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8469 (tp) REVERT: G 5 GLN cc_start: 0.8333 (mt0) cc_final: 0.7692 (mt0) REVERT: G 9 GLN cc_start: 0.7014 (tm-30) cc_final: 0.6554 (tm-30) REVERT: G 17 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8379 (tt) REVERT: G 19 LYS cc_start: 0.8257 (tttm) cc_final: 0.7983 (tttm) REVERT: G 24 ARG cc_start: 0.7689 (tpt170) cc_final: 0.7103 (tpt170) REVERT: G 28 PHE cc_start: 0.7242 (t80) cc_final: 0.6958 (t80) REVERT: G 29 GLU cc_start: 0.7765 (tp30) cc_final: 0.6593 (tp30) REVERT: G 30 LYS cc_start: 0.8608 (tttt) cc_final: 0.8232 (tttt) REVERT: G 32 ASN cc_start: 0.8144 (m-40) cc_final: 0.6842 (p0) REVERT: G 42 LEU cc_start: 0.8395 (mp) cc_final: 0.8153 (mm) REVERT: G 77 ASP cc_start: 0.8518 (t0) cc_final: 0.4746 (p0) REVERT: G 81 TRP cc_start: 0.7243 (m100) cc_final: 0.7021 (m100) REVERT: G 84 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8917 (tp) REVERT: G 87 GLN cc_start: 0.8481 (tp40) cc_final: 0.8132 (tp40) REVERT: G 88 GLU cc_start: 0.8052 (pt0) cc_final: 0.7821 (pt0) REVERT: G 99 GLN cc_start: 0.7699 (tm-30) cc_final: 0.7351 (tm-30) REVERT: G 101 ASP cc_start: 0.7726 (t70) cc_final: 0.7111 (t0) REVERT: G 103 GLN cc_start: 0.8292 (mm-40) cc_final: 0.8071 (mm-40) REVERT: G 125 TYR cc_start: 0.8867 (t80) cc_final: 0.8599 (t80) REVERT: G 130 LYS cc_start: 0.8715 (tttt) cc_final: 0.8137 (ttpp) REVERT: G 136 GLN cc_start: 0.8449 (tp40) cc_final: 0.8136 (tp-100) REVERT: G 142 GLN cc_start: 0.7796 (OUTLIER) cc_final: 0.7462 (mm-40) REVERT: G 162 ASP cc_start: 0.8190 (m-30) cc_final: 0.7889 (m-30) REVERT: G 169 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8335 (mm) REVERT: G 181 GLN cc_start: 0.8397 (OUTLIER) cc_final: 0.7803 (tm-30) REVERT: G 215 GLU cc_start: 0.7560 (tm-30) cc_final: 0.6722 (tm-30) REVERT: G 217 GLU cc_start: 0.8002 (tm-30) cc_final: 0.7582 (mm-30) REVERT: G 225 GLN cc_start: 0.8379 (tm-30) cc_final: 0.8125 (tm-30) REVERT: G 230 GLN cc_start: 0.8550 (OUTLIER) cc_final: 0.7999 (pp30) REVERT: G 231 ASP cc_start: 0.8225 (m-30) cc_final: 0.7699 (m-30) REVERT: G 232 LEU cc_start: 0.9176 (tt) cc_final: 0.8923 (tp) REVERT: G 237 ILE cc_start: 0.8869 (OUTLIER) cc_final: 0.8611 (tp) REVERT: G 299 ASN cc_start: 0.8307 (m110) cc_final: 0.7818 (m-40) REVERT: G 303 LYS cc_start: 0.8753 (mtpp) cc_final: 0.7748 (mtpp) REVERT: G 304 GLN cc_start: 0.8322 (pt0) cc_final: 0.7821 (pp30) REVERT: G 307 TYR cc_start: 0.7996 (m-80) cc_final: 0.7608 (m-80) REVERT: G 315 GLN cc_start: 0.8656 (tp40) cc_final: 0.8141 (tp-100) REVERT: G 317 GLU cc_start: 0.7938 (tp30) cc_final: 0.7118 (tp30) REVERT: G 321 ARG cc_start: 0.8443 (mtt180) cc_final: 0.7956 (mtt180) REVERT: G 344 TYR cc_start: 0.8187 (m-80) cc_final: 0.7515 (m-80) REVERT: G 401 LYS cc_start: 0.8469 (tptm) cc_final: 0.7735 (tppp) REVERT: G 407 LEU cc_start: 0.8003 (OUTLIER) cc_final: 0.7429 (pt) REVERT: G 411 ASP cc_start: 0.5457 (t0) cc_final: 0.5118 (t0) REVERT: H 9 GLN cc_start: 0.8630 (tp-100) cc_final: 0.8155 (tp40) REVERT: H 14 ASN cc_start: 0.8103 (t0) cc_final: 0.7670 (t0) REVERT: H 29 GLU cc_start: 0.7941 (tp30) cc_final: 0.7212 (tp30) REVERT: H 30 LYS cc_start: 0.8667 (ttpt) cc_final: 0.7280 (ttpt) REVERT: H 88 GLU cc_start: 0.8398 (mt-10) cc_final: 0.8117 (mt-10) REVERT: H 89 LYS cc_start: 0.8824 (mmmt) cc_final: 0.8387 (mmmt) REVERT: H 94 GLN cc_start: 0.8293 (tp40) cc_final: 0.7866 (tt0) REVERT: H 131 GLU cc_start: 0.8028 (tp30) cc_final: 0.7695 (tp30) REVERT: H 135 ARG cc_start: 0.8078 (OUTLIER) cc_final: 0.7473 (mmm160) REVERT: H 136 GLN cc_start: 0.8303 (tp-100) cc_final: 0.8072 (tp-100) REVERT: H 142 GLN cc_start: 0.8047 (mm-40) cc_final: 0.7650 (mm-40) REVERT: H 162 ASP cc_start: 0.8081 (m-30) cc_final: 0.7694 (m-30) REVERT: H 173 ASN cc_start: 0.8457 (m-40) cc_final: 0.8233 (m-40) REVERT: H 180 GLU cc_start: 0.8518 (mm-30) cc_final: 0.7916 (tm-30) REVERT: H 184 GLN cc_start: 0.8456 (tt0) cc_final: 0.7613 (tp-100) REVERT: H 218 LYS cc_start: 0.8774 (mmtt) cc_final: 0.8481 (mmtt) REVERT: H 224 LEU cc_start: 0.8634 (mp) cc_final: 0.8143 (mm) REVERT: H 230 GLN cc_start: 0.8223 (tp40) cc_final: 0.7640 (tp-100) REVERT: H 231 ASP cc_start: 0.7755 (t0) cc_final: 0.7470 (t0) REVERT: H 234 ARG cc_start: 0.8075 (mmm-85) cc_final: 0.7502 (mmm-85) REVERT: H 238 ARG cc_start: 0.8259 (mtt180) cc_final: 0.7923 (mtp85) REVERT: H 239 GLN cc_start: 0.8552 (tm-30) cc_final: 0.8299 (pp30) REVERT: H 297 MET cc_start: 0.6543 (ttm) cc_final: 0.6153 (ttm) REVERT: H 301 GLN cc_start: 0.8429 (mt0) cc_final: 0.7974 (mp10) REVERT: H 303 LYS cc_start: 0.8446 (mttt) cc_final: 0.7915 (mttt) REVERT: H 314 GLU cc_start: 0.7555 (mm-30) cc_final: 0.7167 (mm-30) REVERT: H 317 GLU cc_start: 0.7697 (tp30) cc_final: 0.7185 (tp30) REVERT: H 321 ARG cc_start: 0.8308 (mtt180) cc_final: 0.7587 (mtt180) REVERT: H 331 PHE cc_start: 0.9052 (t80) cc_final: 0.8787 (t80) REVERT: H 340 SER cc_start: 0.8756 (m) cc_final: 0.8182 (p) REVERT: H 358 MET cc_start: 0.7925 (mmm) cc_final: 0.7566 (mmm) REVERT: H 367 ARG cc_start: 0.8026 (tpp80) cc_final: 0.7733 (mtm-85) REVERT: H 374 ASP cc_start: 0.7782 (t0) cc_final: 0.7448 (t0) REVERT: H 390 ARG cc_start: 0.8658 (mtt-85) cc_final: 0.8407 (ttm170) REVERT: H 392 ASN cc_start: 0.8407 (m-40) cc_final: 0.7900 (t0) REVERT: H 396 ASN cc_start: 0.8192 (m-40) cc_final: 0.7723 (m-40) REVERT: H 397 GLN cc_start: 0.8111 (tt0) cc_final: 0.7408 (tm-30) REVERT: H 398 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8406 (mp) REVERT: H 412 LEU cc_start: 0.8475 (tp) cc_final: 0.8237 (tt) REVERT: I 8 GLN cc_start: 0.8463 (mm-40) cc_final: 0.7642 (mm-40) REVERT: I 11 ARG cc_start: 0.7922 (ttp80) cc_final: 0.6905 (ttp80) REVERT: I 16 GLU cc_start: 0.7942 (mp0) cc_final: 0.7440 (mp0) REVERT: I 24 ARG cc_start: 0.7923 (ttp-170) cc_final: 0.7457 (ttp-170) REVERT: I 31 ILE cc_start: 0.9075 (mt) cc_final: 0.8792 (mm) REVERT: I 42 LEU cc_start: 0.7605 (tt) cc_final: 0.7382 (tp) REVERT: I 76 PHE cc_start: 0.7551 (t80) cc_final: 0.6756 (t80) REVERT: I 95 ASP cc_start: 0.8245 (t0) cc_final: 0.7255 (t0) REVERT: I 99 GLN cc_start: 0.8321 (mt0) cc_final: 0.7857 (mt0) REVERT: I 103 GLN cc_start: 0.8519 (mt0) cc_final: 0.8272 (mm-40) REVERT: I 124 SER cc_start: 0.8612 (t) cc_final: 0.8380 (p) REVERT: I 160 GLN cc_start: 0.8197 (mm-40) cc_final: 0.7971 (mm-40) REVERT: I 185 ILE cc_start: 0.9239 (mt) cc_final: 0.8951 (tt) REVERT: I 215 GLU cc_start: 0.8076 (tp30) cc_final: 0.7584 (tp30) REVERT: I 217 GLU cc_start: 0.7564 (mm-30) cc_final: 0.7254 (mm-30) REVERT: I 224 LEU cc_start: 0.8768 (tp) cc_final: 0.8105 (mm) REVERT: I 225 GLN cc_start: 0.7982 (tm-30) cc_final: 0.7351 (tm-30) REVERT: I 227 ARG cc_start: 0.7731 (mtm-85) cc_final: 0.7207 (mtm-85) REVERT: I 235 GLU cc_start: 0.7915 (tp30) cc_final: 0.7534 (tp30) REVERT: I 236 GLN cc_start: 0.8334 (mt0) cc_final: 0.7983 (mt0) REVERT: I 238 ARG cc_start: 0.8052 (mpt180) cc_final: 0.7740 (mpt180) REVERT: I 241 GLN cc_start: 0.7973 (OUTLIER) cc_final: 0.7576 (mm110) REVERT: I 259 THR cc_start: 0.3507 (OUTLIER) cc_final: 0.3285 (m) REVERT: I 301 GLN cc_start: 0.8422 (tt0) cc_final: 0.8048 (mt0) REVERT: I 306 GLN cc_start: 0.8470 (pt0) cc_final: 0.8076 (pp30) REVERT: I 384 GLN cc_start: 0.7794 (tm-30) cc_final: 0.7369 (tm-30) REVERT: I 392 ASN cc_start: 0.8203 (m-40) cc_final: 0.6827 (m-40) REVERT: I 396 ASN cc_start: 0.8272 (m-40) cc_final: 0.7763 (m-40) outliers start: 175 outliers final: 111 residues processed: 1316 average time/residue: 0.2230 time to fit residues: 442.1032 Evaluate side-chains 1382 residues out of total 3232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 1241 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 194 GLU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 288 LYS Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 133 LYS Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 294 MET Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 344 SER Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 124 GLN Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 266 MET Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 340 SER Chi-restraints excluded: chain C residue 360 ARG Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 84 LYS Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 169 SER Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 288 LYS Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 353 GLN Chi-restraints excluded: chain D residue 379 LYS Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 65 MET Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 85 GLU Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 196 GLN Chi-restraints excluded: chain E residue 214 GLU Chi-restraints excluded: chain E residue 261 THR Chi-restraints excluded: chain E residue 275 THR Chi-restraints excluded: chain E residue 284 LYS Chi-restraints excluded: chain E residue 288 LYS Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain E residue 309 THR Chi-restraints excluded: chain E residue 344 SER Chi-restraints excluded: chain E residue 371 GLU Chi-restraints excluded: chain E residue 373 SER Chi-restraints excluded: chain E residue 386 LYS Chi-restraints excluded: chain F residue 110 SER Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 133 LYS Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 153 ASN Chi-restraints excluded: chain F residue 159 GLU Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 194 GLU Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 237 ILE Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 288 LYS Chi-restraints excluded: chain F residue 303 LEU Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain F residue 353 GLN Chi-restraints excluded: chain F residue 367 SER Chi-restraints excluded: chain F residue 386 LYS Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 122 LEU Chi-restraints excluded: chain J residue 166 HIS Chi-restraints excluded: chain J residue 213 ILE Chi-restraints excluded: chain J residue 219 MET Chi-restraints excluded: chain J residue 293 GLN Chi-restraints excluded: chain J residue 320 LEU Chi-restraints excluded: chain J residue 368 GLN Chi-restraints excluded: chain J residue 408 LEU Chi-restraints excluded: chain J residue 455 MET Chi-restraints excluded: chain J residue 466 GLN Chi-restraints excluded: chain J residue 494 LEU Chi-restraints excluded: chain G residue 3 LEU Chi-restraints excluded: chain G residue 11 ARG Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 142 GLN Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain G residue 181 GLN Chi-restraints excluded: chain G residue 203 THR Chi-restraints excluded: chain G residue 230 GLN Chi-restraints excluded: chain G residue 237 ILE Chi-restraints excluded: chain G residue 244 HIS Chi-restraints excluded: chain G residue 245 LEU Chi-restraints excluded: chain G residue 272 THR Chi-restraints excluded: chain G residue 318 SER Chi-restraints excluded: chain G residue 334 ILE Chi-restraints excluded: chain G residue 342 ASN Chi-restraints excluded: chain G residue 407 LEU Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 35 ARG Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 135 ARG Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 205 LYS Chi-restraints excluded: chain H residue 221 LEU Chi-restraints excluded: chain H residue 364 VAL Chi-restraints excluded: chain H residue 398 LEU Chi-restraints excluded: chain H residue 404 LEU Chi-restraints excluded: chain I residue 118 ASN Chi-restraints excluded: chain I residue 130 LYS Chi-restraints excluded: chain I residue 188 ASN Chi-restraints excluded: chain I residue 203 THR Chi-restraints excluded: chain I residue 241 GLN Chi-restraints excluded: chain I residue 259 THR Chi-restraints excluded: chain I residue 272 THR Chi-restraints excluded: chain I residue 292 ILE Chi-restraints excluded: chain I residue 297 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 41 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 303 optimal weight: 6.9990 chunk 323 optimal weight: 9.9990 chunk 91 optimal weight: 1.9990 chunk 235 optimal weight: 2.9990 chunk 214 optimal weight: 0.6980 chunk 244 optimal weight: 3.9990 chunk 199 optimal weight: 0.7980 chunk 234 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 ASN B 161 GLN B 317 GLN C 251 ASN D 184 ASN D 353 GLN F 251 ASN F 306 GLN F 327 GLN F 346 ASN J 34 ASN J 478 ASN G 108 ASN ** G 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 320 HIS I 70 GLN I 320 HIS I 325 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.111032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.093190 restraints weight = 58678.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.096131 restraints weight = 25972.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.097965 restraints weight = 14107.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.099160 restraints weight = 8873.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.099912 restraints weight = 6303.869| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.6386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 30315 Z= 0.261 Angle : 0.668 11.185 41246 Z= 0.357 Chirality : 0.045 0.171 4889 Planarity : 0.006 0.147 5392 Dihedral : 4.514 23.941 4179 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 6.37 % Allowed : 22.09 % Favored : 71.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.43 (0.14), residues: 3860 helix: 2.64 (0.11), residues: 2016 sheet: -0.37 (0.22), residues: 512 loop : -1.25 (0.16), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 322 TYR 0.030 0.002 TYR I 190 PHE 0.027 0.002 PHE J 339 TRP 0.032 0.002 TRP C 312 HIS 0.006 0.001 HIS J 429 Details of bonding type rmsd covalent geometry : bond 0.00544 (30315) covalent geometry : angle 0.66785 (41246) hydrogen bonds : bond 0.07104 ( 1888) hydrogen bonds : angle 4.61718 ( 5523) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7720 Ramachandran restraints generated. 3860 Oldfield, 0 Emsley, 3860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7720 Ramachandran restraints generated. 3860 Oldfield, 0 Emsley, 3860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1478 residues out of total 3232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 206 poor density : 1272 time to evaluate : 1.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.6971 (mm-30) cc_final: 0.6759 (mm-30) REVERT: A 54 ASP cc_start: 0.7696 (t0) cc_final: 0.7321 (t70) REVERT: A 57 VAL cc_start: 0.8568 (t) cc_final: 0.8271 (p) REVERT: A 79 ASN cc_start: 0.7775 (t0) cc_final: 0.7502 (t0) REVERT: A 130 GLU cc_start: 0.7598 (mm-30) cc_final: 0.7181 (mm-30) REVERT: A 138 LYS cc_start: 0.8230 (mttt) cc_final: 0.7942 (tttp) REVERT: A 143 TYR cc_start: 0.8178 (t80) cc_final: 0.7885 (t80) REVERT: A 146 ARG cc_start: 0.7835 (ttm-80) cc_final: 0.7538 (mtm-85) REVERT: A 154 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8429 (mp) REVERT: A 161 GLN cc_start: 0.7441 (pt0) cc_final: 0.7026 (pt0) REVERT: A 171 GLN cc_start: 0.8032 (tp40) cc_final: 0.6944 (tp40) REVERT: A 173 GLN cc_start: 0.7917 (mm-40) cc_final: 0.7704 (mm-40) REVERT: A 175 ASP cc_start: 0.6884 (OUTLIER) cc_final: 0.6146 (m-30) REVERT: A 228 ARG cc_start: 0.7698 (mtm-85) cc_final: 0.7332 (mtm-85) REVERT: A 237 ILE cc_start: 0.8083 (mm) cc_final: 0.7752 (pt) REVERT: A 259 LYS cc_start: 0.8162 (mtmm) cc_final: 0.7750 (mtmm) REVERT: A 284 LYS cc_start: 0.7424 (mtpp) cc_final: 0.7163 (mtpp) REVERT: A 317 GLN cc_start: 0.7620 (mm-40) cc_final: 0.7356 (mm-40) REVERT: A 347 THR cc_start: 0.7309 (OUTLIER) cc_final: 0.6834 (p) REVERT: A 379 LYS cc_start: 0.7994 (tttt) cc_final: 0.7732 (tttt) REVERT: A 381 ILE cc_start: 0.8539 (mt) cc_final: 0.8150 (mp) REVERT: B 50 GLU cc_start: 0.7667 (mm-30) cc_final: 0.7277 (mm-30) REVERT: B 51 GLU cc_start: 0.6728 (mp0) cc_final: 0.6459 (mp0) REVERT: B 66 SER cc_start: 0.7809 (t) cc_final: 0.7555 (p) REVERT: B 93 ASP cc_start: 0.7940 (t0) cc_final: 0.7667 (t70) REVERT: B 98 ARG cc_start: 0.7341 (tpp80) cc_final: 0.7073 (ttm-80) REVERT: B 123 LYS cc_start: 0.7647 (mttp) cc_final: 0.7234 (mttp) REVERT: B 130 GLU cc_start: 0.7265 (mm-30) cc_final: 0.6859 (tm-30) REVERT: B 145 ARG cc_start: 0.7965 (mtt-85) cc_final: 0.7068 (mtt-85) REVERT: B 158 GLU cc_start: 0.7027 (tt0) cc_final: 0.6503 (tm-30) REVERT: B 159 GLU cc_start: 0.7770 (tp30) cc_final: 0.7509 (tp30) REVERT: B 162 HIS cc_start: 0.7830 (m-70) cc_final: 0.6986 (m90) REVERT: B 171 GLN cc_start: 0.8100 (tp40) cc_final: 0.7727 (tp40) REVERT: B 179 GLN cc_start: 0.7699 (mm-40) cc_final: 0.7235 (mm-40) REVERT: B 194 GLU cc_start: 0.7478 (pp20) cc_final: 0.7258 (pp20) REVERT: B 207 ARG cc_start: 0.7415 (mtt90) cc_final: 0.7072 (mtt-85) REVERT: B 294 MET cc_start: 0.7089 (OUTLIER) cc_final: 0.6597 (mtp) REVERT: B 328 LYS cc_start: 0.8274 (mmpt) cc_final: 0.7945 (mmpt) REVERT: B 329 GLN cc_start: 0.7143 (mt0) cc_final: 0.6789 (mp10) REVERT: B 330 LEU cc_start: 0.8279 (tt) cc_final: 0.7904 (tp) REVERT: B 332 GLN cc_start: 0.7573 (mm-40) cc_final: 0.6874 (tp40) REVERT: B 333 TYR cc_start: 0.7958 (m-10) cc_final: 0.7699 (m-10) REVERT: B 379 LYS cc_start: 0.8281 (tttt) cc_final: 0.8007 (ttmt) REVERT: B 386 LYS cc_start: 0.8152 (tttt) cc_final: 0.7770 (tttt) REVERT: C 53 ASP cc_start: 0.6832 (t0) cc_final: 0.6576 (t0) REVERT: C 54 ASP cc_start: 0.7392 (t0) cc_final: 0.7170 (t0) REVERT: C 103 LYS cc_start: 0.7975 (tttt) cc_final: 0.7656 (tttt) REVERT: C 117 GLN cc_start: 0.7396 (mt0) cc_final: 0.6802 (mt0) REVERT: C 121 ASN cc_start: 0.7275 (m-40) cc_final: 0.6826 (m-40) REVERT: C 133 LYS cc_start: 0.8271 (mtpt) cc_final: 0.7978 (mtpt) REVERT: C 138 LYS cc_start: 0.7801 (tttt) cc_final: 0.7460 (ptmm) REVERT: C 158 GLU cc_start: 0.7724 (tt0) cc_final: 0.7470 (tt0) REVERT: C 164 ARG cc_start: 0.6829 (ttp80) cc_final: 0.6320 (ttp80) REVERT: C 195 ASP cc_start: 0.7547 (m-30) cc_final: 0.6992 (m-30) REVERT: C 200 GLN cc_start: 0.6973 (mt0) cc_final: 0.6510 (mt0) REVERT: C 229 ARG cc_start: 0.7552 (OUTLIER) cc_final: 0.6319 (ttm-80) REVERT: C 231 VAL cc_start: 0.8338 (OUTLIER) cc_final: 0.8065 (p) REVERT: C 257 ASN cc_start: 0.7898 (m-40) cc_final: 0.7401 (m110) REVERT: C 262 GLN cc_start: 0.7157 (pm20) cc_final: 0.6707 (mp10) REVERT: C 296 THR cc_start: 0.7588 (p) cc_final: 0.7246 (t) REVERT: C 332 GLN cc_start: 0.7391 (tm-30) cc_final: 0.6977 (tp40) REVERT: C 340 SER cc_start: 0.8386 (OUTLIER) cc_final: 0.8143 (p) REVERT: C 353 GLN cc_start: 0.5480 (tm-30) cc_final: 0.5161 (tm-30) REVERT: C 360 ARG cc_start: 0.7347 (OUTLIER) cc_final: 0.7053 (ptp-170) REVERT: C 379 LYS cc_start: 0.7812 (ttmt) cc_final: 0.7569 (ttmt) REVERT: D 50 GLU cc_start: 0.6762 (OUTLIER) cc_final: 0.6352 (tp30) REVERT: D 54 ASP cc_start: 0.6857 (t0) cc_final: 0.5896 (t0) REVERT: D 61 GLN cc_start: 0.8032 (OUTLIER) cc_final: 0.7732 (pm20) REVERT: D 73 THR cc_start: 0.8550 (OUTLIER) cc_final: 0.8290 (m) REVERT: D 110 SER cc_start: 0.8547 (t) cc_final: 0.8347 (m) REVERT: D 117 GLN cc_start: 0.7928 (tt0) cc_final: 0.7328 (tt0) REVERT: D 121 ASN cc_start: 0.7946 (m-40) cc_final: 0.7525 (m-40) REVERT: D 138 LYS cc_start: 0.8244 (tttt) cc_final: 0.7922 (tttt) REVERT: D 147 VAL cc_start: 0.8863 (t) cc_final: 0.8648 (t) REVERT: D 157 ARG cc_start: 0.7236 (mtm110) cc_final: 0.6896 (mtm110) REVERT: D 161 GLN cc_start: 0.7358 (mp10) cc_final: 0.7109 (mp10) REVERT: D 164 ARG cc_start: 0.7934 (ttp80) cc_final: 0.7339 (ttm-80) REVERT: D 189 LEU cc_start: 0.7584 (tp) cc_final: 0.7354 (tt) REVERT: D 228 ARG cc_start: 0.7006 (mtp85) cc_final: 0.6601 (mtt90) REVERT: D 257 ASN cc_start: 0.8020 (m-40) cc_final: 0.6898 (m110) REVERT: D 294 MET cc_start: 0.7559 (mmm) cc_final: 0.7287 (mmm) REVERT: D 309 THR cc_start: 0.7828 (p) cc_final: 0.7382 (m) REVERT: D 311 ASN cc_start: 0.7559 (p0) cc_final: 0.7331 (p0) REVERT: D 314 LYS cc_start: 0.7126 (tttt) cc_final: 0.6746 (tptt) REVERT: D 324 GLU cc_start: 0.6786 (tm-30) cc_final: 0.6492 (tm-30) REVERT: D 331 GLU cc_start: 0.7048 (mp0) cc_final: 0.6645 (mp0) REVERT: D 332 GLN cc_start: 0.7379 (tp40) cc_final: 0.6941 (tp40) REVERT: D 378 ASN cc_start: 0.7908 (m-40) cc_final: 0.7062 (m-40) REVERT: D 382 ASP cc_start: 0.7227 (m-30) cc_final: 0.6725 (m-30) REVERT: D 385 VAL cc_start: 0.8498 (t) cc_final: 0.8173 (p) REVERT: E 53 ASP cc_start: 0.7072 (t70) cc_final: 0.5531 (t0) REVERT: E 85 GLU cc_start: 0.6916 (OUTLIER) cc_final: 0.6453 (tm-30) REVERT: E 142 ASP cc_start: 0.7402 (m-30) cc_final: 0.7054 (m-30) REVERT: E 153 ASN cc_start: 0.7782 (t0) cc_final: 0.7143 (p0) REVERT: E 154 LEU cc_start: 0.8221 (mt) cc_final: 0.7913 (mm) REVERT: E 161 GLN cc_start: 0.7860 (tt0) cc_final: 0.7625 (mm-40) REVERT: E 187 MET cc_start: 0.7310 (mmt) cc_final: 0.5206 (mmt) REVERT: E 192 LYS cc_start: 0.7636 (mmmm) cc_final: 0.7230 (mmmm) REVERT: E 196 GLN cc_start: 0.7882 (OUTLIER) cc_final: 0.7201 (mp10) REVERT: E 217 ARG cc_start: 0.6929 (mtt-85) cc_final: 0.6536 (mtt-85) REVERT: E 251 ASN cc_start: 0.7316 (t0) cc_final: 0.6973 (t0) REVERT: E 294 MET cc_start: 0.6647 (mmm) cc_final: 0.6415 (mmm) REVERT: F 50 GLU cc_start: 0.7640 (mm-30) cc_final: 0.7152 (mm-30) REVERT: F 80 THR cc_start: 0.8108 (t) cc_final: 0.7826 (p) REVERT: F 124 GLN cc_start: 0.7508 (mt0) cc_final: 0.7197 (mt0) REVERT: F 126 GLN cc_start: 0.7109 (tp40) cc_final: 0.6697 (tp40) REVERT: F 133 LYS cc_start: 0.8031 (OUTLIER) cc_final: 0.7632 (tttt) REVERT: F 138 LYS cc_start: 0.8558 (ttpt) cc_final: 0.8215 (tttp) REVERT: F 141 SER cc_start: 0.8396 (m) cc_final: 0.8099 (t) REVERT: F 143 TYR cc_start: 0.7895 (t80) cc_final: 0.7579 (t80) REVERT: F 145 ARG cc_start: 0.7414 (mtm-85) cc_final: 0.7008 (ttm170) REVERT: F 157 ARG cc_start: 0.7297 (mtm-85) cc_final: 0.7051 (mtm-85) REVERT: F 158 GLU cc_start: 0.7228 (tp30) cc_final: 0.6453 (tp30) REVERT: F 161 GLN cc_start: 0.7477 (tp40) cc_final: 0.6781 (tp40) REVERT: F 164 ARG cc_start: 0.7660 (ttm-80) cc_final: 0.7211 (ttm-80) REVERT: F 178 ILE cc_start: 0.8078 (mt) cc_final: 0.7878 (mm) REVERT: F 192 LYS cc_start: 0.8063 (mttp) cc_final: 0.7734 (mttp) REVERT: F 200 GLN cc_start: 0.7144 (mp10) cc_final: 0.6547 (mp10) REVERT: F 205 GLU cc_start: 0.7489 (mm-30) cc_final: 0.7263 (mt-10) REVERT: F 214 GLU cc_start: 0.7596 (tp30) cc_final: 0.6877 (mp0) REVERT: F 217 ARG cc_start: 0.6903 (mtt180) cc_final: 0.6487 (ptp-170) REVERT: F 259 LYS cc_start: 0.7682 (mmtp) cc_final: 0.7147 (mttp) REVERT: F 288 LYS cc_start: 0.8321 (OUTLIER) cc_final: 0.7834 (mtmt) REVERT: F 317 GLN cc_start: 0.7249 (mm-40) cc_final: 0.6942 (mp10) REVERT: F 371 GLU cc_start: 0.6189 (tp30) cc_final: 0.5772 (tp30) REVERT: F 372 ILE cc_start: 0.8692 (mp) cc_final: 0.7979 (mm) REVERT: F 379 LYS cc_start: 0.7749 (tptm) cc_final: 0.7232 (tptm) REVERT: F 383 ASP cc_start: 0.7157 (m-30) cc_final: 0.6796 (m-30) REVERT: J 21 LEU cc_start: 0.8242 (mt) cc_final: 0.7998 (mm) REVERT: J 66 ILE cc_start: 0.8611 (mt) cc_final: 0.8249 (mm) REVERT: J 87 ILE cc_start: 0.8660 (tt) cc_final: 0.8424 (pt) REVERT: J 114 ILE cc_start: 0.8296 (mm) cc_final: 0.7971 (mm) REVERT: J 120 ILE cc_start: 0.7938 (mt) cc_final: 0.7680 (mm) REVERT: J 122 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.7682 (mp) REVERT: J 124 GLN cc_start: 0.7837 (tt0) cc_final: 0.7262 (tt0) REVERT: J 126 LEU cc_start: 0.8445 (mt) cc_final: 0.7898 (mm) REVERT: J 145 MET cc_start: 0.6700 (tmm) cc_final: 0.6188 (tmm) REVERT: J 161 ILE cc_start: 0.8396 (mm) cc_final: 0.8041 (mp) REVERT: J 181 VAL cc_start: 0.8662 (t) cc_final: 0.8415 (p) REVERT: J 213 ILE cc_start: 0.8331 (OUTLIER) cc_final: 0.8061 (mt) REVERT: J 217 GLN cc_start: 0.7885 (tp40) cc_final: 0.7264 (tt0) REVERT: J 233 GLU cc_start: 0.7647 (mp0) cc_final: 0.7275 (mp0) REVERT: J 251 TRP cc_start: 0.7165 (t-100) cc_final: 0.6844 (t-100) REVERT: J 252 GLU cc_start: 0.7272 (mm-30) cc_final: 0.6850 (tp30) REVERT: J 268 ARG cc_start: 0.7717 (ttt180) cc_final: 0.7488 (ttt180) REVERT: J 271 THR cc_start: 0.8336 (m) cc_final: 0.8096 (p) REVERT: J 297 GLU cc_start: 0.7398 (tt0) cc_final: 0.7128 (tt0) REVERT: J 308 LEU cc_start: 0.8030 (mt) cc_final: 0.7774 (mm) REVERT: J 327 PHE cc_start: 0.6701 (t80) cc_final: 0.5945 (t80) REVERT: J 333 MET cc_start: 0.7351 (mtm) cc_final: 0.7111 (mtm) REVERT: J 342 ILE cc_start: 0.8248 (mm) cc_final: 0.7989 (tt) REVERT: J 359 MET cc_start: 0.7239 (mtm) cc_final: 0.6680 (mtm) REVERT: J 361 PHE cc_start: 0.7307 (t80) cc_final: 0.6995 (t80) REVERT: J 368 GLN cc_start: 0.7154 (OUTLIER) cc_final: 0.6730 (mt0) REVERT: J 384 THR cc_start: 0.8282 (m) cc_final: 0.8037 (p) REVERT: J 395 LEU cc_start: 0.7943 (mt) cc_final: 0.7560 (mt) REVERT: J 402 SER cc_start: 0.8096 (t) cc_final: 0.7862 (m) REVERT: J 403 ASN cc_start: 0.8295 (m-40) cc_final: 0.7760 (m110) REVERT: J 408 LEU cc_start: 0.7460 (OUTLIER) cc_final: 0.7165 (tt) REVERT: J 421 TRP cc_start: 0.8233 (t60) cc_final: 0.7862 (t60) REVERT: J 424 ARG cc_start: 0.7466 (mmm160) cc_final: 0.6758 (mmm160) REVERT: J 428 HIS cc_start: 0.8256 (m-70) cc_final: 0.7968 (m-70) REVERT: J 457 GLN cc_start: 0.7659 (mm-40) cc_final: 0.7248 (tp-100) REVERT: J 458 GLN cc_start: 0.8302 (tt0) cc_final: 0.7950 (tt0) REVERT: J 459 GLN cc_start: 0.8037 (mt0) cc_final: 0.7756 (mt0) REVERT: J 466 GLN cc_start: 0.7736 (OUTLIER) cc_final: 0.7301 (mp10) REVERT: J 467 GLN cc_start: 0.8002 (mm-40) cc_final: 0.7547 (mm110) REVERT: J 471 GLN cc_start: 0.7815 (mm-40) cc_final: 0.7210 (mm-40) REVERT: J 488 PHE cc_start: 0.8201 (m-80) cc_final: 0.7571 (m-80) REVERT: J 489 LEU cc_start: 0.8428 (mt) cc_final: 0.8161 (mt) REVERT: J 491 LEU cc_start: 0.7933 (mt) cc_final: 0.7558 (pp) REVERT: G 3 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8498 (tp) REVERT: G 5 GLN cc_start: 0.8347 (mt0) cc_final: 0.7645 (mt0) REVERT: G 9 GLN cc_start: 0.7089 (tm-30) cc_final: 0.6614 (tm-30) REVERT: G 17 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8250 (tt) REVERT: G 19 LYS cc_start: 0.8294 (tttm) cc_final: 0.7987 (tttm) REVERT: G 24 ARG cc_start: 0.7819 (tpt170) cc_final: 0.7237 (tpt170) REVERT: G 28 PHE cc_start: 0.7326 (t80) cc_final: 0.7021 (t80) REVERT: G 29 GLU cc_start: 0.7852 (tp30) cc_final: 0.6672 (tp30) REVERT: G 30 LYS cc_start: 0.8785 (tttt) cc_final: 0.8362 (tttt) REVERT: G 31 ILE cc_start: 0.8761 (mt) cc_final: 0.8517 (mm) REVERT: G 32 ASN cc_start: 0.8215 (m-40) cc_final: 0.6872 (p0) REVERT: G 42 LEU cc_start: 0.8400 (mp) cc_final: 0.8153 (mm) REVERT: G 77 ASP cc_start: 0.8697 (t0) cc_final: 0.5024 (p0) REVERT: G 81 TRP cc_start: 0.7282 (m100) cc_final: 0.7076 (m100) REVERT: G 87 GLN cc_start: 0.8486 (tp40) cc_final: 0.7989 (tp40) REVERT: G 88 GLU cc_start: 0.8097 (pt0) cc_final: 0.7874 (pt0) REVERT: G 99 GLN cc_start: 0.7763 (tm-30) cc_final: 0.7346 (tm-30) REVERT: G 101 ASP cc_start: 0.7716 (t70) cc_final: 0.7232 (t0) REVERT: G 103 GLN cc_start: 0.8279 (mm-40) cc_final: 0.8074 (mm-40) REVERT: G 125 TYR cc_start: 0.8886 (t80) cc_final: 0.8615 (t80) REVERT: G 130 LYS cc_start: 0.8710 (tttt) cc_final: 0.8157 (ttpp) REVERT: G 136 GLN cc_start: 0.8447 (tp40) cc_final: 0.8133 (tp-100) REVERT: G 142 GLN cc_start: 0.7798 (OUTLIER) cc_final: 0.7462 (mm-40) REVERT: G 162 ASP cc_start: 0.8214 (m-30) cc_final: 0.7944 (m-30) REVERT: G 168 GLU cc_start: 0.8315 (tt0) cc_final: 0.8088 (tt0) REVERT: G 169 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8378 (mm) REVERT: G 181 GLN cc_start: 0.8381 (OUTLIER) cc_final: 0.7786 (tm-30) REVERT: G 215 GLU cc_start: 0.7603 (tm-30) cc_final: 0.6790 (tm-30) REVERT: G 217 GLU cc_start: 0.8026 (tm-30) cc_final: 0.7639 (mm-30) REVERT: G 225 GLN cc_start: 0.8379 (tm-30) cc_final: 0.8148 (tm-30) REVERT: G 230 GLN cc_start: 0.8582 (OUTLIER) cc_final: 0.8032 (pp30) REVERT: G 231 ASP cc_start: 0.8201 (m-30) cc_final: 0.7711 (m-30) REVERT: G 232 LEU cc_start: 0.9282 (OUTLIER) cc_final: 0.8702 (tt) REVERT: G 236 GLN cc_start: 0.8302 (mt0) cc_final: 0.7758 (mm-40) REVERT: G 237 ILE cc_start: 0.8876 (OUTLIER) cc_final: 0.8627 (tp) REVERT: G 279 MET cc_start: 0.4310 (tpt) cc_final: 0.3643 (tpt) REVERT: G 299 ASN cc_start: 0.8373 (m110) cc_final: 0.7865 (m-40) REVERT: G 303 LYS cc_start: 0.8766 (mtpp) cc_final: 0.7780 (mtpp) REVERT: G 304 GLN cc_start: 0.8300 (pt0) cc_final: 0.7802 (pp30) REVERT: G 307 TYR cc_start: 0.8037 (m-80) cc_final: 0.7600 (m-80) REVERT: G 315 GLN cc_start: 0.8658 (tp40) cc_final: 0.8151 (tp-100) REVERT: G 317 GLU cc_start: 0.7961 (tp30) cc_final: 0.7183 (tp30) REVERT: G 321 ARG cc_start: 0.8459 (mtt180) cc_final: 0.8052 (mtt180) REVERT: G 344 TYR cc_start: 0.8214 (m-80) cc_final: 0.7644 (m-80) REVERT: G 401 LYS cc_start: 0.8494 (tptm) cc_final: 0.7747 (tppp) REVERT: G 407 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7559 (pt) REVERT: G 411 ASP cc_start: 0.5801 (t0) cc_final: 0.5551 (t0) REVERT: H 5 GLN cc_start: 0.8456 (mp10) cc_final: 0.8246 (mp10) REVERT: H 14 ASN cc_start: 0.8158 (t0) cc_final: 0.7764 (t0) REVERT: H 29 GLU cc_start: 0.7964 (tp30) cc_final: 0.7502 (tp30) REVERT: H 30 LYS cc_start: 0.8668 (ttpt) cc_final: 0.7667 (ttpt) REVERT: H 87 GLN cc_start: 0.7903 (tp-100) cc_final: 0.7103 (tp40) REVERT: H 88 GLU cc_start: 0.8443 (mt-10) cc_final: 0.8085 (mt-10) REVERT: H 94 GLN cc_start: 0.8192 (tp40) cc_final: 0.7790 (tt0) REVERT: H 95 ASP cc_start: 0.8733 (m-30) cc_final: 0.8530 (m-30) REVERT: H 131 GLU cc_start: 0.8056 (tp30) cc_final: 0.7750 (tp30) REVERT: H 135 ARG cc_start: 0.8091 (OUTLIER) cc_final: 0.7487 (mmm160) REVERT: H 136 GLN cc_start: 0.8345 (tp-100) cc_final: 0.7942 (tp40) REVERT: H 142 GLN cc_start: 0.8077 (mm-40) cc_final: 0.7579 (mm-40) REVERT: H 162 ASP cc_start: 0.8167 (m-30) cc_final: 0.7917 (m-30) REVERT: H 173 ASN cc_start: 0.8471 (m-40) cc_final: 0.8078 (m-40) REVERT: H 180 GLU cc_start: 0.8596 (mm-30) cc_final: 0.7946 (tm-30) REVERT: H 184 GLN cc_start: 0.8518 (tt0) cc_final: 0.7742 (tp-100) REVERT: H 218 LYS cc_start: 0.8791 (mmtt) cc_final: 0.8523 (mmtt) REVERT: H 230 GLN cc_start: 0.8243 (tp40) cc_final: 0.7563 (tp40) REVERT: H 231 ASP cc_start: 0.7869 (t0) cc_final: 0.7357 (t0) REVERT: H 236 GLN cc_start: 0.8257 (mt0) cc_final: 0.7845 (tm-30) REVERT: H 297 MET cc_start: 0.6536 (ttm) cc_final: 0.6169 (tmm) REVERT: H 301 GLN cc_start: 0.8403 (mt0) cc_final: 0.7863 (mp10) REVERT: H 303 LYS cc_start: 0.8523 (mttt) cc_final: 0.8000 (mttt) REVERT: H 306 GLN cc_start: 0.8352 (OUTLIER) cc_final: 0.8101 (mm-40) REVERT: H 314 GLU cc_start: 0.7520 (mm-30) cc_final: 0.7133 (mm-30) REVERT: H 317 GLU cc_start: 0.7734 (tp30) cc_final: 0.7224 (tp30) REVERT: H 320 HIS cc_start: 0.8322 (OUTLIER) cc_final: 0.8025 (t70) REVERT: H 321 ARG cc_start: 0.8344 (mtt180) cc_final: 0.7655 (mtt180) REVERT: H 331 PHE cc_start: 0.9050 (t80) cc_final: 0.8812 (t80) REVERT: H 340 SER cc_start: 0.8756 (m) cc_final: 0.8213 (p) REVERT: H 341 ILE cc_start: 0.8877 (OUTLIER) cc_final: 0.8643 (tt) REVERT: H 358 MET cc_start: 0.7934 (mmm) cc_final: 0.7507 (mmm) REVERT: H 367 ARG cc_start: 0.7990 (tpp80) cc_final: 0.7655 (mtm-85) REVERT: H 374 ASP cc_start: 0.7761 (t0) cc_final: 0.7460 (t0) REVERT: H 390 ARG cc_start: 0.8683 (mtt-85) cc_final: 0.8462 (ttm170) REVERT: H 392 ASN cc_start: 0.8430 (m-40) cc_final: 0.7937 (t0) REVERT: H 396 ASN cc_start: 0.8204 (m-40) cc_final: 0.7790 (m-40) REVERT: H 397 GLN cc_start: 0.8103 (tt0) cc_final: 0.7443 (tm-30) REVERT: H 398 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8385 (mp) REVERT: H 412 LEU cc_start: 0.8447 (tp) cc_final: 0.8206 (tt) REVERT: I 4 MET cc_start: 0.7726 (tmm) cc_final: 0.7350 (tmm) REVERT: I 16 GLU cc_start: 0.7984 (mp0) cc_final: 0.7470 (mp0) REVERT: I 24 ARG cc_start: 0.7937 (ttp-170) cc_final: 0.7616 (ttp-110) REVERT: I 28 PHE cc_start: 0.8214 (m-80) cc_final: 0.7892 (m-80) REVERT: I 31 ILE cc_start: 0.9083 (mt) cc_final: 0.8841 (mm) REVERT: I 42 LEU cc_start: 0.7649 (tt) cc_final: 0.7433 (tp) REVERT: I 76 PHE cc_start: 0.7567 (t80) cc_final: 0.6887 (t80) REVERT: I 99 GLN cc_start: 0.8369 (mt0) cc_final: 0.8079 (mt0) REVERT: I 103 GLN cc_start: 0.8528 (mt0) cc_final: 0.8304 (mm-40) REVERT: I 124 SER cc_start: 0.8625 (t) cc_final: 0.8393 (p) REVERT: I 135 ARG cc_start: 0.8085 (tpp-160) cc_final: 0.7787 (tpp-160) REVERT: I 160 GLN cc_start: 0.8251 (mm-40) cc_final: 0.8007 (mm-40) REVERT: I 185 ILE cc_start: 0.9257 (mt) cc_final: 0.9006 (tt) REVERT: I 215 GLU cc_start: 0.8164 (tp30) cc_final: 0.7665 (tp30) REVERT: I 217 GLU cc_start: 0.7591 (mm-30) cc_final: 0.7254 (mm-30) REVERT: I 224 LEU cc_start: 0.8817 (tp) cc_final: 0.8231 (mm) REVERT: I 225 GLN cc_start: 0.8072 (tm-30) cc_final: 0.7417 (tm-30) REVERT: I 227 ARG cc_start: 0.7816 (mtm-85) cc_final: 0.7288 (mtm-85) REVERT: I 235 GLU cc_start: 0.7951 (tp30) cc_final: 0.7558 (tp30) REVERT: I 236 GLN cc_start: 0.8357 (mt0) cc_final: 0.8021 (mt0) REVERT: I 238 ARG cc_start: 0.8116 (mpt180) cc_final: 0.7865 (mpt180) REVERT: I 241 GLN cc_start: 0.8041 (OUTLIER) cc_final: 0.7648 (mm110) REVERT: I 259 THR cc_start: 0.3583 (OUTLIER) cc_final: 0.3381 (m) REVERT: I 301 GLN cc_start: 0.8430 (tt0) cc_final: 0.8070 (mt0) REVERT: I 306 GLN cc_start: 0.8471 (pt0) cc_final: 0.8216 (pp30) REVERT: I 396 ASN cc_start: 0.8291 (m-40) cc_final: 0.7771 (m-40) outliers start: 206 outliers final: 135 residues processed: 1355 average time/residue: 0.2299 time to fit residues: 471.6259 Evaluate side-chains 1427 residues out of total 3232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 1256 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 194 GLU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 133 LYS Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 161 GLN Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 294 MET Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 344 SER Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 124 GLN Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 187 MET Chi-restraints excluded: chain C residue 229 ARG Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 266 MET Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 340 SER Chi-restraints excluded: chain C residue 360 ARG Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain D residue 61 GLN Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 84 LYS Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 169 SER Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 288 LYS Chi-restraints excluded: chain D residue 306 GLN Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 372 ILE Chi-restraints excluded: chain D residue 379 LYS Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 65 MET Chi-restraints excluded: chain E residue 85 GLU Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 196 GLN Chi-restraints excluded: chain E residue 214 GLU Chi-restraints excluded: chain E residue 227 SER Chi-restraints excluded: chain E residue 261 THR Chi-restraints excluded: chain E residue 273 THR Chi-restraints excluded: chain E residue 275 THR Chi-restraints excluded: chain E residue 284 LYS Chi-restraints excluded: chain E residue 288 LYS Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain E residue 311 ASN Chi-restraints excluded: chain E residue 344 SER Chi-restraints excluded: chain E residue 371 GLU Chi-restraints excluded: chain E residue 373 SER Chi-restraints excluded: chain E residue 386 LYS Chi-restraints excluded: chain F residue 69 SER Chi-restraints excluded: chain F residue 110 SER Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 133 LYS Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 153 ASN Chi-restraints excluded: chain F residue 159 GLU Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 194 GLU Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 237 ILE Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 288 LYS Chi-restraints excluded: chain F residue 303 LEU Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain F residue 353 GLN Chi-restraints excluded: chain F residue 367 SER Chi-restraints excluded: chain F residue 380 LEU Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain J residue 122 LEU Chi-restraints excluded: chain J residue 166 HIS Chi-restraints excluded: chain J residue 213 ILE Chi-restraints excluded: chain J residue 219 MET Chi-restraints excluded: chain J residue 293 GLN Chi-restraints excluded: chain J residue 320 LEU Chi-restraints excluded: chain J residue 324 ILE Chi-restraints excluded: chain J residue 368 GLN Chi-restraints excluded: chain J residue 408 LEU Chi-restraints excluded: chain J residue 419 THR Chi-restraints excluded: chain J residue 466 GLN Chi-restraints excluded: chain J residue 483 MET Chi-restraints excluded: chain J residue 490 VAL Chi-restraints excluded: chain J residue 494 LEU Chi-restraints excluded: chain G residue 3 LEU Chi-restraints excluded: chain G residue 11 ARG Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 142 GLN Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain G residue 177 ASN Chi-restraints excluded: chain G residue 181 GLN Chi-restraints excluded: chain G residue 203 THR Chi-restraints excluded: chain G residue 230 GLN Chi-restraints excluded: chain G residue 232 LEU Chi-restraints excluded: chain G residue 237 ILE Chi-restraints excluded: chain G residue 245 LEU Chi-restraints excluded: chain G residue 272 THR Chi-restraints excluded: chain G residue 318 SER Chi-restraints excluded: chain G residue 334 ILE Chi-restraints excluded: chain G residue 342 ASN Chi-restraints excluded: chain G residue 345 LYS Chi-restraints excluded: chain G residue 407 LEU Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 135 ARG Chi-restraints excluded: chain H residue 143 ARG Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 205 LYS Chi-restraints excluded: chain H residue 221 LEU Chi-restraints excluded: chain H residue 245 LEU Chi-restraints excluded: chain H residue 250 LEU Chi-restraints excluded: chain H residue 306 GLN Chi-restraints excluded: chain H residue 320 HIS Chi-restraints excluded: chain H residue 341 ILE Chi-restraints excluded: chain H residue 364 VAL Chi-restraints excluded: chain H residue 398 LEU Chi-restraints excluded: chain H residue 404 LEU Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 203 THR Chi-restraints excluded: chain I residue 232 LEU Chi-restraints excluded: chain I residue 241 GLN Chi-restraints excluded: chain I residue 259 THR Chi-restraints excluded: chain I residue 272 THR Chi-restraints excluded: chain I residue 279 MET Chi-restraints excluded: chain I residue 292 ILE Chi-restraints excluded: chain I residue 297 MET Chi-restraints excluded: chain I residue 328 ARG Chi-restraints excluded: chain I residue 398 LEU Chi-restraints excluded: chain I residue 409 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 291 optimal weight: 3.9990 chunk 136 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 235 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 206 optimal weight: 0.9990 chunk 326 optimal weight: 2.9990 chunk 301 optimal weight: 2.9990 chunk 376 optimal weight: 0.4980 chunk 349 optimal weight: 2.9990 chunk 88 optimal weight: 0.0060 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 ASN ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 161 GLN C 61 GLN C 251 ASN E 185 GLN E 306 GLN F 251 ASN F 346 ASN J 130 ASN J 478 ASN G 156 ASN ** G 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 294 GLN I 70 GLN I 118 ASN ** I 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 320 HIS I 325 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.113090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.095277 restraints weight = 58660.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.098236 restraints weight = 25844.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.100067 restraints weight = 13984.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.101292 restraints weight = 8801.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.102032 restraints weight = 6212.511| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.6515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 30315 Z= 0.161 Angle : 0.633 13.782 41246 Z= 0.329 Chirality : 0.043 0.177 4889 Planarity : 0.005 0.096 5392 Dihedral : 4.203 20.564 4179 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 5.32 % Allowed : 24.60 % Favored : 70.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.75 (0.14), residues: 3860 helix: 2.96 (0.11), residues: 2005 sheet: -0.20 (0.23), residues: 501 loop : -1.17 (0.16), residues: 1354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 18 TYR 0.024 0.002 TYR D 143 PHE 0.029 0.001 PHE J 339 TRP 0.057 0.002 TRP E 312 HIS 0.013 0.001 HIS H 320 Details of bonding type rmsd covalent geometry : bond 0.00334 (30315) covalent geometry : angle 0.63308 (41246) hydrogen bonds : bond 0.06423 ( 1888) hydrogen bonds : angle 4.31609 ( 5523) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7720 Ramachandran restraints generated. 3860 Oldfield, 0 Emsley, 3860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7720 Ramachandran restraints generated. 3860 Oldfield, 0 Emsley, 3860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1447 residues out of total 3232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 1275 time to evaluate : 1.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.6990 (mm-30) cc_final: 0.6761 (mm-30) REVERT: A 79 ASN cc_start: 0.7720 (t0) cc_final: 0.7413 (t0) REVERT: A 130 GLU cc_start: 0.7521 (mm-30) cc_final: 0.7110 (mm-30) REVERT: A 138 LYS cc_start: 0.8208 (tttt) cc_final: 0.7869 (tttm) REVERT: A 143 TYR cc_start: 0.8141 (t80) cc_final: 0.7750 (t80) REVERT: A 154 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8444 (mp) REVERT: A 161 GLN cc_start: 0.7380 (pt0) cc_final: 0.6949 (pt0) REVERT: A 171 GLN cc_start: 0.7986 (tp40) cc_final: 0.6964 (tp40) REVERT: A 175 ASP cc_start: 0.6850 (OUTLIER) cc_final: 0.6206 (m-30) REVERT: A 178 ILE cc_start: 0.8459 (tt) cc_final: 0.8129 (pt) REVERT: A 214 GLU cc_start: 0.7712 (mm-30) cc_final: 0.7325 (mm-30) REVERT: A 228 ARG cc_start: 0.7452 (mtm-85) cc_final: 0.7087 (mtm-85) REVERT: A 237 ILE cc_start: 0.8045 (mm) cc_final: 0.7825 (pt) REVERT: A 259 LYS cc_start: 0.8128 (mtmm) cc_final: 0.7739 (mtmm) REVERT: A 284 LYS cc_start: 0.7378 (mtpp) cc_final: 0.7146 (mtpp) REVERT: A 317 GLN cc_start: 0.7634 (mm-40) cc_final: 0.7259 (mm-40) REVERT: A 331 GLU cc_start: 0.6807 (pp20) cc_final: 0.6193 (pp20) REVERT: A 347 THR cc_start: 0.7282 (OUTLIER) cc_final: 0.6839 (p) REVERT: A 379 LYS cc_start: 0.7982 (tttt) cc_final: 0.7712 (tttt) REVERT: A 381 ILE cc_start: 0.8512 (mt) cc_final: 0.8215 (mt) REVERT: B 50 GLU cc_start: 0.7657 (mm-30) cc_final: 0.7206 (mm-30) REVERT: B 51 GLU cc_start: 0.6688 (mp0) cc_final: 0.6408 (mp0) REVERT: B 66 SER cc_start: 0.7797 (t) cc_final: 0.7497 (p) REVERT: B 93 ASP cc_start: 0.7906 (t0) cc_final: 0.7602 (t70) REVERT: B 98 ARG cc_start: 0.7186 (tpp80) cc_final: 0.6976 (ttm-80) REVERT: B 123 LYS cc_start: 0.7517 (mttp) cc_final: 0.7124 (mttp) REVERT: B 130 GLU cc_start: 0.7269 (mm-30) cc_final: 0.6840 (tm-30) REVERT: B 145 ARG cc_start: 0.7868 (mtt-85) cc_final: 0.6904 (mtt-85) REVERT: B 158 GLU cc_start: 0.6912 (tt0) cc_final: 0.6257 (tm-30) REVERT: B 159 GLU cc_start: 0.7706 (tp30) cc_final: 0.7384 (tp30) REVERT: B 161 GLN cc_start: 0.8192 (mm110) cc_final: 0.7491 (mm-40) REVERT: B 162 HIS cc_start: 0.7806 (m-70) cc_final: 0.6957 (m90) REVERT: B 165 ASP cc_start: 0.7142 (m-30) cc_final: 0.6880 (m-30) REVERT: B 171 GLN cc_start: 0.8059 (tp40) cc_final: 0.7675 (tp40) REVERT: B 184 ASN cc_start: 0.8058 (t0) cc_final: 0.7805 (t0) REVERT: B 207 ARG cc_start: 0.7375 (mtt90) cc_final: 0.7116 (mtt-85) REVERT: B 217 ARG cc_start: 0.6645 (mtm-85) cc_final: 0.6427 (mtm-85) REVERT: B 293 ASP cc_start: 0.6927 (t0) cc_final: 0.6671 (t0) REVERT: B 294 MET cc_start: 0.7086 (OUTLIER) cc_final: 0.6607 (ptp) REVERT: B 318 ARG cc_start: 0.8143 (ptp-110) cc_final: 0.7886 (ptp90) REVERT: B 328 LYS cc_start: 0.8212 (mmpt) cc_final: 0.7905 (mmpt) REVERT: B 329 GLN cc_start: 0.7039 (mt0) cc_final: 0.6724 (mp10) REVERT: B 330 LEU cc_start: 0.8225 (tt) cc_final: 0.7980 (tt) REVERT: B 332 GLN cc_start: 0.7584 (mm-40) cc_final: 0.6920 (tp40) REVERT: B 333 TYR cc_start: 0.7895 (m-10) cc_final: 0.7619 (m-10) REVERT: B 379 LYS cc_start: 0.8243 (tttt) cc_final: 0.7987 (ttmt) REVERT: B 386 LYS cc_start: 0.8062 (tttt) cc_final: 0.7718 (tttt) REVERT: C 53 ASP cc_start: 0.6777 (t0) cc_final: 0.6490 (t0) REVERT: C 54 ASP cc_start: 0.7270 (t0) cc_final: 0.6996 (t0) REVERT: C 62 ILE cc_start: 0.7837 (OUTLIER) cc_final: 0.7422 (tp) REVERT: C 103 LYS cc_start: 0.7984 (tttt) cc_final: 0.7623 (tttt) REVERT: C 111 SER cc_start: 0.8610 (m) cc_final: 0.8197 (p) REVERT: C 117 GLN cc_start: 0.7345 (mt0) cc_final: 0.6733 (mt0) REVERT: C 121 ASN cc_start: 0.7297 (m-40) cc_final: 0.6932 (m-40) REVERT: C 133 LYS cc_start: 0.8317 (mtpt) cc_final: 0.7987 (mtpt) REVERT: C 158 GLU cc_start: 0.7647 (tt0) cc_final: 0.7419 (tt0) REVERT: C 161 GLN cc_start: 0.7561 (tp40) cc_final: 0.5909 (tp-100) REVERT: C 164 ARG cc_start: 0.6627 (ttp80) cc_final: 0.6026 (ttp80) REVERT: C 168 THR cc_start: 0.8301 (OUTLIER) cc_final: 0.8014 (p) REVERT: C 179 GLN cc_start: 0.8127 (mm-40) cc_final: 0.7765 (mm-40) REVERT: C 231 VAL cc_start: 0.8282 (OUTLIER) cc_final: 0.7915 (p) REVERT: C 257 ASN cc_start: 0.7915 (m-40) cc_final: 0.7421 (m110) REVERT: C 262 GLN cc_start: 0.7075 (OUTLIER) cc_final: 0.6679 (mp10) REVERT: C 296 THR cc_start: 0.7612 (p) cc_final: 0.7242 (t) REVERT: C 340 SER cc_start: 0.8327 (m) cc_final: 0.8101 (p) REVERT: C 379 LYS cc_start: 0.7823 (ttmt) cc_final: 0.7560 (ttmt) REVERT: D 50 GLU cc_start: 0.6711 (OUTLIER) cc_final: 0.6300 (tp30) REVERT: D 54 ASP cc_start: 0.6866 (t0) cc_final: 0.5490 (t0) REVERT: D 61 GLN cc_start: 0.7999 (OUTLIER) cc_final: 0.7751 (pm20) REVERT: D 73 THR cc_start: 0.8587 (OUTLIER) cc_final: 0.8328 (m) REVERT: D 117 GLN cc_start: 0.7877 (tt0) cc_final: 0.7242 (tt0) REVERT: D 121 ASN cc_start: 0.7870 (m-40) cc_final: 0.7433 (m-40) REVERT: D 138 LYS cc_start: 0.8225 (tttt) cc_final: 0.7853 (tttt) REVERT: D 147 VAL cc_start: 0.8832 (t) cc_final: 0.8614 (t) REVERT: D 157 ARG cc_start: 0.7236 (mtm110) cc_final: 0.6791 (mtm110) REVERT: D 161 GLN cc_start: 0.7348 (mp10) cc_final: 0.7001 (mp10) REVERT: D 164 ARG cc_start: 0.7958 (ttp80) cc_final: 0.7369 (ttm-80) REVERT: D 187 MET cc_start: 0.7655 (mmm) cc_final: 0.6932 (mmt) REVERT: D 219 ILE cc_start: 0.7847 (mm) cc_final: 0.7555 (tp) REVERT: D 228 ARG cc_start: 0.6977 (mtp85) cc_final: 0.6578 (mtt90) REVERT: D 255 ASP cc_start: 0.7192 (m-30) cc_final: 0.6906 (m-30) REVERT: D 257 ASN cc_start: 0.8036 (m-40) cc_final: 0.6891 (m110) REVERT: D 294 MET cc_start: 0.7527 (mmm) cc_final: 0.7181 (mmm) REVERT: D 314 LYS cc_start: 0.7063 (tttt) cc_final: 0.6791 (tptt) REVERT: D 331 GLU cc_start: 0.7042 (mp0) cc_final: 0.6591 (mp0) REVERT: D 332 GLN cc_start: 0.7374 (tp40) cc_final: 0.7045 (tp40) REVERT: D 378 ASN cc_start: 0.7846 (m-40) cc_final: 0.6974 (m-40) REVERT: D 379 LYS cc_start: 0.8054 (OUTLIER) cc_final: 0.7640 (ttmt) REVERT: D 382 ASP cc_start: 0.7220 (m-30) cc_final: 0.6686 (m-30) REVERT: D 385 VAL cc_start: 0.8474 (t) cc_final: 0.8154 (p) REVERT: E 53 ASP cc_start: 0.7165 (t70) cc_final: 0.5528 (t0) REVERT: E 85 GLU cc_start: 0.6920 (OUTLIER) cc_final: 0.6489 (tm-30) REVERT: E 142 ASP cc_start: 0.7349 (m-30) cc_final: 0.7012 (m-30) REVERT: E 153 ASN cc_start: 0.7745 (t0) cc_final: 0.7381 (p0) REVERT: E 157 ARG cc_start: 0.7234 (mtp180) cc_final: 0.6762 (mtp180) REVERT: E 164 ARG cc_start: 0.7157 (ttp80) cc_final: 0.6607 (ttp80) REVERT: E 200 GLN cc_start: 0.7382 (mm-40) cc_final: 0.6983 (mt0) REVERT: E 211 LEU cc_start: 0.8315 (mt) cc_final: 0.8056 (mm) REVERT: E 217 ARG cc_start: 0.6897 (mtt-85) cc_final: 0.6497 (mtt-85) REVERT: E 228 ARG cc_start: 0.7058 (mtm-85) cc_final: 0.6802 (mtt180) REVERT: E 251 ASN cc_start: 0.7292 (t0) cc_final: 0.6958 (t0) REVERT: E 279 TYR cc_start: 0.7853 (m-80) cc_final: 0.7385 (m-80) REVERT: E 294 MET cc_start: 0.6667 (mmm) cc_final: 0.6421 (mmm) REVERT: E 312 TRP cc_start: 0.8092 (t60) cc_final: 0.7803 (t60) REVERT: F 50 GLU cc_start: 0.7658 (mm-30) cc_final: 0.7102 (mm-30) REVERT: F 124 GLN cc_start: 0.7498 (mt0) cc_final: 0.7277 (tt0) REVERT: F 126 GLN cc_start: 0.6991 (tp40) cc_final: 0.6599 (tp40) REVERT: F 133 LYS cc_start: 0.7957 (OUTLIER) cc_final: 0.7527 (tttt) REVERT: F 138 LYS cc_start: 0.8500 (ttpt) cc_final: 0.8175 (tttp) REVERT: F 141 SER cc_start: 0.8342 (m) cc_final: 0.8074 (t) REVERT: F 143 TYR cc_start: 0.7879 (t80) cc_final: 0.7622 (t80) REVERT: F 145 ARG cc_start: 0.7376 (mtm-85) cc_final: 0.6978 (ttm170) REVERT: F 157 ARG cc_start: 0.7309 (mtm-85) cc_final: 0.7070 (mtm-85) REVERT: F 158 GLU cc_start: 0.7198 (tp30) cc_final: 0.6331 (tp30) REVERT: F 161 GLN cc_start: 0.7326 (tp40) cc_final: 0.6828 (tp40) REVERT: F 164 ARG cc_start: 0.7651 (ttm-80) cc_final: 0.7182 (ttm-80) REVERT: F 178 ILE cc_start: 0.8021 (mt) cc_final: 0.7812 (mm) REVERT: F 192 LYS cc_start: 0.8028 (mttp) cc_final: 0.7711 (mttp) REVERT: F 200 GLN cc_start: 0.7043 (mp10) cc_final: 0.6417 (mp10) REVERT: F 205 GLU cc_start: 0.7459 (mm-30) cc_final: 0.7230 (mt-10) REVERT: F 214 GLU cc_start: 0.7558 (tp30) cc_final: 0.6762 (mp0) REVERT: F 217 ARG cc_start: 0.6863 (mtt180) cc_final: 0.6491 (ptp-170) REVERT: F 259 LYS cc_start: 0.7709 (mmtp) cc_final: 0.7190 (mttp) REVERT: F 272 VAL cc_start: 0.7920 (t) cc_final: 0.7634 (p) REVERT: F 288 LYS cc_start: 0.8320 (OUTLIER) cc_final: 0.7835 (mtmt) REVERT: F 317 GLN cc_start: 0.7203 (mm-40) cc_final: 0.6805 (mp10) REVERT: F 371 GLU cc_start: 0.6165 (tp30) cc_final: 0.5762 (tp30) REVERT: F 372 ILE cc_start: 0.8705 (mp) cc_final: 0.7957 (mm) REVERT: F 379 LYS cc_start: 0.7720 (tptm) cc_final: 0.7170 (tptm) REVERT: F 383 ASP cc_start: 0.7153 (m-30) cc_final: 0.6812 (m-30) REVERT: J 21 LEU cc_start: 0.8217 (mt) cc_final: 0.8001 (mm) REVERT: J 66 ILE cc_start: 0.8612 (mt) cc_final: 0.8227 (mm) REVERT: J 87 ILE cc_start: 0.8617 (tt) cc_final: 0.8386 (pt) REVERT: J 104 MET cc_start: 0.6617 (ttp) cc_final: 0.6124 (tmm) REVERT: J 114 ILE cc_start: 0.8284 (mm) cc_final: 0.7939 (mm) REVERT: J 122 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7737 (mp) REVERT: J 124 GLN cc_start: 0.7821 (tt0) cc_final: 0.7197 (tt0) REVERT: J 145 MET cc_start: 0.6697 (tmm) cc_final: 0.6073 (tmm) REVERT: J 161 ILE cc_start: 0.8383 (mm) cc_final: 0.8045 (mp) REVERT: J 181 VAL cc_start: 0.8603 (t) cc_final: 0.8397 (p) REVERT: J 184 MET cc_start: 0.7611 (mtm) cc_final: 0.7339 (mtm) REVERT: J 213 ILE cc_start: 0.8322 (OUTLIER) cc_final: 0.8064 (mt) REVERT: J 217 GLN cc_start: 0.7738 (tp40) cc_final: 0.7073 (tt0) REVERT: J 233 GLU cc_start: 0.7598 (mp0) cc_final: 0.7217 (mp0) REVERT: J 251 TRP cc_start: 0.7142 (t-100) cc_final: 0.6894 (t-100) REVERT: J 252 GLU cc_start: 0.7267 (mm-30) cc_final: 0.6852 (tp30) REVERT: J 268 ARG cc_start: 0.7680 (ttt180) cc_final: 0.7361 (mmm-85) REVERT: J 271 THR cc_start: 0.8316 (m) cc_final: 0.8101 (p) REVERT: J 297 GLU cc_start: 0.7405 (tt0) cc_final: 0.7125 (tt0) REVERT: J 308 LEU cc_start: 0.7989 (mt) cc_final: 0.7727 (mm) REVERT: J 327 PHE cc_start: 0.6693 (t80) cc_final: 0.5964 (t80) REVERT: J 333 MET cc_start: 0.7254 (mtm) cc_final: 0.7032 (mtm) REVERT: J 342 ILE cc_start: 0.8140 (mm) cc_final: 0.7838 (tt) REVERT: J 356 GLU cc_start: 0.6752 (OUTLIER) cc_final: 0.6256 (tm-30) REVERT: J 359 MET cc_start: 0.7169 (mtm) cc_final: 0.6793 (mtm) REVERT: J 361 PHE cc_start: 0.7381 (t80) cc_final: 0.7067 (t80) REVERT: J 368 GLN cc_start: 0.7081 (OUTLIER) cc_final: 0.6805 (mt0) REVERT: J 384 THR cc_start: 0.8222 (m) cc_final: 0.7973 (p) REVERT: J 395 LEU cc_start: 0.7882 (mt) cc_final: 0.7505 (mt) REVERT: J 402 SER cc_start: 0.8040 (t) cc_final: 0.7827 (m) REVERT: J 403 ASN cc_start: 0.8203 (m-40) cc_final: 0.7749 (m110) REVERT: J 408 LEU cc_start: 0.7379 (OUTLIER) cc_final: 0.7088 (tt) REVERT: J 416 ILE cc_start: 0.8226 (mt) cc_final: 0.7974 (tp) REVERT: J 420 MET cc_start: 0.7489 (OUTLIER) cc_final: 0.7220 (tpt) REVERT: J 421 TRP cc_start: 0.8194 (t60) cc_final: 0.7831 (t60) REVERT: J 424 ARG cc_start: 0.7425 (mmm160) cc_final: 0.5589 (mmm160) REVERT: J 428 HIS cc_start: 0.8263 (m-70) cc_final: 0.7949 (m-70) REVERT: J 457 GLN cc_start: 0.7598 (mm-40) cc_final: 0.7190 (tp-100) REVERT: J 458 GLN cc_start: 0.8177 (tt0) cc_final: 0.7842 (tt0) REVERT: J 459 GLN cc_start: 0.7914 (mt0) cc_final: 0.7671 (mt0) REVERT: J 466 GLN cc_start: 0.7718 (OUTLIER) cc_final: 0.7126 (mp10) REVERT: J 471 GLN cc_start: 0.7732 (mm-40) cc_final: 0.7207 (mm-40) REVERT: J 488 PHE cc_start: 0.8119 (m-80) cc_final: 0.7580 (m-10) REVERT: J 489 LEU cc_start: 0.8407 (mt) cc_final: 0.8144 (mt) REVERT: J 491 LEU cc_start: 0.7806 (mt) cc_final: 0.7491 (mt) REVERT: G 3 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8538 (tp) REVERT: G 5 GLN cc_start: 0.8331 (mt0) cc_final: 0.7593 (mt0) REVERT: G 9 GLN cc_start: 0.7036 (tm-30) cc_final: 0.6620 (tm-30) REVERT: G 11 ARG cc_start: 0.8336 (OUTLIER) cc_final: 0.8085 (ttp-110) REVERT: G 17 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8472 (tt) REVERT: G 19 LYS cc_start: 0.8272 (tttm) cc_final: 0.7903 (tttm) REVERT: G 29 GLU cc_start: 0.7750 (tp30) cc_final: 0.6544 (tp30) REVERT: G 31 ILE cc_start: 0.8619 (mt) cc_final: 0.8367 (mm) REVERT: G 32 ASN cc_start: 0.8175 (m-40) cc_final: 0.6795 (p0) REVERT: G 42 LEU cc_start: 0.8391 (mp) cc_final: 0.8141 (mm) REVERT: G 78 MET cc_start: 0.7110 (ptp) cc_final: 0.6898 (ptp) REVERT: G 87 GLN cc_start: 0.8429 (tp40) cc_final: 0.7988 (tp40) REVERT: G 88 GLU cc_start: 0.8057 (pt0) cc_final: 0.7831 (pt0) REVERT: G 99 GLN cc_start: 0.7722 (tm-30) cc_final: 0.7286 (tm-30) REVERT: G 101 ASP cc_start: 0.7695 (t70) cc_final: 0.7164 (t0) REVERT: G 125 TYR cc_start: 0.8874 (t80) cc_final: 0.8544 (t80) REVERT: G 130 LYS cc_start: 0.8664 (tttt) cc_final: 0.8215 (ttpp) REVERT: G 136 GLN cc_start: 0.8417 (tp40) cc_final: 0.8097 (tp-100) REVERT: G 142 GLN cc_start: 0.7789 (OUTLIER) cc_final: 0.7465 (mm-40) REVERT: G 162 ASP cc_start: 0.8238 (m-30) cc_final: 0.7890 (m-30) REVERT: G 169 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8362 (mm) REVERT: G 181 GLN cc_start: 0.8333 (OUTLIER) cc_final: 0.7801 (tm-30) REVERT: G 215 GLU cc_start: 0.7577 (tm-30) cc_final: 0.6780 (tm-30) REVERT: G 217 GLU cc_start: 0.8013 (tm-30) cc_final: 0.7569 (mm-30) REVERT: G 225 GLN cc_start: 0.8372 (tm-30) cc_final: 0.8103 (tm-30) REVERT: G 230 GLN cc_start: 0.8549 (OUTLIER) cc_final: 0.7877 (pp30) REVERT: G 231 ASP cc_start: 0.8207 (m-30) cc_final: 0.7630 (m-30) REVERT: G 237 ILE cc_start: 0.8867 (OUTLIER) cc_final: 0.8204 (tp) REVERT: G 279 MET cc_start: 0.4131 (tpt) cc_final: 0.3411 (tpt) REVERT: G 299 ASN cc_start: 0.8352 (m110) cc_final: 0.7892 (m-40) REVERT: G 303 LYS cc_start: 0.8734 (mtpp) cc_final: 0.7743 (mtpp) REVERT: G 304 GLN cc_start: 0.8274 (pt0) cc_final: 0.7739 (pp30) REVERT: G 307 TYR cc_start: 0.8023 (m-80) cc_final: 0.7529 (m-80) REVERT: G 314 GLU cc_start: 0.7916 (mm-30) cc_final: 0.7397 (mm-30) REVERT: G 317 GLU cc_start: 0.7917 (tp30) cc_final: 0.7131 (tp30) REVERT: G 321 ARG cc_start: 0.8394 (mtt180) cc_final: 0.8063 (mtt180) REVERT: G 333 ASN cc_start: 0.8624 (m-40) cc_final: 0.8324 (m-40) REVERT: G 344 TYR cc_start: 0.8160 (m-80) cc_final: 0.7569 (m-80) REVERT: G 401 LYS cc_start: 0.8404 (tptm) cc_final: 0.7624 (tppp) REVERT: G 407 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7393 (pt) REVERT: G 411 ASP cc_start: 0.5839 (t0) cc_final: 0.5621 (t70) REVERT: H 14 ASN cc_start: 0.8142 (t0) cc_final: 0.7642 (t0) REVERT: H 16 GLU cc_start: 0.8203 (mp0) cc_final: 0.7558 (mp0) REVERT: H 19 LYS cc_start: 0.8330 (tttt) cc_final: 0.7927 (tptt) REVERT: H 29 GLU cc_start: 0.8010 (tp30) cc_final: 0.7563 (tp30) REVERT: H 88 GLU cc_start: 0.8364 (mt-10) cc_final: 0.8022 (mt-10) REVERT: H 89 LYS cc_start: 0.8788 (mmmt) cc_final: 0.8411 (mmmt) REVERT: H 94 GLN cc_start: 0.8165 (tp40) cc_final: 0.7686 (tt0) REVERT: H 95 ASP cc_start: 0.8711 (m-30) cc_final: 0.7917 (m-30) REVERT: H 131 GLU cc_start: 0.8056 (tp30) cc_final: 0.7742 (tp30) REVERT: H 135 ARG cc_start: 0.8037 (OUTLIER) cc_final: 0.7465 (mmm160) REVERT: H 142 GLN cc_start: 0.8029 (mm-40) cc_final: 0.7527 (mm-40) REVERT: H 162 ASP cc_start: 0.8128 (m-30) cc_final: 0.7845 (m-30) REVERT: H 169 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.7931 (tp) REVERT: H 173 ASN cc_start: 0.8443 (m-40) cc_final: 0.8137 (m-40) REVERT: H 180 GLU cc_start: 0.8590 (mm-30) cc_final: 0.7905 (tm-30) REVERT: H 184 GLN cc_start: 0.8480 (tt0) cc_final: 0.7711 (tp-100) REVERT: H 230 GLN cc_start: 0.8187 (tp40) cc_final: 0.7574 (tp-100) REVERT: H 231 ASP cc_start: 0.7795 (t0) cc_final: 0.7487 (t0) REVERT: H 236 GLN cc_start: 0.8127 (mt0) cc_final: 0.7921 (mt0) REVERT: H 239 GLN cc_start: 0.8516 (tm-30) cc_final: 0.8313 (pp30) REVERT: H 297 MET cc_start: 0.6407 (ttm) cc_final: 0.6075 (tmm) REVERT: H 301 GLN cc_start: 0.8356 (mt0) cc_final: 0.7749 (mp10) REVERT: H 303 LYS cc_start: 0.8486 (mttt) cc_final: 0.7975 (mttt) REVERT: H 306 GLN cc_start: 0.8261 (OUTLIER) cc_final: 0.8031 (mm-40) REVERT: H 314 GLU cc_start: 0.7534 (mm-30) cc_final: 0.7086 (mm-30) REVERT: H 317 GLU cc_start: 0.7699 (tp30) cc_final: 0.7081 (tp30) REVERT: H 321 ARG cc_start: 0.8357 (mtt180) cc_final: 0.7456 (mtt180) REVERT: H 331 PHE cc_start: 0.9026 (t80) cc_final: 0.8818 (t80) REVERT: H 340 SER cc_start: 0.8739 (m) cc_final: 0.8176 (p) REVERT: H 341 ILE cc_start: 0.8888 (OUTLIER) cc_final: 0.8600 (tp) REVERT: H 358 MET cc_start: 0.7854 (mmm) cc_final: 0.7645 (tpp) REVERT: H 374 ASP cc_start: 0.7796 (t0) cc_final: 0.7444 (t0) REVERT: H 392 ASN cc_start: 0.8399 (m-40) cc_final: 0.7890 (t0) REVERT: H 396 ASN cc_start: 0.8164 (m-40) cc_final: 0.7735 (m110) REVERT: H 397 GLN cc_start: 0.8104 (tt0) cc_final: 0.7440 (tm-30) REVERT: H 412 LEU cc_start: 0.8439 (tp) cc_final: 0.8209 (tp) REVERT: I 4 MET cc_start: 0.7656 (OUTLIER) cc_final: 0.7304 (tmm) REVERT: I 16 GLU cc_start: 0.7970 (mp0) cc_final: 0.7443 (mp0) REVERT: I 24 ARG cc_start: 0.7966 (ttp-170) cc_final: 0.7575 (ttp-110) REVERT: I 31 ILE cc_start: 0.9053 (mt) cc_final: 0.8785 (mm) REVERT: I 76 PHE cc_start: 0.7543 (t80) cc_final: 0.6731 (t80) REVERT: I 89 LYS cc_start: 0.8431 (mmtp) cc_final: 0.8173 (mmtp) REVERT: I 99 GLN cc_start: 0.8345 (mt0) cc_final: 0.8068 (mt0) REVERT: I 124 SER cc_start: 0.8611 (t) cc_final: 0.8398 (p) REVERT: I 160 GLN cc_start: 0.8171 (mm-40) cc_final: 0.7959 (mm-40) REVERT: I 185 ILE cc_start: 0.9195 (mt) cc_final: 0.8969 (tt) REVERT: I 215 GLU cc_start: 0.8110 (tp30) cc_final: 0.7634 (tp30) REVERT: I 217 GLU cc_start: 0.7573 (mm-30) cc_final: 0.7218 (mm-30) REVERT: I 224 LEU cc_start: 0.8754 (tp) cc_final: 0.8172 (mm) REVERT: I 225 GLN cc_start: 0.7979 (tm-30) cc_final: 0.7334 (tm-30) REVERT: I 227 ARG cc_start: 0.7745 (mtm-85) cc_final: 0.7279 (mtm-85) REVERT: I 234 ARG cc_start: 0.7619 (OUTLIER) cc_final: 0.7359 (mtt180) REVERT: I 235 GLU cc_start: 0.7937 (tp30) cc_final: 0.7555 (tp30) REVERT: I 236 GLN cc_start: 0.8327 (mt0) cc_final: 0.7945 (mt0) REVERT: I 241 GLN cc_start: 0.7931 (OUTLIER) cc_final: 0.7557 (mm110) REVERT: I 301 GLN cc_start: 0.8430 (tt0) cc_final: 0.8047 (mt0) REVERT: I 306 GLN cc_start: 0.8403 (pt0) cc_final: 0.7866 (mp10) REVERT: I 314 GLU cc_start: 0.7248 (mt-10) cc_final: 0.6832 (mt-10) REVERT: I 315 GLN cc_start: 0.8044 (mt0) cc_final: 0.7317 (mp10) REVERT: I 362 TYR cc_start: 0.8464 (t80) cc_final: 0.8231 (t80) REVERT: I 392 ASN cc_start: 0.8134 (m-40) cc_final: 0.6604 (m-40) REVERT: I 396 ASN cc_start: 0.8283 (m-40) cc_final: 0.7753 (m110) outliers start: 172 outliers final: 108 residues processed: 1340 average time/residue: 0.2117 time to fit residues: 430.5596 Evaluate side-chains 1391 residues out of total 3232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 1245 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 158 GLU Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 222 MET Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain B residue 133 LYS Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 294 MET Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 124 GLN Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 266 MET Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 360 ARG Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain D residue 61 GLN Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 84 LYS Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 169 SER Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 288 LYS Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 379 LYS Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 65 MET Chi-restraints excluded: chain E residue 85 GLU Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 273 THR Chi-restraints excluded: chain E residue 275 THR Chi-restraints excluded: chain E residue 284 LYS Chi-restraints excluded: chain E residue 288 LYS Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain E residue 309 THR Chi-restraints excluded: chain E residue 311 ASN Chi-restraints excluded: chain E residue 342 LEU Chi-restraints excluded: chain E residue 344 SER Chi-restraints excluded: chain E residue 346 ASN Chi-restraints excluded: chain E residue 373 SER Chi-restraints excluded: chain E residue 386 LYS Chi-restraints excluded: chain F residue 69 SER Chi-restraints excluded: chain F residue 110 SER Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 133 LYS Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 194 GLU Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 288 LYS Chi-restraints excluded: chain F residue 303 LEU Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain F residue 353 GLN Chi-restraints excluded: chain F residue 367 SER Chi-restraints excluded: chain F residue 380 LEU Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 39 THR Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain J residue 122 LEU Chi-restraints excluded: chain J residue 166 HIS Chi-restraints excluded: chain J residue 213 ILE Chi-restraints excluded: chain J residue 219 MET Chi-restraints excluded: chain J residue 356 GLU Chi-restraints excluded: chain J residue 368 GLN Chi-restraints excluded: chain J residue 408 LEU Chi-restraints excluded: chain J residue 420 MET Chi-restraints excluded: chain J residue 466 GLN Chi-restraints excluded: chain J residue 490 VAL Chi-restraints excluded: chain G residue 3 LEU Chi-restraints excluded: chain G residue 11 ARG Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 142 GLN Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain G residue 181 GLN Chi-restraints excluded: chain G residue 203 THR Chi-restraints excluded: chain G residue 230 GLN Chi-restraints excluded: chain G residue 237 ILE Chi-restraints excluded: chain G residue 245 LEU Chi-restraints excluded: chain G residue 272 THR Chi-restraints excluded: chain G residue 318 SER Chi-restraints excluded: chain G residue 334 ILE Chi-restraints excluded: chain G residue 342 ASN Chi-restraints excluded: chain G residue 407 LEU Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 35 ARG Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 135 ARG Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 169 LEU Chi-restraints excluded: chain H residue 205 LYS Chi-restraints excluded: chain H residue 221 LEU Chi-restraints excluded: chain H residue 245 LEU Chi-restraints excluded: chain H residue 250 LEU Chi-restraints excluded: chain H residue 306 GLN Chi-restraints excluded: chain H residue 341 ILE Chi-restraints excluded: chain H residue 404 LEU Chi-restraints excluded: chain H residue 413 LEU Chi-restraints excluded: chain I residue 4 MET Chi-restraints excluded: chain I residue 118 ASN Chi-restraints excluded: chain I residue 203 THR Chi-restraints excluded: chain I residue 234 ARG Chi-restraints excluded: chain I residue 241 GLN Chi-restraints excluded: chain I residue 250 LEU Chi-restraints excluded: chain I residue 272 THR Chi-restraints excluded: chain I residue 279 MET Chi-restraints excluded: chain I residue 292 ILE Chi-restraints excluded: chain I residue 297 MET Chi-restraints excluded: chain I residue 328 ARG Chi-restraints excluded: chain I residue 394 LEU Chi-restraints excluded: chain I residue 398 LEU Chi-restraints excluded: chain I residue 409 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 218 optimal weight: 0.9990 chunk 339 optimal weight: 0.7980 chunk 145 optimal weight: 2.9990 chunk 326 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 188 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 294 optimal weight: 4.9990 chunk 273 optimal weight: 0.6980 chunk 319 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 161 GLN E 185 GLN E 236 GLN F 251 ASN G 156 ASN ** G 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 70 GLN I 103 GLN ** I 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 320 HIS I 325 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.112798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.095082 restraints weight = 58769.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.098057 restraints weight = 25816.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.099918 restraints weight = 13941.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.101072 restraints weight = 8701.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.101860 restraints weight = 6192.993| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.6668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 30315 Z= 0.175 Angle : 0.663 12.646 41246 Z= 0.341 Chirality : 0.043 0.187 4889 Planarity : 0.005 0.115 5392 Dihedral : 4.195 20.541 4179 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 5.38 % Allowed : 25.25 % Favored : 69.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.73 (0.14), residues: 3860 helix: 2.88 (0.11), residues: 2027 sheet: -0.16 (0.23), residues: 501 loop : -1.17 (0.16), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG J 424 TYR 0.025 0.002 TYR J 344 PHE 0.031 0.001 PHE J 339 TRP 0.041 0.002 TRP E 312 HIS 0.004 0.001 HIS J 429 Details of bonding type rmsd covalent geometry : bond 0.00372 (30315) covalent geometry : angle 0.66316 (41246) hydrogen bonds : bond 0.06384 ( 1888) hydrogen bonds : angle 4.33687 ( 5523) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7720 Ramachandran restraints generated. 3860 Oldfield, 0 Emsley, 3860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7720 Ramachandran restraints generated. 3860 Oldfield, 0 Emsley, 3860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1424 residues out of total 3232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 174 poor density : 1250 time to evaluate : 1.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.6992 (mm-30) cc_final: 0.6751 (mm-30) REVERT: A 130 GLU cc_start: 0.7538 (mm-30) cc_final: 0.7133 (mm-30) REVERT: A 138 LYS cc_start: 0.8200 (tttt) cc_final: 0.7860 (tttm) REVERT: A 154 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8440 (mp) REVERT: A 161 GLN cc_start: 0.7419 (pt0) cc_final: 0.6876 (pt0) REVERT: A 171 GLN cc_start: 0.7970 (tp40) cc_final: 0.6809 (tp40) REVERT: A 175 ASP cc_start: 0.6852 (OUTLIER) cc_final: 0.6058 (m-30) REVERT: A 205 GLU cc_start: 0.7052 (tp30) cc_final: 0.6775 (tp30) REVERT: A 214 GLU cc_start: 0.7669 (mm-30) cc_final: 0.7269 (mm-30) REVERT: A 228 ARG cc_start: 0.7547 (mtm-85) cc_final: 0.7152 (mtm-85) REVERT: A 237 ILE cc_start: 0.8056 (mm) cc_final: 0.7816 (pt) REVERT: A 259 LYS cc_start: 0.8153 (mtmm) cc_final: 0.7767 (mtmm) REVERT: A 284 LYS cc_start: 0.7412 (mtpp) cc_final: 0.7152 (mtpp) REVERT: A 293 ASP cc_start: 0.7488 (t0) cc_final: 0.7237 (t0) REVERT: A 317 GLN cc_start: 0.7599 (mm-40) cc_final: 0.7279 (mm-40) REVERT: A 347 THR cc_start: 0.7285 (OUTLIER) cc_final: 0.6828 (p) REVERT: A 379 LYS cc_start: 0.7977 (tttt) cc_final: 0.7721 (tttt) REVERT: A 381 ILE cc_start: 0.8509 (mt) cc_final: 0.8206 (mt) REVERT: B 50 GLU cc_start: 0.7660 (mm-30) cc_final: 0.7202 (mm-30) REVERT: B 51 GLU cc_start: 0.6684 (mp0) cc_final: 0.6378 (mp0) REVERT: B 65 MET cc_start: 0.6869 (mtm) cc_final: 0.6621 (mtp) REVERT: B 66 SER cc_start: 0.7780 (t) cc_final: 0.7505 (p) REVERT: B 93 ASP cc_start: 0.7896 (t0) cc_final: 0.7589 (t70) REVERT: B 123 LYS cc_start: 0.7548 (mttp) cc_final: 0.7187 (mttp) REVERT: B 130 GLU cc_start: 0.7305 (mm-30) cc_final: 0.6883 (tm-30) REVERT: B 136 LEU cc_start: 0.8514 (tt) cc_final: 0.8279 (tp) REVERT: B 158 GLU cc_start: 0.6895 (tt0) cc_final: 0.6140 (tm-30) REVERT: B 159 GLU cc_start: 0.7734 (tp30) cc_final: 0.7370 (tp30) REVERT: B 162 HIS cc_start: 0.7861 (m-70) cc_final: 0.6810 (m90) REVERT: B 165 ASP cc_start: 0.7157 (m-30) cc_final: 0.6888 (m-30) REVERT: B 171 GLN cc_start: 0.8060 (tp40) cc_final: 0.7665 (tp40) REVERT: B 184 ASN cc_start: 0.8051 (t0) cc_final: 0.7806 (t0) REVERT: B 207 ARG cc_start: 0.7376 (mtt90) cc_final: 0.7118 (mtt-85) REVERT: B 293 ASP cc_start: 0.6873 (t0) cc_final: 0.6644 (t0) REVERT: B 318 ARG cc_start: 0.8150 (ptp-110) cc_final: 0.7891 (ptp90) REVERT: B 328 LYS cc_start: 0.8223 (mmpt) cc_final: 0.7886 (mmpt) REVERT: B 329 GLN cc_start: 0.7068 (mt0) cc_final: 0.6775 (mp10) REVERT: B 330 LEU cc_start: 0.8244 (tt) cc_final: 0.8007 (tt) REVERT: B 332 GLN cc_start: 0.7592 (mm-40) cc_final: 0.6911 (tp40) REVERT: B 333 TYR cc_start: 0.7900 (m-10) cc_final: 0.7631 (m-10) REVERT: B 379 LYS cc_start: 0.8242 (tttt) cc_final: 0.8006 (ttmt) REVERT: B 386 LYS cc_start: 0.8026 (tttt) cc_final: 0.7669 (tttt) REVERT: C 53 ASP cc_start: 0.6767 (t0) cc_final: 0.6506 (t0) REVERT: C 54 ASP cc_start: 0.7292 (t0) cc_final: 0.7029 (t0) REVERT: C 62 ILE cc_start: 0.7837 (OUTLIER) cc_final: 0.7436 (tp) REVERT: C 111 SER cc_start: 0.8608 (m) cc_final: 0.8187 (p) REVERT: C 117 GLN cc_start: 0.7451 (mt0) cc_final: 0.6857 (mt0) REVERT: C 121 ASN cc_start: 0.7298 (m-40) cc_final: 0.6990 (m-40) REVERT: C 133 LYS cc_start: 0.8315 (mtpt) cc_final: 0.7998 (mtpt) REVERT: C 161 GLN cc_start: 0.7650 (tp40) cc_final: 0.6063 (tp40) REVERT: C 164 ARG cc_start: 0.6665 (ttp80) cc_final: 0.6066 (ttp80) REVERT: C 168 THR cc_start: 0.8288 (OUTLIER) cc_final: 0.8024 (p) REVERT: C 179 GLN cc_start: 0.8136 (mm-40) cc_final: 0.7788 (mm-40) REVERT: C 200 GLN cc_start: 0.6945 (mt0) cc_final: 0.6487 (mt0) REVERT: C 231 VAL cc_start: 0.8303 (OUTLIER) cc_final: 0.7964 (p) REVERT: C 257 ASN cc_start: 0.7911 (m-40) cc_final: 0.7447 (m110) REVERT: C 262 GLN cc_start: 0.7099 (OUTLIER) cc_final: 0.6673 (mp10) REVERT: C 296 THR cc_start: 0.7609 (p) cc_final: 0.7240 (t) REVERT: C 322 ARG cc_start: 0.8020 (tpt-90) cc_final: 0.7261 (tpt-90) REVERT: C 379 LYS cc_start: 0.7829 (ttmt) cc_final: 0.7567 (ttmt) REVERT: D 50 GLU cc_start: 0.6703 (OUTLIER) cc_final: 0.6253 (tp30) REVERT: D 54 ASP cc_start: 0.6894 (t0) cc_final: 0.5535 (t0) REVERT: D 61 GLN cc_start: 0.7999 (OUTLIER) cc_final: 0.7731 (pm20) REVERT: D 73 THR cc_start: 0.8599 (OUTLIER) cc_final: 0.8334 (m) REVERT: D 117 GLN cc_start: 0.7861 (tt0) cc_final: 0.7008 (tt0) REVERT: D 121 ASN cc_start: 0.7838 (m-40) cc_final: 0.7426 (m-40) REVERT: D 129 ILE cc_start: 0.8325 (mt) cc_final: 0.8044 (mp) REVERT: D 138 LYS cc_start: 0.8213 (tttt) cc_final: 0.7855 (tttt) REVERT: D 145 ARG cc_start: 0.7982 (mtm-85) cc_final: 0.7777 (mtm180) REVERT: D 157 ARG cc_start: 0.7226 (mtm110) cc_final: 0.6668 (mtm110) REVERT: D 161 GLN cc_start: 0.7374 (mp10) cc_final: 0.6967 (mp10) REVERT: D 187 MET cc_start: 0.7645 (mmm) cc_final: 0.6832 (mmt) REVERT: D 228 ARG cc_start: 0.7005 (mtp85) cc_final: 0.6635 (mtt90) REVERT: D 255 ASP cc_start: 0.7207 (m-30) cc_final: 0.6929 (m-30) REVERT: D 257 ASN cc_start: 0.8035 (m-40) cc_final: 0.6869 (m110) REVERT: D 294 MET cc_start: 0.7488 (mmm) cc_final: 0.7129 (mmm) REVERT: D 314 LYS cc_start: 0.7098 (tttt) cc_final: 0.6834 (tptt) REVERT: D 331 GLU cc_start: 0.7085 (mp0) cc_final: 0.6606 (mp0) REVERT: D 332 GLN cc_start: 0.7375 (tp40) cc_final: 0.6934 (tp40) REVERT: D 378 ASN cc_start: 0.7868 (m-40) cc_final: 0.6980 (m-40) REVERT: D 379 LYS cc_start: 0.8055 (OUTLIER) cc_final: 0.7662 (ttmt) REVERT: D 382 ASP cc_start: 0.7226 (m-30) cc_final: 0.6708 (m-30) REVERT: D 385 VAL cc_start: 0.8491 (t) cc_final: 0.8170 (p) REVERT: E 53 ASP cc_start: 0.7131 (t70) cc_final: 0.5492 (t0) REVERT: E 85 GLU cc_start: 0.6925 (OUTLIER) cc_final: 0.6559 (tm-30) REVERT: E 142 ASP cc_start: 0.7347 (m-30) cc_final: 0.7027 (m-30) REVERT: E 157 ARG cc_start: 0.7094 (mtp180) cc_final: 0.6892 (mtp180) REVERT: E 164 ARG cc_start: 0.7124 (ttp80) cc_final: 0.6633 (ttp80) REVERT: E 196 GLN cc_start: 0.7882 (OUTLIER) cc_final: 0.7116 (mp10) REVERT: E 200 GLN cc_start: 0.7391 (mm-40) cc_final: 0.6976 (mt0) REVERT: E 211 LEU cc_start: 0.8313 (mt) cc_final: 0.8032 (mm) REVERT: E 217 ARG cc_start: 0.6911 (mtt-85) cc_final: 0.6492 (mtt-85) REVERT: E 222 MET cc_start: 0.6262 (tpp) cc_final: 0.5956 (mpp) REVERT: E 228 ARG cc_start: 0.7063 (mtm-85) cc_final: 0.6761 (mtt180) REVERT: E 229 ARG cc_start: 0.7987 (ptm-80) cc_final: 0.7771 (ttp80) REVERT: E 236 GLN cc_start: 0.7465 (OUTLIER) cc_final: 0.7169 (tp40) REVERT: E 251 ASN cc_start: 0.7330 (t0) cc_final: 0.7021 (t0) REVERT: E 279 TYR cc_start: 0.7863 (m-80) cc_final: 0.7357 (m-80) REVERT: E 294 MET cc_start: 0.6686 (mmm) cc_final: 0.6385 (mmm) REVERT: E 312 TRP cc_start: 0.8124 (t60) cc_final: 0.7884 (t60) REVERT: F 50 GLU cc_start: 0.7705 (mm-30) cc_final: 0.7163 (mm-30) REVERT: F 105 LYS cc_start: 0.7991 (mttt) cc_final: 0.7744 (mttt) REVERT: F 124 GLN cc_start: 0.7470 (mt0) cc_final: 0.7227 (tt0) REVERT: F 126 GLN cc_start: 0.7015 (tp40) cc_final: 0.6617 (tp40) REVERT: F 133 LYS cc_start: 0.8019 (OUTLIER) cc_final: 0.7573 (tttt) REVERT: F 138 LYS cc_start: 0.8539 (ttpt) cc_final: 0.8194 (tttp) REVERT: F 141 SER cc_start: 0.8291 (m) cc_final: 0.8048 (t) REVERT: F 143 TYR cc_start: 0.7874 (t80) cc_final: 0.7601 (t80) REVERT: F 145 ARG cc_start: 0.7357 (mtm-85) cc_final: 0.7018 (ttm170) REVERT: F 157 ARG cc_start: 0.7309 (mtm-85) cc_final: 0.7103 (mtm-85) REVERT: F 158 GLU cc_start: 0.7219 (tp30) cc_final: 0.6343 (tp30) REVERT: F 161 GLN cc_start: 0.7362 (tp40) cc_final: 0.6785 (tp40) REVERT: F 164 ARG cc_start: 0.7663 (ttm-80) cc_final: 0.7192 (ttm-80) REVERT: F 192 LYS cc_start: 0.8004 (mttp) cc_final: 0.7700 (mttp) REVERT: F 200 GLN cc_start: 0.7032 (mp10) cc_final: 0.6402 (mp10) REVERT: F 205 GLU cc_start: 0.7463 (mm-30) cc_final: 0.7248 (mt-10) REVERT: F 214 GLU cc_start: 0.7590 (tp30) cc_final: 0.6886 (mp0) REVERT: F 217 ARG cc_start: 0.6866 (mtt180) cc_final: 0.6473 (ptp-170) REVERT: F 259 LYS cc_start: 0.7730 (mmtp) cc_final: 0.7213 (mttp) REVERT: F 288 LYS cc_start: 0.8328 (OUTLIER) cc_final: 0.7858 (mtmt) REVERT: F 317 GLN cc_start: 0.7228 (mm-40) cc_final: 0.6787 (mp10) REVERT: F 371 GLU cc_start: 0.6246 (tp30) cc_final: 0.5833 (tp30) REVERT: F 372 ILE cc_start: 0.8743 (mp) cc_final: 0.7952 (mm) REVERT: F 379 LYS cc_start: 0.7738 (tptm) cc_final: 0.7172 (tptm) REVERT: F 383 ASP cc_start: 0.7154 (m-30) cc_final: 0.6810 (m-30) REVERT: J 21 LEU cc_start: 0.8213 (mt) cc_final: 0.7999 (mm) REVERT: J 66 ILE cc_start: 0.8626 (mt) cc_final: 0.8249 (mm) REVERT: J 87 ILE cc_start: 0.8632 (tt) cc_final: 0.8405 (pt) REVERT: J 114 ILE cc_start: 0.8274 (mm) cc_final: 0.7927 (mm) REVERT: J 120 ILE cc_start: 0.7960 (mt) cc_final: 0.7700 (mm) REVERT: J 122 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.7817 (mp) REVERT: J 124 GLN cc_start: 0.7828 (tt0) cc_final: 0.7206 (tt0) REVERT: J 161 ILE cc_start: 0.8394 (mm) cc_final: 0.8043 (mp) REVERT: J 181 VAL cc_start: 0.8619 (t) cc_final: 0.8331 (p) REVERT: J 213 ILE cc_start: 0.8373 (OUTLIER) cc_final: 0.8116 (mt) REVERT: J 217 GLN cc_start: 0.7769 (tp40) cc_final: 0.7076 (tt0) REVERT: J 233 GLU cc_start: 0.7603 (mp0) cc_final: 0.7223 (mp0) REVERT: J 239 VAL cc_start: 0.8489 (p) cc_final: 0.8224 (m) REVERT: J 251 TRP cc_start: 0.7196 (t-100) cc_final: 0.6958 (t-100) REVERT: J 252 GLU cc_start: 0.7267 (mm-30) cc_final: 0.6896 (tp30) REVERT: J 268 ARG cc_start: 0.7636 (ttt180) cc_final: 0.7283 (mmm-85) REVERT: J 271 THR cc_start: 0.8310 (m) cc_final: 0.8095 (p) REVERT: J 297 GLU cc_start: 0.7407 (tt0) cc_final: 0.7174 (tt0) REVERT: J 308 LEU cc_start: 0.7985 (mt) cc_final: 0.7740 (mm) REVERT: J 327 PHE cc_start: 0.6712 (t80) cc_final: 0.5966 (t80) REVERT: J 333 MET cc_start: 0.7247 (mtm) cc_final: 0.6952 (mtm) REVERT: J 342 ILE cc_start: 0.8146 (mm) cc_final: 0.7837 (tt) REVERT: J 361 PHE cc_start: 0.7284 (t80) cc_final: 0.6959 (t80) REVERT: J 368 GLN cc_start: 0.7103 (OUTLIER) cc_final: 0.6832 (mt0) REVERT: J 382 LEU cc_start: 0.8254 (mt) cc_final: 0.7987 (mp) REVERT: J 384 THR cc_start: 0.8284 (m) cc_final: 0.8002 (p) REVERT: J 395 LEU cc_start: 0.7895 (mt) cc_final: 0.7515 (mt) REVERT: J 403 ASN cc_start: 0.8224 (m-40) cc_final: 0.7804 (m110) REVERT: J 408 LEU cc_start: 0.7387 (OUTLIER) cc_final: 0.7087 (tt) REVERT: J 416 ILE cc_start: 0.8257 (mt) cc_final: 0.7982 (tp) REVERT: J 420 MET cc_start: 0.7541 (OUTLIER) cc_final: 0.7302 (tpt) REVERT: J 428 HIS cc_start: 0.8284 (m-70) cc_final: 0.7950 (m-70) REVERT: J 436 VAL cc_start: 0.8017 (t) cc_final: 0.7629 (m) REVERT: J 457 GLN cc_start: 0.7594 (mm-40) cc_final: 0.7189 (tp-100) REVERT: J 458 GLN cc_start: 0.8187 (tt0) cc_final: 0.7844 (tt0) REVERT: J 459 GLN cc_start: 0.7921 (mt0) cc_final: 0.7664 (mt0) REVERT: J 466 GLN cc_start: 0.7626 (OUTLIER) cc_final: 0.7182 (mp10) REVERT: J 471 GLN cc_start: 0.7804 (mm-40) cc_final: 0.7240 (mm-40) REVERT: J 488 PHE cc_start: 0.8125 (m-80) cc_final: 0.7504 (m-10) REVERT: J 489 LEU cc_start: 0.8423 (mt) cc_final: 0.8148 (mt) REVERT: J 491 LEU cc_start: 0.7776 (mt) cc_final: 0.7452 (mt) REVERT: G 3 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8492 (tp) REVERT: G 5 GLN cc_start: 0.8345 (mt0) cc_final: 0.7621 (mt0) REVERT: G 9 GLN cc_start: 0.7016 (tm-30) cc_final: 0.6577 (tm-30) REVERT: G 17 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8477 (tt) REVERT: G 19 LYS cc_start: 0.8284 (tttm) cc_final: 0.7923 (tttm) REVERT: G 29 GLU cc_start: 0.7815 (tp30) cc_final: 0.7223 (tp30) REVERT: G 31 ILE cc_start: 0.8731 (mt) cc_final: 0.8453 (mm) REVERT: G 32 ASN cc_start: 0.8191 (m-40) cc_final: 0.7471 (m110) REVERT: G 78 MET cc_start: 0.6913 (ptp) cc_final: 0.6600 (ptp) REVERT: G 87 GLN cc_start: 0.8470 (tp40) cc_final: 0.8009 (tp40) REVERT: G 88 GLU cc_start: 0.8100 (pt0) cc_final: 0.7862 (pt0) REVERT: G 101 ASP cc_start: 0.7587 (t70) cc_final: 0.7162 (t0) REVERT: G 125 TYR cc_start: 0.8885 (t80) cc_final: 0.8552 (t80) REVERT: G 130 LYS cc_start: 0.8618 (tttt) cc_final: 0.8236 (ttpp) REVERT: G 136 GLN cc_start: 0.8432 (tp40) cc_final: 0.8103 (tp-100) REVERT: G 142 GLN cc_start: 0.7785 (OUTLIER) cc_final: 0.7471 (mm-40) REVERT: G 162 ASP cc_start: 0.8232 (m-30) cc_final: 0.7882 (m-30) REVERT: G 169 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8359 (mm) REVERT: G 181 GLN cc_start: 0.8330 (mm-40) cc_final: 0.7801 (tm-30) REVERT: G 215 GLU cc_start: 0.7576 (tm-30) cc_final: 0.6774 (tm-30) REVERT: G 217 GLU cc_start: 0.8027 (tm-30) cc_final: 0.7549 (mm-30) REVERT: G 225 GLN cc_start: 0.8404 (tm-30) cc_final: 0.8155 (tm-30) REVERT: G 230 GLN cc_start: 0.8528 (OUTLIER) cc_final: 0.7932 (pp30) REVERT: G 231 ASP cc_start: 0.8224 (m-30) cc_final: 0.7652 (m-30) REVERT: G 279 MET cc_start: 0.4222 (tpt) cc_final: 0.3592 (mmm) REVERT: G 290 LEU cc_start: 0.8405 (tp) cc_final: 0.8062 (mp) REVERT: G 299 ASN cc_start: 0.8362 (m110) cc_final: 0.7892 (m-40) REVERT: G 303 LYS cc_start: 0.8737 (mtpp) cc_final: 0.7729 (mtpp) REVERT: G 304 GLN cc_start: 0.8288 (pt0) cc_final: 0.7742 (pp30) REVERT: G 307 TYR cc_start: 0.8051 (m-80) cc_final: 0.7550 (m-80) REVERT: G 314 GLU cc_start: 0.7918 (mm-30) cc_final: 0.7388 (mm-30) REVERT: G 317 GLU cc_start: 0.7934 (tp30) cc_final: 0.7148 (tp30) REVERT: G 321 ARG cc_start: 0.8393 (mtt180) cc_final: 0.8074 (mtt180) REVERT: G 333 ASN cc_start: 0.8616 (m-40) cc_final: 0.8322 (m-40) REVERT: G 344 TYR cc_start: 0.8156 (m-80) cc_final: 0.7542 (m-80) REVERT: G 385 GLU cc_start: 0.7815 (mm-30) cc_final: 0.7224 (mm-30) REVERT: G 401 LYS cc_start: 0.8427 (tptm) cc_final: 0.7750 (tppp) REVERT: G 407 LEU cc_start: 0.7867 (OUTLIER) cc_final: 0.7538 (pt) REVERT: G 411 ASP cc_start: 0.5956 (t0) cc_final: 0.5705 (t0) REVERT: H 14 ASN cc_start: 0.8093 (t0) cc_final: 0.7469 (t0) REVERT: H 16 GLU cc_start: 0.8216 (mp0) cc_final: 0.7567 (mp0) REVERT: H 17 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8681 (mm) REVERT: H 19 LYS cc_start: 0.8284 (tttt) cc_final: 0.7657 (tptt) REVERT: H 29 GLU cc_start: 0.7995 (tp30) cc_final: 0.7458 (tp30) REVERT: H 87 GLN cc_start: 0.8040 (tp-100) cc_final: 0.7331 (tp-100) REVERT: H 88 GLU cc_start: 0.8359 (mt-10) cc_final: 0.7949 (mt-10) REVERT: H 89 LYS cc_start: 0.8756 (mmmt) cc_final: 0.8401 (mmmt) REVERT: H 94 GLN cc_start: 0.8158 (tp40) cc_final: 0.7702 (tt0) REVERT: H 95 ASP cc_start: 0.8737 (m-30) cc_final: 0.7915 (m-30) REVERT: H 129 GLN cc_start: 0.8376 (tt0) cc_final: 0.8077 (tt0) REVERT: H 131 GLU cc_start: 0.8079 (tp30) cc_final: 0.7822 (tp30) REVERT: H 135 ARG cc_start: 0.8034 (OUTLIER) cc_final: 0.7462 (mmm160) REVERT: H 142 GLN cc_start: 0.8081 (mm-40) cc_final: 0.7529 (mm-40) REVERT: H 162 ASP cc_start: 0.8137 (m-30) cc_final: 0.7844 (m-30) REVERT: H 169 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.7951 (tp) REVERT: H 173 ASN cc_start: 0.8437 (m-40) cc_final: 0.8107 (m-40) REVERT: H 180 GLU cc_start: 0.8581 (mm-30) cc_final: 0.7900 (tm-30) REVERT: H 184 GLN cc_start: 0.8481 (tt0) cc_final: 0.7759 (tp-100) REVERT: H 223 LEU cc_start: 0.8884 (mt) cc_final: 0.8660 (mm) REVERT: H 230 GLN cc_start: 0.8203 (tp40) cc_final: 0.7583 (tp-100) REVERT: H 231 ASP cc_start: 0.7823 (t0) cc_final: 0.7527 (t0) REVERT: H 232 LEU cc_start: 0.8722 (tp) cc_final: 0.8204 (tt) REVERT: H 236 GLN cc_start: 0.8142 (mt0) cc_final: 0.7453 (mm-40) REVERT: H 297 MET cc_start: 0.6406 (ttm) cc_final: 0.6028 (tmm) REVERT: H 301 GLN cc_start: 0.8297 (mt0) cc_final: 0.7829 (mp10) REVERT: H 303 LYS cc_start: 0.8474 (mttt) cc_final: 0.7945 (mttt) REVERT: H 306 GLN cc_start: 0.8277 (OUTLIER) cc_final: 0.7953 (mp10) REVERT: H 314 GLU cc_start: 0.7546 (mm-30) cc_final: 0.7114 (mm-30) REVERT: H 317 GLU cc_start: 0.7700 (tp30) cc_final: 0.7080 (tp30) REVERT: H 321 ARG cc_start: 0.8290 (mtt180) cc_final: 0.7581 (mtt180) REVERT: H 340 SER cc_start: 0.8751 (m) cc_final: 0.8168 (p) REVERT: H 341 ILE cc_start: 0.8870 (OUTLIER) cc_final: 0.8607 (tp) REVERT: H 374 ASP cc_start: 0.7788 (t0) cc_final: 0.7432 (t0) REVERT: H 392 ASN cc_start: 0.8409 (m-40) cc_final: 0.7975 (t0) REVERT: H 396 ASN cc_start: 0.8169 (m-40) cc_final: 0.7751 (m110) REVERT: H 397 GLN cc_start: 0.8126 (tt0) cc_final: 0.7436 (tm-30) REVERT: H 412 LEU cc_start: 0.8431 (tp) cc_final: 0.8194 (tp) REVERT: I 4 MET cc_start: 0.7666 (tmm) cc_final: 0.7328 (tmm) REVERT: I 16 GLU cc_start: 0.7975 (mp0) cc_final: 0.7444 (mp0) REVERT: I 24 ARG cc_start: 0.7941 (ttp-170) cc_final: 0.7504 (ttp-110) REVERT: I 28 PHE cc_start: 0.8109 (m-80) cc_final: 0.7882 (m-80) REVERT: I 31 ILE cc_start: 0.9057 (mt) cc_final: 0.8799 (mm) REVERT: I 76 PHE cc_start: 0.7537 (t80) cc_final: 0.6836 (t80) REVERT: I 89 LYS cc_start: 0.8418 (mmtp) cc_final: 0.8174 (mmtp) REVERT: I 97 THR cc_start: 0.8761 (t) cc_final: 0.8546 (p) REVERT: I 99 GLN cc_start: 0.8354 (mt0) cc_final: 0.8057 (mt0) REVERT: I 124 SER cc_start: 0.8606 (t) cc_final: 0.8402 (p) REVERT: I 185 ILE cc_start: 0.9188 (mt) cc_final: 0.8965 (tt) REVERT: I 215 GLU cc_start: 0.8113 (tp30) cc_final: 0.7645 (tp30) REVERT: I 217 GLU cc_start: 0.7554 (mm-30) cc_final: 0.7172 (mm-30) REVERT: I 224 LEU cc_start: 0.8772 (tp) cc_final: 0.8027 (mm) REVERT: I 225 GLN cc_start: 0.8015 (tm-30) cc_final: 0.7374 (tm-30) REVERT: I 227 ARG cc_start: 0.7759 (mtm-85) cc_final: 0.7222 (mtm-85) REVERT: I 235 GLU cc_start: 0.8004 (tp30) cc_final: 0.7514 (tp30) REVERT: I 236 GLN cc_start: 0.8364 (mt0) cc_final: 0.7983 (mt0) REVERT: I 238 ARG cc_start: 0.8026 (mpt180) cc_final: 0.7342 (mpp-170) REVERT: I 301 GLN cc_start: 0.8421 (tt0) cc_final: 0.8062 (mt0) REVERT: I 306 GLN cc_start: 0.8413 (pt0) cc_final: 0.7951 (mp10) REVERT: I 314 GLU cc_start: 0.7211 (mt-10) cc_final: 0.6803 (mt-10) REVERT: I 315 GLN cc_start: 0.7987 (mt0) cc_final: 0.7017 (mp10) REVERT: I 328 ARG cc_start: 0.7959 (OUTLIER) cc_final: 0.7613 (mtt90) REVERT: I 362 TYR cc_start: 0.8472 (t80) cc_final: 0.8235 (t80) REVERT: I 392 ASN cc_start: 0.8125 (m-40) cc_final: 0.6865 (m-40) REVERT: I 396 ASN cc_start: 0.8278 (m-40) cc_final: 0.7735 (m110) outliers start: 174 outliers final: 125 residues processed: 1317 average time/residue: 0.2129 time to fit residues: 424.7915 Evaluate side-chains 1394 residues out of total 3232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 1235 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 194 GLU Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 133 LYS Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 124 GLN Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 266 MET Chi-restraints excluded: chain C residue 282 ASP Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 360 ARG Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain D residue 61 GLN Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 84 LYS Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 169 SER Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 288 LYS Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 379 LYS Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 65 MET Chi-restraints excluded: chain E residue 85 GLU Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 196 GLN Chi-restraints excluded: chain E residue 227 SER Chi-restraints excluded: chain E residue 236 GLN Chi-restraints excluded: chain E residue 273 THR Chi-restraints excluded: chain E residue 275 THR Chi-restraints excluded: chain E residue 284 LYS Chi-restraints excluded: chain E residue 288 LYS Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain E residue 342 LEU Chi-restraints excluded: chain E residue 344 SER Chi-restraints excluded: chain E residue 346 ASN Chi-restraints excluded: chain E residue 355 LEU Chi-restraints excluded: chain E residue 371 GLU Chi-restraints excluded: chain E residue 372 ILE Chi-restraints excluded: chain E residue 373 SER Chi-restraints excluded: chain E residue 386 LYS Chi-restraints excluded: chain F residue 69 SER Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 133 LYS Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 153 ASN Chi-restraints excluded: chain F residue 180 GLN Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 194 GLU Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 288 LYS Chi-restraints excluded: chain F residue 303 LEU Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain F residue 353 GLN Chi-restraints excluded: chain F residue 367 SER Chi-restraints excluded: chain F residue 380 LEU Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain J residue 122 LEU Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 166 HIS Chi-restraints excluded: chain J residue 194 THR Chi-restraints excluded: chain J residue 201 ILE Chi-restraints excluded: chain J residue 213 ILE Chi-restraints excluded: chain J residue 219 MET Chi-restraints excluded: chain J residue 356 GLU Chi-restraints excluded: chain J residue 368 GLN Chi-restraints excluded: chain J residue 408 LEU Chi-restraints excluded: chain J residue 419 THR Chi-restraints excluded: chain J residue 420 MET Chi-restraints excluded: chain J residue 466 GLN Chi-restraints excluded: chain J residue 490 VAL Chi-restraints excluded: chain G residue 3 LEU Chi-restraints excluded: chain G residue 11 ARG Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 142 GLN Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain G residue 203 THR Chi-restraints excluded: chain G residue 230 GLN Chi-restraints excluded: chain G residue 237 ILE Chi-restraints excluded: chain G residue 245 LEU Chi-restraints excluded: chain G residue 272 THR Chi-restraints excluded: chain G residue 318 SER Chi-restraints excluded: chain G residue 334 ILE Chi-restraints excluded: chain G residue 342 ASN Chi-restraints excluded: chain G residue 407 LEU Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 17 LEU Chi-restraints excluded: chain H residue 35 ARG Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 135 ARG Chi-restraints excluded: chain H residue 143 ARG Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 169 LEU Chi-restraints excluded: chain H residue 205 LYS Chi-restraints excluded: chain H residue 214 LYS Chi-restraints excluded: chain H residue 221 LEU Chi-restraints excluded: chain H residue 250 LEU Chi-restraints excluded: chain H residue 298 VAL Chi-restraints excluded: chain H residue 306 GLN Chi-restraints excluded: chain H residue 341 ILE Chi-restraints excluded: chain H residue 359 GLU Chi-restraints excluded: chain H residue 404 LEU Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 118 ASN Chi-restraints excluded: chain I residue 203 THR Chi-restraints excluded: chain I residue 232 LEU Chi-restraints excluded: chain I residue 234 ARG Chi-restraints excluded: chain I residue 241 GLN Chi-restraints excluded: chain I residue 250 LEU Chi-restraints excluded: chain I residue 272 THR Chi-restraints excluded: chain I residue 279 MET Chi-restraints excluded: chain I residue 292 ILE Chi-restraints excluded: chain I residue 297 MET Chi-restraints excluded: chain I residue 328 ARG Chi-restraints excluded: chain I residue 398 LEU Chi-restraints excluded: chain I residue 407 LEU Chi-restraints excluded: chain I residue 409 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 95 optimal weight: 0.7980 chunk 201 optimal weight: 0.2980 chunk 200 optimal weight: 0.1980 chunk 311 optimal weight: 2.9990 chunk 319 optimal weight: 3.9990 chunk 202 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 189 optimal weight: 0.9990 chunk 106 optimal weight: 0.6980 chunk 348 optimal weight: 4.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 251 ASN F 327 GLN F 329 GLN ** J 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 478 ASN G 156 ASN ** G 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 2 ASN I 118 ASN ** I 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 320 HIS I 325 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.113928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.095954 restraints weight = 58584.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.098968 restraints weight = 25924.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.100858 restraints weight = 14020.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.101997 restraints weight = 8773.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.102828 restraints weight = 6279.285| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.6782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 30315 Z= 0.151 Angle : 0.675 14.399 41246 Z= 0.344 Chirality : 0.043 0.220 4889 Planarity : 0.005 0.063 5392 Dihedral : 4.080 20.705 4179 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 4.76 % Allowed : 26.52 % Favored : 68.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.82 (0.14), residues: 3860 helix: 2.99 (0.11), residues: 2016 sheet: -0.20 (0.22), residues: 531 loop : -1.14 (0.16), residues: 1313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG J 424 TYR 0.026 0.001 TYR G 293 PHE 0.033 0.001 PHE J 339 TRP 0.034 0.002 TRP E 312 HIS 0.013 0.001 HIS I 320 Details of bonding type rmsd covalent geometry : bond 0.00319 (30315) covalent geometry : angle 0.67524 (41246) hydrogen bonds : bond 0.05990 ( 1888) hydrogen bonds : angle 4.21653 ( 5523) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7720 Ramachandran restraints generated. 3860 Oldfield, 0 Emsley, 3860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7720 Ramachandran restraints generated. 3860 Oldfield, 0 Emsley, 3860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1402 residues out of total 3232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 1248 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.6984 (mm-30) cc_final: 0.6719 (mm-30) REVERT: A 130 GLU cc_start: 0.7520 (mm-30) cc_final: 0.7113 (mm-30) REVERT: A 154 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8471 (mp) REVERT: A 161 GLN cc_start: 0.7389 (pt0) cc_final: 0.6810 (pt0) REVERT: A 171 GLN cc_start: 0.7946 (tp40) cc_final: 0.6815 (tp40) REVERT: A 175 ASP cc_start: 0.6816 (OUTLIER) cc_final: 0.6091 (m-30) REVERT: A 178 ILE cc_start: 0.8439 (tt) cc_final: 0.8110 (pt) REVERT: A 214 GLU cc_start: 0.7659 (mm-30) cc_final: 0.7266 (mm-30) REVERT: A 228 ARG cc_start: 0.7432 (mtm-85) cc_final: 0.7119 (mtm-85) REVERT: A 259 LYS cc_start: 0.8142 (mtmm) cc_final: 0.7771 (mtmm) REVERT: A 284 LYS cc_start: 0.7384 (mtpp) cc_final: 0.7136 (mtpp) REVERT: A 293 ASP cc_start: 0.7497 (t0) cc_final: 0.7217 (t0) REVERT: A 317 GLN cc_start: 0.7574 (mm-40) cc_final: 0.7235 (mm-40) REVERT: A 324 GLU cc_start: 0.6235 (tp30) cc_final: 0.5998 (tp30) REVERT: A 347 THR cc_start: 0.7207 (OUTLIER) cc_final: 0.6860 (p) REVERT: A 379 LYS cc_start: 0.7967 (tttt) cc_final: 0.7718 (tttt) REVERT: A 381 ILE cc_start: 0.8511 (mt) cc_final: 0.8230 (mt) REVERT: B 50 GLU cc_start: 0.7600 (mm-30) cc_final: 0.7209 (mm-30) REVERT: B 51 GLU cc_start: 0.6666 (mp0) cc_final: 0.6360 (mp0) REVERT: B 65 MET cc_start: 0.6849 (mtm) cc_final: 0.6559 (mtp) REVERT: B 93 ASP cc_start: 0.7883 (t0) cc_final: 0.7551 (t70) REVERT: B 123 LYS cc_start: 0.7493 (mttp) cc_final: 0.7090 (mttp) REVERT: B 130 GLU cc_start: 0.7303 (mm-30) cc_final: 0.6843 (tm-30) REVERT: B 136 LEU cc_start: 0.8489 (tt) cc_final: 0.8250 (tp) REVERT: B 158 GLU cc_start: 0.6813 (tt0) cc_final: 0.6047 (tm-30) REVERT: B 159 GLU cc_start: 0.7664 (tp30) cc_final: 0.7326 (tp30) REVERT: B 161 GLN cc_start: 0.8161 (OUTLIER) cc_final: 0.7611 (mm-40) REVERT: B 162 HIS cc_start: 0.7873 (m-70) cc_final: 0.6767 (m90) REVERT: B 165 ASP cc_start: 0.7031 (m-30) cc_final: 0.6778 (m-30) REVERT: B 171 GLN cc_start: 0.8026 (tp40) cc_final: 0.7583 (tp40) REVERT: B 225 TYR cc_start: 0.8008 (m-80) cc_final: 0.7671 (m-10) REVERT: B 279 TYR cc_start: 0.7980 (m-80) cc_final: 0.7671 (m-80) REVERT: B 294 MET cc_start: 0.7136 (ptp) cc_final: 0.6874 (ptp) REVERT: B 300 PHE cc_start: 0.7784 (m-10) cc_final: 0.7231 (m-80) REVERT: B 318 ARG cc_start: 0.7957 (ptp-110) cc_final: 0.7460 (mtp85) REVERT: B 328 LYS cc_start: 0.8143 (mmpt) cc_final: 0.7753 (mmpt) REVERT: B 329 GLN cc_start: 0.7034 (mt0) cc_final: 0.6773 (mp10) REVERT: B 330 LEU cc_start: 0.8178 (tt) cc_final: 0.7812 (tp) REVERT: B 332 GLN cc_start: 0.7599 (mm-40) cc_final: 0.6963 (tp40) REVERT: B 333 TYR cc_start: 0.7840 (m-10) cc_final: 0.7402 (m-10) REVERT: B 379 LYS cc_start: 0.8208 (tttt) cc_final: 0.8008 (ttmt) REVERT: C 53 ASP cc_start: 0.6754 (t0) cc_final: 0.6498 (t0) REVERT: C 54 ASP cc_start: 0.7303 (t0) cc_final: 0.7037 (t0) REVERT: C 62 ILE cc_start: 0.7844 (tp) cc_final: 0.7426 (pt) REVERT: C 78 ASP cc_start: 0.6546 (p0) cc_final: 0.6278 (p0) REVERT: C 111 SER cc_start: 0.8626 (m) cc_final: 0.8198 (p) REVERT: C 117 GLN cc_start: 0.7339 (mt0) cc_final: 0.6635 (mt0) REVERT: C 121 ASN cc_start: 0.7305 (m-40) cc_final: 0.6980 (m-40) REVERT: C 133 LYS cc_start: 0.8307 (mtpt) cc_final: 0.8002 (mtpt) REVERT: C 161 GLN cc_start: 0.7594 (tp40) cc_final: 0.6039 (tp40) REVERT: C 164 ARG cc_start: 0.6572 (ttp80) cc_final: 0.5997 (ttp80) REVERT: C 168 THR cc_start: 0.8267 (OUTLIER) cc_final: 0.8022 (p) REVERT: C 200 GLN cc_start: 0.6985 (mt0) cc_final: 0.6487 (mt0) REVERT: C 231 VAL cc_start: 0.8289 (OUTLIER) cc_final: 0.7913 (p) REVERT: C 257 ASN cc_start: 0.7909 (m-40) cc_final: 0.7442 (m110) REVERT: C 262 GLN cc_start: 0.7040 (OUTLIER) cc_final: 0.6657 (mp10) REVERT: C 296 THR cc_start: 0.7600 (p) cc_final: 0.7246 (t) REVERT: C 340 SER cc_start: 0.8334 (OUTLIER) cc_final: 0.8128 (p) REVERT: C 379 LYS cc_start: 0.7825 (ttmt) cc_final: 0.7559 (ttmt) REVERT: D 50 GLU cc_start: 0.6669 (OUTLIER) cc_final: 0.6229 (tp30) REVERT: D 54 ASP cc_start: 0.6835 (t0) cc_final: 0.6085 (t0) REVERT: D 73 THR cc_start: 0.8610 (OUTLIER) cc_final: 0.8328 (m) REVERT: D 117 GLN cc_start: 0.7802 (tt0) cc_final: 0.6996 (tt0) REVERT: D 121 ASN cc_start: 0.7773 (m-40) cc_final: 0.7364 (m-40) REVERT: D 126 GLN cc_start: 0.7638 (tp-100) cc_final: 0.7397 (tp-100) REVERT: D 129 ILE cc_start: 0.8315 (mt) cc_final: 0.8006 (mp) REVERT: D 138 LYS cc_start: 0.8195 (tttt) cc_final: 0.7816 (tttt) REVERT: D 145 ARG cc_start: 0.7942 (mtm-85) cc_final: 0.7739 (mtm180) REVERT: D 157 ARG cc_start: 0.7241 (mtm110) cc_final: 0.6611 (mtm110) REVERT: D 161 GLN cc_start: 0.7369 (mp10) cc_final: 0.6933 (mp10) REVERT: D 187 MET cc_start: 0.7563 (mmm) cc_final: 0.6769 (mmm) REVERT: D 228 ARG cc_start: 0.7030 (mtp85) cc_final: 0.6624 (mtt90) REVERT: D 255 ASP cc_start: 0.7200 (m-30) cc_final: 0.6910 (m-30) REVERT: D 276 THR cc_start: 0.8054 (m) cc_final: 0.7817 (t) REVERT: D 294 MET cc_start: 0.7515 (mmm) cc_final: 0.7158 (mmm) REVERT: D 314 LYS cc_start: 0.6968 (tttt) cc_final: 0.6705 (tptt) REVERT: D 327 GLN cc_start: 0.7758 (mm110) cc_final: 0.7556 (mm-40) REVERT: D 331 GLU cc_start: 0.7063 (mp0) cc_final: 0.6558 (mp0) REVERT: D 332 GLN cc_start: 0.7380 (tp40) cc_final: 0.7041 (tp40) REVERT: D 378 ASN cc_start: 0.7837 (m-40) cc_final: 0.6895 (m-40) REVERT: D 379 LYS cc_start: 0.8060 (OUTLIER) cc_final: 0.7539 (mmmm) REVERT: D 382 ASP cc_start: 0.7221 (m-30) cc_final: 0.6626 (m-30) REVERT: D 385 VAL cc_start: 0.8491 (t) cc_final: 0.8165 (p) REVERT: E 53 ASP cc_start: 0.7098 (t70) cc_final: 0.5400 (t0) REVERT: E 61 GLN cc_start: 0.7406 (mp10) cc_final: 0.7097 (mp10) REVERT: E 85 GLU cc_start: 0.6959 (OUTLIER) cc_final: 0.6563 (tm-30) REVERT: E 126 GLN cc_start: 0.8050 (tm-30) cc_final: 0.7841 (tm-30) REVERT: E 142 ASP cc_start: 0.7295 (m-30) cc_final: 0.6941 (m-30) REVERT: E 153 ASN cc_start: 0.7791 (t0) cc_final: 0.7467 (t0) REVERT: E 164 ARG cc_start: 0.7115 (ttp80) cc_final: 0.6711 (ttp80) REVERT: E 196 GLN cc_start: 0.7863 (OUTLIER) cc_final: 0.7090 (mp10) REVERT: E 200 GLN cc_start: 0.7362 (mm-40) cc_final: 0.6936 (mt0) REVERT: E 211 LEU cc_start: 0.8310 (mt) cc_final: 0.8038 (mm) REVERT: E 217 ARG cc_start: 0.6919 (mtt-85) cc_final: 0.6518 (mtt-85) REVERT: E 222 MET cc_start: 0.6400 (tpp) cc_final: 0.5871 (mpp) REVERT: E 228 ARG cc_start: 0.6960 (mtm-85) cc_final: 0.6751 (mtt180) REVERT: E 236 GLN cc_start: 0.7479 (mm-40) cc_final: 0.7155 (tp40) REVERT: E 251 ASN cc_start: 0.7294 (t0) cc_final: 0.6988 (t0) REVERT: E 294 MET cc_start: 0.6694 (mmm) cc_final: 0.6389 (mmm) REVERT: E 312 TRP cc_start: 0.8053 (t60) cc_final: 0.7825 (t60) REVERT: F 50 GLU cc_start: 0.7730 (mm-30) cc_final: 0.7158 (mm-30) REVERT: F 98 ARG cc_start: 0.6996 (ttm110) cc_final: 0.6712 (ttm110) REVERT: F 105 LYS cc_start: 0.7906 (mttt) cc_final: 0.7683 (mttt) REVERT: F 124 GLN cc_start: 0.7434 (mt0) cc_final: 0.7167 (tt0) REVERT: F 126 GLN cc_start: 0.7035 (tp40) cc_final: 0.6638 (tp40) REVERT: F 133 LYS cc_start: 0.7971 (OUTLIER) cc_final: 0.7516 (tttt) REVERT: F 138 LYS cc_start: 0.8509 (ttpt) cc_final: 0.8154 (tttp) REVERT: F 157 ARG cc_start: 0.7341 (mtm-85) cc_final: 0.7118 (mtm-85) REVERT: F 158 GLU cc_start: 0.7189 (tp30) cc_final: 0.6312 (tp30) REVERT: F 161 GLN cc_start: 0.7324 (tp40) cc_final: 0.6828 (tp40) REVERT: F 164 ARG cc_start: 0.7619 (ttm-80) cc_final: 0.7292 (ttm110) REVERT: F 179 GLN cc_start: 0.7871 (OUTLIER) cc_final: 0.7169 (mp10) REVERT: F 192 LYS cc_start: 0.7968 (mttp) cc_final: 0.7679 (mttp) REVERT: F 200 GLN cc_start: 0.6992 (mp10) cc_final: 0.6385 (mp10) REVERT: F 205 GLU cc_start: 0.7449 (mm-30) cc_final: 0.7221 (mt-10) REVERT: F 214 GLU cc_start: 0.7572 (tp30) cc_final: 0.6861 (mp0) REVERT: F 217 ARG cc_start: 0.6787 (mtt180) cc_final: 0.6274 (ptp-110) REVERT: F 259 LYS cc_start: 0.7738 (mmtp) cc_final: 0.7445 (mttp) REVERT: F 288 LYS cc_start: 0.8339 (OUTLIER) cc_final: 0.7850 (mtmt) REVERT: F 317 GLN cc_start: 0.7189 (mm-40) cc_final: 0.6941 (mp10) REVERT: F 371 GLU cc_start: 0.6242 (tp30) cc_final: 0.5822 (tp30) REVERT: F 372 ILE cc_start: 0.8744 (mp) cc_final: 0.7926 (mm) REVERT: F 379 LYS cc_start: 0.7707 (tptm) cc_final: 0.7135 (tptm) REVERT: F 383 ASP cc_start: 0.7166 (m-30) cc_final: 0.6791 (m-30) REVERT: J 21 LEU cc_start: 0.8211 (mt) cc_final: 0.7986 (mm) REVERT: J 66 ILE cc_start: 0.8612 (mt) cc_final: 0.8240 (mm) REVERT: J 87 ILE cc_start: 0.8624 (tt) cc_final: 0.8403 (pt) REVERT: J 114 ILE cc_start: 0.8265 (mm) cc_final: 0.7920 (mm) REVERT: J 122 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.7743 (mp) REVERT: J 124 GLN cc_start: 0.7807 (tt0) cc_final: 0.7202 (tt0) REVERT: J 126 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.8026 (mm) REVERT: J 161 ILE cc_start: 0.8399 (mm) cc_final: 0.8032 (mp) REVERT: J 213 ILE cc_start: 0.8356 (OUTLIER) cc_final: 0.8094 (mt) REVERT: J 217 GLN cc_start: 0.7744 (tp40) cc_final: 0.7033 (tt0) REVERT: J 233 GLU cc_start: 0.7572 (mp0) cc_final: 0.7172 (mp0) REVERT: J 239 VAL cc_start: 0.8483 (p) cc_final: 0.8228 (m) REVERT: J 252 GLU cc_start: 0.7354 (mm-30) cc_final: 0.6981 (tp30) REVERT: J 268 ARG cc_start: 0.7602 (ttt180) cc_final: 0.7200 (mmm-85) REVERT: J 297 GLU cc_start: 0.7439 (tt0) cc_final: 0.7152 (tt0) REVERT: J 308 LEU cc_start: 0.7990 (mt) cc_final: 0.7749 (mm) REVERT: J 327 PHE cc_start: 0.6699 (t80) cc_final: 0.5747 (t80) REVERT: J 331 LEU cc_start: 0.8232 (mt) cc_final: 0.7535 (mt) REVERT: J 333 MET cc_start: 0.7154 (mtm) cc_final: 0.6848 (mtm) REVERT: J 342 ILE cc_start: 0.8075 (mm) cc_final: 0.7749 (tt) REVERT: J 368 GLN cc_start: 0.6994 (OUTLIER) cc_final: 0.6657 (mt0) REVERT: J 384 THR cc_start: 0.8253 (m) cc_final: 0.7989 (p) REVERT: J 395 LEU cc_start: 0.7872 (mt) cc_final: 0.7467 (mt) REVERT: J 403 ASN cc_start: 0.8205 (m-40) cc_final: 0.7781 (m110) REVERT: J 408 LEU cc_start: 0.7381 (OUTLIER) cc_final: 0.7066 (tt) REVERT: J 416 ILE cc_start: 0.8299 (mt) cc_final: 0.8015 (tp) REVERT: J 420 MET cc_start: 0.7521 (OUTLIER) cc_final: 0.7275 (tpt) REVERT: J 436 VAL cc_start: 0.8016 (t) cc_final: 0.7619 (m) REVERT: J 457 GLN cc_start: 0.7573 (mm-40) cc_final: 0.7311 (tp40) REVERT: J 458 GLN cc_start: 0.8174 (tt0) cc_final: 0.7833 (tt0) REVERT: J 466 GLN cc_start: 0.7619 (OUTLIER) cc_final: 0.7011 (mp10) REVERT: J 471 GLN cc_start: 0.7760 (mm-40) cc_final: 0.7269 (mm-40) REVERT: J 488 PHE cc_start: 0.8050 (m-80) cc_final: 0.7428 (m-10) REVERT: J 489 LEU cc_start: 0.8406 (mt) cc_final: 0.8114 (mt) REVERT: J 491 LEU cc_start: 0.7697 (mt) cc_final: 0.7401 (tt) REVERT: G 3 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8464 (tp) REVERT: G 5 GLN cc_start: 0.8334 (mt0) cc_final: 0.7631 (mt0) REVERT: G 17 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8401 (tt) REVERT: G 19 LYS cc_start: 0.8242 (tttm) cc_final: 0.7902 (tttm) REVERT: G 24 ARG cc_start: 0.7731 (tpt170) cc_final: 0.7328 (tpt170) REVERT: G 29 GLU cc_start: 0.7812 (tp30) cc_final: 0.6611 (tp30) REVERT: G 31 ILE cc_start: 0.8651 (mt) cc_final: 0.8375 (mm) REVERT: G 32 ASN cc_start: 0.8168 (m-40) cc_final: 0.6876 (p0) REVERT: G 78 MET cc_start: 0.6930 (ptp) cc_final: 0.6643 (ptp) REVERT: G 87 GLN cc_start: 0.8475 (tp40) cc_final: 0.7986 (tp40) REVERT: G 88 GLU cc_start: 0.8078 (pt0) cc_final: 0.7876 (pt0) REVERT: G 101 ASP cc_start: 0.7715 (t70) cc_final: 0.7149 (t0) REVERT: G 125 TYR cc_start: 0.8892 (t80) cc_final: 0.8524 (t80) REVERT: G 130 LYS cc_start: 0.8606 (tttt) cc_final: 0.8215 (ttpp) REVERT: G 136 GLN cc_start: 0.8412 (tp40) cc_final: 0.8088 (tp-100) REVERT: G 142 GLN cc_start: 0.7807 (OUTLIER) cc_final: 0.7521 (mm-40) REVERT: G 162 ASP cc_start: 0.8205 (m-30) cc_final: 0.7860 (m-30) REVERT: G 169 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8352 (mm) REVERT: G 181 GLN cc_start: 0.8306 (mm-40) cc_final: 0.7819 (tm-30) REVERT: G 215 GLU cc_start: 0.7570 (tm-30) cc_final: 0.6789 (tm-30) REVERT: G 217 GLU cc_start: 0.8021 (tm-30) cc_final: 0.7585 (tm-30) REVERT: G 225 GLN cc_start: 0.8406 (tm-30) cc_final: 0.8162 (tm-30) REVERT: G 230 GLN cc_start: 0.8545 (OUTLIER) cc_final: 0.7906 (pp30) REVERT: G 231 ASP cc_start: 0.8218 (m-30) cc_final: 0.7651 (m-30) REVERT: G 232 LEU cc_start: 0.9220 (tp) cc_final: 0.8914 (tt) REVERT: G 279 MET cc_start: 0.4350 (tpt) cc_final: 0.3726 (mmm) REVERT: G 290 LEU cc_start: 0.8492 (tp) cc_final: 0.8142 (mp) REVERT: G 299 ASN cc_start: 0.8393 (m110) cc_final: 0.7911 (m-40) REVERT: G 303 LYS cc_start: 0.8681 (mtpp) cc_final: 0.7727 (mtpp) REVERT: G 304 GLN cc_start: 0.8251 (pt0) cc_final: 0.7676 (pp30) REVERT: G 307 TYR cc_start: 0.7976 (m-80) cc_final: 0.7512 (m-80) REVERT: G 314 GLU cc_start: 0.7901 (mm-30) cc_final: 0.7367 (mm-30) REVERT: G 317 GLU cc_start: 0.7919 (tp30) cc_final: 0.7111 (tp30) REVERT: G 321 ARG cc_start: 0.8368 (mtt180) cc_final: 0.8019 (mtt180) REVERT: G 333 ASN cc_start: 0.8593 (m-40) cc_final: 0.8234 (m-40) REVERT: G 344 TYR cc_start: 0.8130 (m-80) cc_final: 0.7486 (m-80) REVERT: G 401 LYS cc_start: 0.8424 (tptm) cc_final: 0.8061 (tppp) REVERT: H 14 ASN cc_start: 0.8136 (t0) cc_final: 0.7437 (t0) REVERT: H 16 GLU cc_start: 0.8211 (mp0) cc_final: 0.7516 (mp0) REVERT: H 17 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8623 (mm) REVERT: H 29 GLU cc_start: 0.8000 (tp30) cc_final: 0.7381 (tp30) REVERT: H 87 GLN cc_start: 0.8080 (tp-100) cc_final: 0.7342 (tp-100) REVERT: H 88 GLU cc_start: 0.8394 (mt-10) cc_final: 0.7963 (mt-10) REVERT: H 89 LYS cc_start: 0.8740 (mmmt) cc_final: 0.8378 (mmmt) REVERT: H 94 GLN cc_start: 0.8158 (tp40) cc_final: 0.7697 (tt0) REVERT: H 95 ASP cc_start: 0.8718 (m-30) cc_final: 0.7905 (m-30) REVERT: H 129 GLN cc_start: 0.8111 (tt0) cc_final: 0.7903 (tt0) REVERT: H 131 GLU cc_start: 0.8029 (tp30) cc_final: 0.7774 (tp30) REVERT: H 135 ARG cc_start: 0.8029 (OUTLIER) cc_final: 0.7453 (mmm160) REVERT: H 162 ASP cc_start: 0.8136 (m-30) cc_final: 0.7832 (m-30) REVERT: H 180 GLU cc_start: 0.8553 (mm-30) cc_final: 0.7882 (tm-30) REVERT: H 184 GLN cc_start: 0.8510 (tt0) cc_final: 0.8134 (tm-30) REVERT: H 190 TYR cc_start: 0.7263 (m-80) cc_final: 0.7013 (m-10) REVERT: H 223 LEU cc_start: 0.8850 (mt) cc_final: 0.8639 (mm) REVERT: H 230 GLN cc_start: 0.8197 (tp40) cc_final: 0.7556 (tp-100) REVERT: H 231 ASP cc_start: 0.7842 (t0) cc_final: 0.7544 (t0) REVERT: H 232 LEU cc_start: 0.8700 (tp) cc_final: 0.8206 (tt) REVERT: H 236 GLN cc_start: 0.8119 (mt0) cc_final: 0.7451 (mm-40) REVERT: H 237 ILE cc_start: 0.8900 (mt) cc_final: 0.8630 (pt) REVERT: H 297 MET cc_start: 0.6365 (ttm) cc_final: 0.6027 (tmm) REVERT: H 301 GLN cc_start: 0.8315 (mt0) cc_final: 0.7798 (mp10) REVERT: H 303 LYS cc_start: 0.8411 (mttt) cc_final: 0.7865 (mttt) REVERT: H 306 GLN cc_start: 0.8264 (OUTLIER) cc_final: 0.7901 (mp10) REVERT: H 314 GLU cc_start: 0.7443 (mm-30) cc_final: 0.7109 (mm-30) REVERT: H 317 GLU cc_start: 0.7682 (tp30) cc_final: 0.7087 (tp30) REVERT: H 321 ARG cc_start: 0.8276 (mtt180) cc_final: 0.7543 (mtt180) REVERT: H 340 SER cc_start: 0.8730 (m) cc_final: 0.8149 (p) REVERT: H 341 ILE cc_start: 0.8870 (OUTLIER) cc_final: 0.8608 (tp) REVERT: H 374 ASP cc_start: 0.7687 (t0) cc_final: 0.7349 (t0) REVERT: H 392 ASN cc_start: 0.8350 (m-40) cc_final: 0.7913 (t0) REVERT: H 396 ASN cc_start: 0.8085 (m-40) cc_final: 0.7648 (m110) REVERT: H 397 GLN cc_start: 0.8128 (tt0) cc_final: 0.7419 (tm-30) REVERT: H 412 LEU cc_start: 0.8421 (tp) cc_final: 0.8178 (tp) REVERT: I 4 MET cc_start: 0.7662 (tmm) cc_final: 0.7329 (tmm) REVERT: I 16 GLU cc_start: 0.7960 (mp0) cc_final: 0.7446 (mp0) REVERT: I 24 ARG cc_start: 0.7971 (ttp-170) cc_final: 0.7508 (ttp-110) REVERT: I 28 PHE cc_start: 0.8080 (m-80) cc_final: 0.7878 (m-80) REVERT: I 31 ILE cc_start: 0.9056 (mt) cc_final: 0.8840 (mm) REVERT: I 76 PHE cc_start: 0.7557 (t80) cc_final: 0.6808 (t80) REVERT: I 124 SER cc_start: 0.8606 (t) cc_final: 0.8390 (p) REVERT: I 162 ASP cc_start: 0.8847 (m-30) cc_final: 0.7872 (m-30) REVERT: I 185 ILE cc_start: 0.9148 (mt) cc_final: 0.8919 (tt) REVERT: I 188 ASN cc_start: 0.7849 (p0) cc_final: 0.7387 (p0) REVERT: I 215 GLU cc_start: 0.8093 (tp30) cc_final: 0.7633 (tp30) REVERT: I 217 GLU cc_start: 0.7554 (mm-30) cc_final: 0.7168 (mm-30) REVERT: I 225 GLN cc_start: 0.7986 (tm-30) cc_final: 0.7351 (tm-30) REVERT: I 235 GLU cc_start: 0.7997 (tp30) cc_final: 0.7453 (tp30) REVERT: I 236 GLN cc_start: 0.8378 (mt0) cc_final: 0.7967 (mt0) REVERT: I 238 ARG cc_start: 0.8037 (mpt180) cc_final: 0.7348 (mpp-170) REVERT: I 301 GLN cc_start: 0.8461 (tt0) cc_final: 0.8122 (mt0) REVERT: I 306 GLN cc_start: 0.8413 (pt0) cc_final: 0.7920 (mp10) REVERT: I 314 GLU cc_start: 0.7152 (mt-10) cc_final: 0.6773 (mt-10) REVERT: I 315 GLN cc_start: 0.7984 (mt0) cc_final: 0.7530 (mp10) REVERT: I 328 ARG cc_start: 0.7955 (OUTLIER) cc_final: 0.7623 (mtt90) REVERT: I 362 TYR cc_start: 0.8470 (t80) cc_final: 0.8216 (t80) REVERT: I 392 ASN cc_start: 0.8092 (m-40) cc_final: 0.6862 (m-40) REVERT: I 396 ASN cc_start: 0.8271 (m-40) cc_final: 0.7728 (m110) outliers start: 154 outliers final: 103 residues processed: 1305 average time/residue: 0.2319 time to fit residues: 455.7217 Evaluate side-chains 1362 residues out of total 3232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 1226 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 158 GLU Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 133 LYS Chi-restraints excluded: chain B residue 161 GLN Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 124 GLN Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 266 MET Chi-restraints excluded: chain C residue 282 ASP Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 340 SER Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 84 LYS Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 288 LYS Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 379 LYS Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 65 MET Chi-restraints excluded: chain E residue 85 GLU Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 196 GLN Chi-restraints excluded: chain E residue 261 THR Chi-restraints excluded: chain E residue 275 THR Chi-restraints excluded: chain E residue 284 LYS Chi-restraints excluded: chain E residue 288 LYS Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain E residue 344 SER Chi-restraints excluded: chain E residue 346 ASN Chi-restraints excluded: chain E residue 373 SER Chi-restraints excluded: chain E residue 386 LYS Chi-restraints excluded: chain F residue 69 SER Chi-restraints excluded: chain F residue 110 SER Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 133 LYS Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 179 GLN Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 194 GLU Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 288 LYS Chi-restraints excluded: chain F residue 303 LEU Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain F residue 353 GLN Chi-restraints excluded: chain F residue 367 SER Chi-restraints excluded: chain F residue 380 LEU Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain J residue 122 LEU Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 166 HIS Chi-restraints excluded: chain J residue 194 THR Chi-restraints excluded: chain J residue 213 ILE Chi-restraints excluded: chain J residue 219 MET Chi-restraints excluded: chain J residue 293 GLN Chi-restraints excluded: chain J residue 368 GLN Chi-restraints excluded: chain J residue 408 LEU Chi-restraints excluded: chain J residue 420 MET Chi-restraints excluded: chain J residue 466 GLN Chi-restraints excluded: chain J residue 490 VAL Chi-restraints excluded: chain G residue 3 LEU Chi-restraints excluded: chain G residue 11 ARG Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 142 GLN Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain G residue 203 THR Chi-restraints excluded: chain G residue 230 GLN Chi-restraints excluded: chain G residue 237 ILE Chi-restraints excluded: chain G residue 245 LEU Chi-restraints excluded: chain G residue 272 THR Chi-restraints excluded: chain G residue 318 SER Chi-restraints excluded: chain G residue 342 ASN Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 17 LEU Chi-restraints excluded: chain H residue 35 ARG Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 135 ARG Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 214 LYS Chi-restraints excluded: chain H residue 221 LEU Chi-restraints excluded: chain H residue 250 LEU Chi-restraints excluded: chain H residue 298 VAL Chi-restraints excluded: chain H residue 306 GLN Chi-restraints excluded: chain H residue 341 ILE Chi-restraints excluded: chain H residue 404 LEU Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 118 ASN Chi-restraints excluded: chain I residue 203 THR Chi-restraints excluded: chain I residue 232 LEU Chi-restraints excluded: chain I residue 234 ARG Chi-restraints excluded: chain I residue 241 GLN Chi-restraints excluded: chain I residue 250 LEU Chi-restraints excluded: chain I residue 272 THR Chi-restraints excluded: chain I residue 279 MET Chi-restraints excluded: chain I residue 297 MET Chi-restraints excluded: chain I residue 328 ARG Chi-restraints excluded: chain I residue 398 LEU Chi-restraints excluded: chain I residue 409 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 44 optimal weight: 0.9980 chunk 130 optimal weight: 0.6980 chunk 190 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 358 optimal weight: 0.0050 chunk 346 optimal weight: 10.0000 chunk 340 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 chunk 339 optimal weight: 9.9990 chunk 322 optimal weight: 4.9990 chunk 222 optimal weight: 0.0980 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 GLN ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 185 GLN E 236 GLN F 182 ASN F 251 ASN ** J 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 478 ASN G 156 ASN ** G 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 173 ASN I 2 ASN I 118 ASN ** I 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 320 HIS I 325 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.114291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.096414 restraints weight = 58599.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.099424 restraints weight = 25989.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.101290 restraints weight = 14072.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.102518 restraints weight = 8815.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.103243 restraints weight = 6224.879| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.6891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 30315 Z= 0.151 Angle : 0.689 13.096 41246 Z= 0.350 Chirality : 0.043 0.215 4889 Planarity : 0.005 0.072 5392 Dihedral : 4.049 22.236 4179 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 4.39 % Allowed : 27.72 % Favored : 67.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.85 (0.14), residues: 3860 helix: 2.96 (0.11), residues: 2016 sheet: -0.08 (0.23), residues: 501 loop : -1.06 (0.16), residues: 1343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG J 424 TYR 0.028 0.001 TYR H 125 PHE 0.033 0.002 PHE J 339 TRP 0.045 0.002 TRP C 312 HIS 0.012 0.001 HIS I 320 Details of bonding type rmsd covalent geometry : bond 0.00325 (30315) covalent geometry : angle 0.68897 (41246) hydrogen bonds : bond 0.05815 ( 1888) hydrogen bonds : angle 4.20004 ( 5523) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7720 Ramachandran restraints generated. 3860 Oldfield, 0 Emsley, 3860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7720 Ramachandran restraints generated. 3860 Oldfield, 0 Emsley, 3860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1388 residues out of total 3232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 1246 time to evaluate : 1.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.6997 (mm-30) cc_final: 0.6732 (mm-30) REVERT: A 130 GLU cc_start: 0.7513 (mm-30) cc_final: 0.7124 (mm-30) REVERT: A 154 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8439 (mp) REVERT: A 161 GLN cc_start: 0.7425 (pt0) cc_final: 0.6829 (pt0) REVERT: A 171 GLN cc_start: 0.7948 (tp40) cc_final: 0.6840 (tp40) REVERT: A 175 ASP cc_start: 0.6821 (OUTLIER) cc_final: 0.6136 (m-30) REVERT: A 178 ILE cc_start: 0.8425 (tt) cc_final: 0.8082 (pt) REVERT: A 228 ARG cc_start: 0.7406 (mtm-85) cc_final: 0.7164 (mtm-85) REVERT: A 251 ASN cc_start: 0.7446 (m-40) cc_final: 0.7239 (t0) REVERT: A 259 LYS cc_start: 0.8130 (mtmm) cc_final: 0.7766 (mtmm) REVERT: A 284 LYS cc_start: 0.7390 (mtpp) cc_final: 0.7166 (mtpp) REVERT: A 293 ASP cc_start: 0.7495 (t0) cc_final: 0.7207 (t0) REVERT: A 317 GLN cc_start: 0.7568 (mm-40) cc_final: 0.7223 (mm-40) REVERT: A 324 GLU cc_start: 0.6199 (tp30) cc_final: 0.5933 (tp30) REVERT: A 347 THR cc_start: 0.7225 (OUTLIER) cc_final: 0.6853 (p) REVERT: A 379 LYS cc_start: 0.7950 (tttt) cc_final: 0.7675 (tttt) REVERT: A 381 ILE cc_start: 0.8504 (mt) cc_final: 0.8201 (mt) REVERT: B 50 GLU cc_start: 0.7617 (mm-30) cc_final: 0.7201 (mm-30) REVERT: B 51 GLU cc_start: 0.6619 (mp0) cc_final: 0.6281 (mp0) REVERT: B 54 ASP cc_start: 0.7330 (t70) cc_final: 0.7088 (t0) REVERT: B 65 MET cc_start: 0.6818 (mtm) cc_final: 0.6549 (mtp) REVERT: B 93 ASP cc_start: 0.7878 (t0) cc_final: 0.7533 (t70) REVERT: B 123 LYS cc_start: 0.7495 (mttp) cc_final: 0.7026 (mttp) REVERT: B 130 GLU cc_start: 0.7319 (mm-30) cc_final: 0.6850 (tm-30) REVERT: B 158 GLU cc_start: 0.6766 (tt0) cc_final: 0.5993 (tm-30) REVERT: B 159 GLU cc_start: 0.7673 (tp30) cc_final: 0.7338 (tp30) REVERT: B 161 GLN cc_start: 0.8113 (OUTLIER) cc_final: 0.7301 (mm-40) REVERT: B 162 HIS cc_start: 0.7883 (m-70) cc_final: 0.6786 (m90) REVERT: B 165 ASP cc_start: 0.6989 (m-30) cc_final: 0.6698 (m-30) REVERT: B 171 GLN cc_start: 0.8014 (tp40) cc_final: 0.7560 (tp40) REVERT: B 225 TYR cc_start: 0.8005 (m-80) cc_final: 0.7663 (m-10) REVERT: B 279 TYR cc_start: 0.8010 (m-80) cc_final: 0.7710 (m-80) REVERT: B 300 PHE cc_start: 0.7783 (m-10) cc_final: 0.7211 (m-80) REVERT: B 328 LYS cc_start: 0.8130 (mmpt) cc_final: 0.7743 (mmpt) REVERT: B 329 GLN cc_start: 0.7028 (mt0) cc_final: 0.6781 (mp10) REVERT: B 330 LEU cc_start: 0.8150 (tt) cc_final: 0.7809 (tp) REVERT: B 332 GLN cc_start: 0.7515 (mm-40) cc_final: 0.6914 (tp40) REVERT: B 333 TYR cc_start: 0.7845 (m-10) cc_final: 0.7409 (m-10) REVERT: B 350 ARG cc_start: 0.7842 (mtm-85) cc_final: 0.7143 (mtt90) REVERT: C 53 ASP cc_start: 0.6739 (t0) cc_final: 0.6444 (t0) REVERT: C 54 ASP cc_start: 0.7232 (t0) cc_final: 0.6991 (t0) REVERT: C 62 ILE cc_start: 0.7812 (OUTLIER) cc_final: 0.7433 (pt) REVERT: C 78 ASP cc_start: 0.6509 (p0) cc_final: 0.6264 (p0) REVERT: C 113 ARG cc_start: 0.8324 (mtt180) cc_final: 0.8091 (mtt-85) REVERT: C 117 GLN cc_start: 0.7327 (mt0) cc_final: 0.7006 (mt0) REVERT: C 133 LYS cc_start: 0.8292 (mtpt) cc_final: 0.7984 (mtpt) REVERT: C 145 ARG cc_start: 0.7589 (tpp80) cc_final: 0.7305 (ttp80) REVERT: C 161 GLN cc_start: 0.7570 (tp40) cc_final: 0.6042 (tp40) REVERT: C 164 ARG cc_start: 0.6531 (ttp80) cc_final: 0.5960 (ttp80) REVERT: C 168 THR cc_start: 0.8267 (OUTLIER) cc_final: 0.8018 (p) REVERT: C 196 GLN cc_start: 0.7649 (mm-40) cc_final: 0.7194 (mm-40) REVERT: C 200 GLN cc_start: 0.6983 (mt0) cc_final: 0.6489 (mt0) REVERT: C 231 VAL cc_start: 0.8299 (OUTLIER) cc_final: 0.7899 (p) REVERT: C 257 ASN cc_start: 0.7873 (m-40) cc_final: 0.7432 (m110) REVERT: C 262 GLN cc_start: 0.7027 (OUTLIER) cc_final: 0.6714 (mt0) REVERT: C 296 THR cc_start: 0.7607 (p) cc_final: 0.7275 (t) REVERT: C 329 GLN cc_start: 0.8099 (mm-40) cc_final: 0.7798 (mm-40) REVERT: C 360 ARG cc_start: 0.7071 (OUTLIER) cc_final: 0.6834 (ptp-170) REVERT: C 379 LYS cc_start: 0.7762 (ttmt) cc_final: 0.7499 (ttmt) REVERT: D 50 GLU cc_start: 0.6611 (OUTLIER) cc_final: 0.6227 (tp30) REVERT: D 53 ASP cc_start: 0.7735 (p0) cc_final: 0.7460 (p0) REVERT: D 54 ASP cc_start: 0.6768 (t0) cc_final: 0.6148 (t0) REVERT: D 73 THR cc_start: 0.8619 (OUTLIER) cc_final: 0.8346 (m) REVERT: D 117 GLN cc_start: 0.7804 (tt0) cc_final: 0.7058 (tt0) REVERT: D 121 ASN cc_start: 0.7757 (m-40) cc_final: 0.7339 (m-40) REVERT: D 126 GLN cc_start: 0.7629 (tp-100) cc_final: 0.7393 (tp-100) REVERT: D 129 ILE cc_start: 0.8296 (mt) cc_final: 0.7995 (mp) REVERT: D 138 LYS cc_start: 0.8230 (tttt) cc_final: 0.7898 (tttt) REVERT: D 161 GLN cc_start: 0.7325 (mp10) cc_final: 0.6878 (mp10) REVERT: D 187 MET cc_start: 0.7499 (mmm) cc_final: 0.6719 (mmm) REVERT: D 228 ARG cc_start: 0.7046 (mtp85) cc_final: 0.6774 (mtt90) REVERT: D 255 ASP cc_start: 0.7198 (m-30) cc_final: 0.6897 (m-30) REVERT: D 276 THR cc_start: 0.8052 (m) cc_final: 0.7826 (t) REVERT: D 294 MET cc_start: 0.7501 (mmm) cc_final: 0.7109 (mmm) REVERT: D 314 LYS cc_start: 0.6963 (tttt) cc_final: 0.6688 (tptt) REVERT: D 331 GLU cc_start: 0.7070 (mp0) cc_final: 0.6542 (mp0) REVERT: D 332 GLN cc_start: 0.7389 (tp40) cc_final: 0.7106 (tp40) REVERT: D 378 ASN cc_start: 0.7821 (m-40) cc_final: 0.6897 (m-40) REVERT: D 379 LYS cc_start: 0.8056 (OUTLIER) cc_final: 0.7538 (mmmm) REVERT: D 382 ASP cc_start: 0.7213 (m-30) cc_final: 0.6626 (m-30) REVERT: D 385 VAL cc_start: 0.8489 (t) cc_final: 0.8157 (p) REVERT: E 53 ASP cc_start: 0.7155 (t70) cc_final: 0.5448 (t0) REVERT: E 61 GLN cc_start: 0.7410 (mp10) cc_final: 0.7095 (mp10) REVERT: E 85 GLU cc_start: 0.6924 (OUTLIER) cc_final: 0.6533 (tm-30) REVERT: E 142 ASP cc_start: 0.7322 (m-30) cc_final: 0.6944 (m-30) REVERT: E 145 ARG cc_start: 0.7868 (mtt-85) cc_final: 0.7198 (mtm-85) REVERT: E 164 ARG cc_start: 0.7084 (ttp80) cc_final: 0.6757 (ttp80) REVERT: E 189 LEU cc_start: 0.8248 (mt) cc_final: 0.7925 (mt) REVERT: E 196 GLN cc_start: 0.7786 (OUTLIER) cc_final: 0.7083 (mp10) REVERT: E 200 GLN cc_start: 0.7319 (mm-40) cc_final: 0.6861 (mt0) REVERT: E 211 LEU cc_start: 0.8272 (mt) cc_final: 0.8017 (mm) REVERT: E 215 ARG cc_start: 0.7799 (mtt90) cc_final: 0.7573 (mmt90) REVERT: E 217 ARG cc_start: 0.6929 (mtt-85) cc_final: 0.6515 (mtt-85) REVERT: E 222 MET cc_start: 0.6296 (tpp) cc_final: 0.5776 (mpp) REVERT: E 228 ARG cc_start: 0.7003 (mtm-85) cc_final: 0.6782 (mtt180) REVERT: E 251 ASN cc_start: 0.7296 (t0) cc_final: 0.6981 (t0) REVERT: E 294 MET cc_start: 0.6754 (mmm) cc_final: 0.6484 (mmm) REVERT: E 312 TRP cc_start: 0.8012 (t60) cc_final: 0.7797 (t60) REVERT: F 50 GLU cc_start: 0.7744 (mm-30) cc_final: 0.7149 (mm-30) REVERT: F 98 ARG cc_start: 0.6997 (ttm110) cc_final: 0.6730 (ttm110) REVERT: F 105 LYS cc_start: 0.7902 (mttt) cc_final: 0.7633 (mttt) REVERT: F 124 GLN cc_start: 0.7435 (mt0) cc_final: 0.7202 (tt0) REVERT: F 126 GLN cc_start: 0.7024 (tp40) cc_final: 0.6649 (tp40) REVERT: F 133 LYS cc_start: 0.8004 (mttt) cc_final: 0.7565 (tttt) REVERT: F 138 LYS cc_start: 0.8443 (ttpt) cc_final: 0.8098 (tttp) REVERT: F 145 ARG cc_start: 0.7372 (ttm-80) cc_final: 0.7027 (ttm170) REVERT: F 158 GLU cc_start: 0.7187 (tp30) cc_final: 0.6303 (tp30) REVERT: F 161 GLN cc_start: 0.7329 (tp40) cc_final: 0.6914 (tp40) REVERT: F 179 GLN cc_start: 0.7822 (OUTLIER) cc_final: 0.7619 (mm-40) REVERT: F 192 LYS cc_start: 0.7953 (mttp) cc_final: 0.7668 (mttp) REVERT: F 200 GLN cc_start: 0.6967 (mp10) cc_final: 0.6355 (mp10) REVERT: F 205 GLU cc_start: 0.7449 (mm-30) cc_final: 0.7227 (mt-10) REVERT: F 214 GLU cc_start: 0.7594 (tp30) cc_final: 0.6866 (mp0) REVERT: F 217 ARG cc_start: 0.6762 (mtt180) cc_final: 0.6354 (ptp-170) REVERT: F 259 LYS cc_start: 0.7738 (mmtp) cc_final: 0.7461 (mttp) REVERT: F 288 LYS cc_start: 0.8368 (OUTLIER) cc_final: 0.7906 (mtmt) REVERT: F 317 GLN cc_start: 0.7217 (mm-40) cc_final: 0.6956 (mp10) REVERT: F 371 GLU cc_start: 0.6234 (tp30) cc_final: 0.5833 (tp30) REVERT: F 372 ILE cc_start: 0.8719 (mp) cc_final: 0.7888 (mm) REVERT: F 379 LYS cc_start: 0.7699 (tptm) cc_final: 0.7119 (tptm) REVERT: F 383 ASP cc_start: 0.7157 (m-30) cc_final: 0.6783 (m-30) REVERT: J 21 LEU cc_start: 0.8196 (mt) cc_final: 0.7996 (mm) REVERT: J 40 ILE cc_start: 0.8320 (mt) cc_final: 0.8069 (pt) REVERT: J 53 TRP cc_start: 0.8699 (m100) cc_final: 0.8316 (m100) REVERT: J 83 LEU cc_start: 0.8511 (mt) cc_final: 0.8154 (pp) REVERT: J 87 ILE cc_start: 0.8653 (tt) cc_final: 0.8419 (pt) REVERT: J 114 ILE cc_start: 0.8248 (mm) cc_final: 0.7902 (mm) REVERT: J 122 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7777 (mp) REVERT: J 124 GLN cc_start: 0.7807 (tt0) cc_final: 0.7191 (tt0) REVERT: J 161 ILE cc_start: 0.8391 (mm) cc_final: 0.8023 (mp) REVERT: J 213 ILE cc_start: 0.8358 (OUTLIER) cc_final: 0.8102 (mt) REVERT: J 217 GLN cc_start: 0.7747 (tp40) cc_final: 0.7119 (tt0) REVERT: J 233 GLU cc_start: 0.7547 (mp0) cc_final: 0.7154 (mp0) REVERT: J 252 GLU cc_start: 0.7382 (mm-30) cc_final: 0.6935 (tp30) REVERT: J 297 GLU cc_start: 0.7420 (tt0) cc_final: 0.7197 (tt0) REVERT: J 308 LEU cc_start: 0.7991 (mt) cc_final: 0.7738 (mm) REVERT: J 327 PHE cc_start: 0.6697 (t80) cc_final: 0.5734 (t80) REVERT: J 331 LEU cc_start: 0.8237 (mt) cc_final: 0.7512 (mt) REVERT: J 333 MET cc_start: 0.7143 (mtm) cc_final: 0.6774 (mtm) REVERT: J 342 ILE cc_start: 0.8051 (mm) cc_final: 0.7734 (tt) REVERT: J 378 PHE cc_start: 0.7715 (t80) cc_final: 0.7386 (t80) REVERT: J 384 THR cc_start: 0.8263 (m) cc_final: 0.7957 (p) REVERT: J 390 LEU cc_start: 0.8577 (tp) cc_final: 0.7924 (mt) REVERT: J 395 LEU cc_start: 0.7819 (mt) cc_final: 0.7384 (mt) REVERT: J 403 ASN cc_start: 0.8197 (m-40) cc_final: 0.7799 (m110) REVERT: J 408 LEU cc_start: 0.7352 (OUTLIER) cc_final: 0.7026 (tt) REVERT: J 416 ILE cc_start: 0.8309 (mt) cc_final: 0.8035 (tp) REVERT: J 420 MET cc_start: 0.7485 (OUTLIER) cc_final: 0.7276 (tpt) REVERT: J 424 ARG cc_start: 0.7758 (ttm-80) cc_final: 0.7096 (tpm-80) REVERT: J 428 HIS cc_start: 0.8356 (m-70) cc_final: 0.8117 (m-70) REVERT: J 436 VAL cc_start: 0.8067 (t) cc_final: 0.7670 (m) REVERT: J 458 GLN cc_start: 0.8188 (tt0) cc_final: 0.7848 (tt0) REVERT: J 471 GLN cc_start: 0.7720 (mm-40) cc_final: 0.7274 (mm-40) REVERT: J 482 TRP cc_start: 0.7954 (t60) cc_final: 0.7674 (t60) REVERT: J 484 SER cc_start: 0.7970 (m) cc_final: 0.7627 (p) REVERT: J 489 LEU cc_start: 0.8388 (mt) cc_final: 0.8108 (mt) REVERT: J 491 LEU cc_start: 0.7607 (mt) cc_final: 0.7402 (tt) REVERT: G 3 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8501 (tp) REVERT: G 5 GLN cc_start: 0.8347 (mt0) cc_final: 0.7659 (mt0) REVERT: G 19 LYS cc_start: 0.8201 (tttm) cc_final: 0.7855 (tttm) REVERT: G 29 GLU cc_start: 0.7750 (tp30) cc_final: 0.6558 (tp30) REVERT: G 31 ILE cc_start: 0.8650 (mt) cc_final: 0.8370 (mm) REVERT: G 32 ASN cc_start: 0.8101 (m-40) cc_final: 0.6883 (p0) REVERT: G 35 ARG cc_start: 0.7670 (ttm110) cc_final: 0.7441 (ttm110) REVERT: G 80 LYS cc_start: 0.8359 (mttp) cc_final: 0.8101 (mttp) REVERT: G 87 GLN cc_start: 0.8441 (tp40) cc_final: 0.7890 (tp40) REVERT: G 88 GLU cc_start: 0.8055 (pt0) cc_final: 0.7818 (pt0) REVERT: G 94 GLN cc_start: 0.8307 (tp40) cc_final: 0.8097 (mm-40) REVERT: G 98 TYR cc_start: 0.8222 (t80) cc_final: 0.7613 (t80) REVERT: G 101 ASP cc_start: 0.7553 (t70) cc_final: 0.7084 (t0) REVERT: G 125 TYR cc_start: 0.8898 (t80) cc_final: 0.8558 (t80) REVERT: G 130 LYS cc_start: 0.8651 (tttt) cc_final: 0.8211 (ttpp) REVERT: G 142 GLN cc_start: 0.7800 (OUTLIER) cc_final: 0.7539 (mm-40) REVERT: G 162 ASP cc_start: 0.8213 (m-30) cc_final: 0.7872 (m-30) REVERT: G 169 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8498 (mm) REVERT: G 181 GLN cc_start: 0.8295 (mm-40) cc_final: 0.7818 (tm-30) REVERT: G 215 GLU cc_start: 0.7564 (tm-30) cc_final: 0.6835 (tm-30) REVERT: G 217 GLU cc_start: 0.8019 (tm-30) cc_final: 0.7519 (tm-30) REVERT: G 225 GLN cc_start: 0.8399 (tm-30) cc_final: 0.8156 (tm-30) REVERT: G 230 GLN cc_start: 0.8528 (OUTLIER) cc_final: 0.7931 (pp30) REVERT: G 231 ASP cc_start: 0.8168 (m-30) cc_final: 0.7744 (m-30) REVERT: G 279 MET cc_start: 0.4323 (tpt) cc_final: 0.3722 (mmm) REVERT: G 290 LEU cc_start: 0.8692 (tp) cc_final: 0.8359 (mp) REVERT: G 299 ASN cc_start: 0.8413 (m110) cc_final: 0.7906 (m110) REVERT: G 303 LYS cc_start: 0.8661 (mtpp) cc_final: 0.7727 (mtpp) REVERT: G 307 TYR cc_start: 0.7898 (m-80) cc_final: 0.7466 (m-80) REVERT: G 317 GLU cc_start: 0.7891 (tp30) cc_final: 0.7085 (tp30) REVERT: G 321 ARG cc_start: 0.8348 (mtt180) cc_final: 0.8007 (mtt180) REVERT: G 333 ASN cc_start: 0.8596 (m-40) cc_final: 0.8253 (m-40) REVERT: G 344 TYR cc_start: 0.8117 (m-80) cc_final: 0.7469 (m-80) REVERT: G 385 GLU cc_start: 0.7830 (mm-30) cc_final: 0.7244 (mm-30) REVERT: H 14 ASN cc_start: 0.8121 (t0) cc_final: 0.7393 (t0) REVERT: H 17 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8524 (mm) REVERT: H 19 LYS cc_start: 0.8183 (tttt) cc_final: 0.7886 (tttt) REVERT: H 29 GLU cc_start: 0.7986 (tp30) cc_final: 0.7302 (tp30) REVERT: H 87 GLN cc_start: 0.8025 (tp-100) cc_final: 0.7303 (tp-100) REVERT: H 88 GLU cc_start: 0.8345 (mt-10) cc_final: 0.7999 (mt-10) REVERT: H 89 LYS cc_start: 0.8708 (mmmt) cc_final: 0.8344 (mmmt) REVERT: H 94 GLN cc_start: 0.8137 (tp40) cc_final: 0.7669 (tt0) REVERT: H 95 ASP cc_start: 0.8700 (m-30) cc_final: 0.8074 (m-30) REVERT: H 129 GLN cc_start: 0.8289 (tt0) cc_final: 0.8071 (tt0) REVERT: H 131 GLU cc_start: 0.8027 (tp30) cc_final: 0.7761 (tp30) REVERT: H 135 ARG cc_start: 0.8036 (OUTLIER) cc_final: 0.7459 (mmm160) REVERT: H 136 GLN cc_start: 0.8329 (tp-100) cc_final: 0.7877 (tp40) REVERT: H 162 ASP cc_start: 0.8121 (m-30) cc_final: 0.7796 (m-30) REVERT: H 180 GLU cc_start: 0.8542 (mm-30) cc_final: 0.7896 (tp30) REVERT: H 184 GLN cc_start: 0.8468 (tt0) cc_final: 0.8104 (tm-30) REVERT: H 190 TYR cc_start: 0.7302 (m-80) cc_final: 0.7070 (m-10) REVERT: H 218 LYS cc_start: 0.8743 (mmtt) cc_final: 0.8474 (mmtt) REVERT: H 230 GLN cc_start: 0.8145 (tp40) cc_final: 0.7503 (tp-100) REVERT: H 231 ASP cc_start: 0.7812 (t0) cc_final: 0.7505 (t0) REVERT: H 232 LEU cc_start: 0.8692 (tp) cc_final: 0.8191 (tt) REVERT: H 236 GLN cc_start: 0.8119 (mt0) cc_final: 0.7385 (mm-40) REVERT: H 237 ILE cc_start: 0.8877 (mt) cc_final: 0.8585 (pt) REVERT: H 288 PHE cc_start: 0.7757 (t80) cc_final: 0.7551 (t80) REVERT: H 297 MET cc_start: 0.6368 (ttm) cc_final: 0.6021 (tmm) REVERT: H 301 GLN cc_start: 0.8293 (mt0) cc_final: 0.7812 (mp10) REVERT: H 303 LYS cc_start: 0.8400 (mttt) cc_final: 0.7889 (mttt) REVERT: H 306 GLN cc_start: 0.8237 (OUTLIER) cc_final: 0.7909 (mp10) REVERT: H 314 GLU cc_start: 0.7404 (mm-30) cc_final: 0.7075 (mm-30) REVERT: H 317 GLU cc_start: 0.7670 (tp30) cc_final: 0.7060 (tp30) REVERT: H 321 ARG cc_start: 0.8273 (mtt180) cc_final: 0.7512 (mtt180) REVERT: H 340 SER cc_start: 0.8725 (m) cc_final: 0.8131 (p) REVERT: H 341 ILE cc_start: 0.8855 (OUTLIER) cc_final: 0.8554 (tp) REVERT: H 374 ASP cc_start: 0.7537 (t0) cc_final: 0.7194 (t0) REVERT: H 392 ASN cc_start: 0.8378 (m-40) cc_final: 0.7944 (t0) REVERT: H 396 ASN cc_start: 0.8070 (m-40) cc_final: 0.7655 (m110) REVERT: H 397 GLN cc_start: 0.8116 (tt0) cc_final: 0.7429 (tm-30) REVERT: H 412 LEU cc_start: 0.8416 (tp) cc_final: 0.8172 (tp) REVERT: I 4 MET cc_start: 0.7695 (tmm) cc_final: 0.7390 (tmm) REVERT: I 16 GLU cc_start: 0.7918 (mp0) cc_final: 0.7414 (mp0) REVERT: I 24 ARG cc_start: 0.7988 (ttp-170) cc_final: 0.7527 (ttp-110) REVERT: I 28 PHE cc_start: 0.8060 (m-80) cc_final: 0.7827 (m-80) REVERT: I 30 LYS cc_start: 0.8830 (mttt) cc_final: 0.8607 (mttt) REVERT: I 31 ILE cc_start: 0.9049 (mt) cc_final: 0.8844 (mm) REVERT: I 42 LEU cc_start: 0.7863 (mp) cc_final: 0.7614 (tp) REVERT: I 76 PHE cc_start: 0.7575 (t80) cc_final: 0.6821 (t80) REVERT: I 124 SER cc_start: 0.8621 (t) cc_final: 0.8345 (p) REVERT: I 162 ASP cc_start: 0.8838 (m-30) cc_final: 0.7855 (m-30) REVERT: I 174 ASN cc_start: 0.8635 (t0) cc_final: 0.8375 (t0) REVERT: I 185 ILE cc_start: 0.9133 (mt) cc_final: 0.8930 (tt) REVERT: I 188 ASN cc_start: 0.7839 (p0) cc_final: 0.7425 (p0) REVERT: I 215 GLU cc_start: 0.8072 (tp30) cc_final: 0.7616 (tp30) REVERT: I 217 GLU cc_start: 0.7550 (mm-30) cc_final: 0.7136 (mm-30) REVERT: I 224 LEU cc_start: 0.8890 (mt) cc_final: 0.7814 (mm) REVERT: I 225 GLN cc_start: 0.7882 (tm-30) cc_final: 0.7350 (tm-30) REVERT: I 227 ARG cc_start: 0.7641 (mtm-85) cc_final: 0.7414 (mtm-85) REVERT: I 234 ARG cc_start: 0.7600 (OUTLIER) cc_final: 0.7352 (mtt180) REVERT: I 235 GLU cc_start: 0.7975 (tp30) cc_final: 0.7375 (tp30) REVERT: I 236 GLN cc_start: 0.8277 (mt0) cc_final: 0.7896 (mt0) REVERT: I 238 ARG cc_start: 0.8003 (mpt180) cc_final: 0.7332 (mpp-170) REVERT: I 301 GLN cc_start: 0.8453 (tt0) cc_final: 0.8121 (mt0) REVERT: I 306 GLN cc_start: 0.8389 (pt0) cc_final: 0.7917 (mp10) REVERT: I 314 GLU cc_start: 0.7089 (mt-10) cc_final: 0.6739 (mt-10) REVERT: I 315 GLN cc_start: 0.7959 (mt0) cc_final: 0.7431 (mp10) REVERT: I 362 TYR cc_start: 0.8403 (t80) cc_final: 0.8140 (t80) REVERT: I 392 ASN cc_start: 0.8073 (m-40) cc_final: 0.6932 (m-40) REVERT: I 396 ASN cc_start: 0.8242 (m-40) cc_final: 0.7686 (m-40) outliers start: 142 outliers final: 95 residues processed: 1301 average time/residue: 0.2402 time to fit residues: 470.5795 Evaluate side-chains 1348 residues out of total 3232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 1224 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 158 GLU Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain B residue 161 GLN Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 124 GLN Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 266 MET Chi-restraints excluded: chain C residue 282 ASP Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 360 ARG Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 84 LYS Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 169 SER Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 288 LYS Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 379 LYS Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 85 GLU Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 196 GLN Chi-restraints excluded: chain E residue 227 SER Chi-restraints excluded: chain E residue 261 THR Chi-restraints excluded: chain E residue 273 THR Chi-restraints excluded: chain E residue 275 THR Chi-restraints excluded: chain E residue 284 LYS Chi-restraints excluded: chain E residue 288 LYS Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain E residue 344 SER Chi-restraints excluded: chain E residue 346 ASN Chi-restraints excluded: chain E residue 371 GLU Chi-restraints excluded: chain E residue 372 ILE Chi-restraints excluded: chain E residue 373 SER Chi-restraints excluded: chain E residue 386 LYS Chi-restraints excluded: chain F residue 69 SER Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 179 GLN Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 194 GLU Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 288 LYS Chi-restraints excluded: chain F residue 303 LEU Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain F residue 353 GLN Chi-restraints excluded: chain F residue 367 SER Chi-restraints excluded: chain F residue 380 LEU Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain J residue 122 LEU Chi-restraints excluded: chain J residue 166 HIS Chi-restraints excluded: chain J residue 194 THR Chi-restraints excluded: chain J residue 213 ILE Chi-restraints excluded: chain J residue 219 MET Chi-restraints excluded: chain J residue 408 LEU Chi-restraints excluded: chain J residue 420 MET Chi-restraints excluded: chain J residue 490 VAL Chi-restraints excluded: chain G residue 3 LEU Chi-restraints excluded: chain G residue 11 ARG Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 142 GLN Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain G residue 203 THR Chi-restraints excluded: chain G residue 230 GLN Chi-restraints excluded: chain G residue 245 LEU Chi-restraints excluded: chain G residue 272 THR Chi-restraints excluded: chain G residue 318 SER Chi-restraints excluded: chain G residue 342 ASN Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 17 LEU Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 135 ARG Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 221 LEU Chi-restraints excluded: chain H residue 250 LEU Chi-restraints excluded: chain H residue 298 VAL Chi-restraints excluded: chain H residue 306 GLN Chi-restraints excluded: chain H residue 341 ILE Chi-restraints excluded: chain H residue 404 LEU Chi-restraints excluded: chain I residue 69 LEU Chi-restraints excluded: chain I residue 118 ASN Chi-restraints excluded: chain I residue 203 THR Chi-restraints excluded: chain I residue 232 LEU Chi-restraints excluded: chain I residue 234 ARG Chi-restraints excluded: chain I residue 241 GLN Chi-restraints excluded: chain I residue 250 LEU Chi-restraints excluded: chain I residue 272 THR Chi-restraints excluded: chain I residue 279 MET Chi-restraints excluded: chain I residue 297 MET Chi-restraints excluded: chain I residue 325 GLN Chi-restraints excluded: chain I residue 398 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 36 optimal weight: 2.9990 chunk 173 optimal weight: 3.9990 chunk 295 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 chunk 205 optimal weight: 4.9990 chunk 20 optimal weight: 0.5980 chunk 325 optimal weight: 8.9990 chunk 189 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 279 optimal weight: 3.9990 chunk 168 optimal weight: 0.8980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 ASN ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 184 ASN D 151 ASN ** D 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 182 ASN F 251 ASN F 329 GLN J 368 GLN ** J 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 449 GLN J 457 GLN J 470 ASN J 478 ASN ** G 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 308 ASN ** I 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 188 ASN ** I 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 320 HIS I 325 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.111484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.093618 restraints weight = 58845.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.096600 restraints weight = 25830.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 67)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.098463 restraints weight = 13927.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.099621 restraints weight = 8731.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.100401 restraints weight = 6224.309| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.7007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 30315 Z= 0.266 Angle : 0.756 13.784 41246 Z= 0.396 Chirality : 0.047 0.297 4889 Planarity : 0.005 0.065 5392 Dihedral : 4.474 22.116 4179 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 4.55 % Allowed : 28.12 % Favored : 67.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.48 (0.14), residues: 3860 helix: 2.60 (0.11), residues: 2023 sheet: -0.15 (0.23), residues: 498 loop : -1.19 (0.16), residues: 1339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG J 424 TYR 0.035 0.002 TYR H 125 PHE 0.048 0.002 PHE B 258 TRP 0.039 0.003 TRP C 312 HIS 0.012 0.001 HIS I 320 Details of bonding type rmsd covalent geometry : bond 0.00561 (30315) covalent geometry : angle 0.75615 (41246) hydrogen bonds : bond 0.06678 ( 1888) hydrogen bonds : angle 4.53708 ( 5523) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8262.64 seconds wall clock time: 142 minutes 8.29 seconds (8528.29 seconds total)