Starting phenix.real_space_refine on Tue May 27 12:05:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zar_39885/05_2025/8zar_39885.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zar_39885/05_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_39885/05_2025/8zar_39885.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zar_39885/05_2025/8zar_39885.map" model { file = "/net/cci-nas-00/data/ceres_data/8zar_39885/05_2025/8zar_39885.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zar_39885/05_2025/8zar_39885.cif" } resolution = 3.59 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.023 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 18.32, per 1000 atoms: 0.61 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: 7.70 Conformation dependent library (CDL) restraints added in 3.9 seconds 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: 3.22 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: 10.55 Time building geometry restraints manager: 8.94 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: 3.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 1.110 Check model and map are aligned: 0.240 Set scattering table: 0.270 Process input model: 65.860 Find NCS groups from input model: 1.090 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.390 ------------------------------------------------------------------------------- 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 : 3.75 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.14), 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 TRP 0.010 0.001 TRP J 482 HIS 0.004 0.001 HIS C 48 PHE 0.011 0.001 PHE J 247 TYR 0.014 0.001 TYR I 7 ARG 0.015 0.001 ARG B 229 Details of bonding type rmsd hydrogen bonds : bond 0.17669 ( 1888) hydrogen bonds : angle 6.09732 ( 5523) covalent geometry : bond 0.00429 (30315) covalent geometry : angle 0.64107 (41246) *********************** 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 : 3.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.6594 (t0) REVERT: A 56 TYR cc_start: 0.6733 (m-80) cc_final: 0.6288 (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: 0.7170 (t0) REVERT: A 187 MET cc_start: 0.8025 (mmm) cc_final: 0.7772 (mmm) REVERT: A 205 GLU cc_start: 0.7527 (tp30) cc_final: 0.7319 (tp30) REVERT: A 216 THR cc_start: 0.8350 (m) cc_final: 0.8069 (t) REVERT: A 225 TYR cc_start: 0.7999 (m-80) cc_final: 0.7222 (m-80) REVERT: A 247 VAL cc_start: 0.8929 (t) cc_final: 0.8572 (m) REVERT: A 259 LYS cc_start: 0.7908 (mtmm) cc_final: 0.7523 (mtmm) REVERT: A 284 LYS cc_start: 0.7786 (mtpp) cc_final: 0.7259 (mtpp) REVERT: A 294 MET cc_start: 0.5498 (mmm) cc_final: 0.5175 (mmm) REVERT: A 326 ASP cc_start: 0.6717 (t70) cc_final: 0.6513 (t0) REVERT: A 340 SER cc_start: 0.7663 (t) cc_final: 0.7369 (p) REVERT: B 50 GLU cc_start: 0.7405 (mm-30) cc_final: 0.7165 (mm-30) REVERT: B 66 SER cc_start: 0.7861 (t) cc_final: 0.7635 (p) REVERT: B 84 LYS cc_start: 0.7702 (mttp) cc_final: 0.7386 (mttp) REVERT: B 133 LYS cc_start: 0.7386 (mtpp) cc_final: 0.7133 (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: 0.4316 (t0) REVERT: B 143 TYR cc_start: 0.7742 (t80) cc_final: 0.7465 (t80) REVERT: B 145 ARG cc_start: 0.7670 (mtm-85) cc_final: 0.7357 (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: 0.6875 (m-30) REVERT: B 187 MET cc_start: 0.7447 (mmm) cc_final: 0.7245 (mtm) REVERT: B 195 ASP cc_start: 0.7266 (m-30) cc_final: 0.6758 (m-30) REVERT: B 207 ARG cc_start: 0.7624 (mtt90) cc_final: 0.7395 (mtt-85) REVERT: B 258 PHE cc_start: 0.7604 (m-80) cc_final: 0.7296 (m-80) REVERT: B 300 PHE cc_start: 0.7742 (m-10) cc_final: 0.7514 (m-10) REVERT: B 332 GLN cc_start: 0.7141 (tm-30) cc_final: 0.6463 (tm-30) REVERT: B 333 TYR cc_start: 0.7787 (m-80) cc_final: 0.7467 (m-80) REVERT: B 368 THR cc_start: 0.7199 (t) cc_final: 0.6872 (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: 0.6725 (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: 0.7619 (m-30) REVERT: C 200 GLN cc_start: 0.7349 (mt0) cc_final: 0.7086 (mt0) REVERT: C 266 MET cc_start: 0.7311 (mtm) cc_final: 0.7069 (mtp) REVERT: D 64 ILE cc_start: 0.8446 (mm) cc_final: 0.8216 (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: 0.6768 (tpp) REVERT: D 218 ILE cc_start: 0.7914 (mt) cc_final: 0.7672 (mt) REVERT: D 219 ILE cc_start: 0.8209 (mm) cc_final: 0.7860 (mm) REVERT: D 225 TYR cc_start: 0.8325 (m-80) cc_final: 0.8045 (m-80) 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: 0.6601 (m110) REVERT: D 288 LYS cc_start: 0.8346 (ptpt) cc_final: 0.7824 (mtmm) REVERT: D 304 PRO cc_start: 0.7330 (Cg_endo) cc_final: 0.7113 (Cg_exo) REVERT: D 313 ILE cc_start: 0.7605 (mp) cc_final: 0.7394 (mp) REVERT: D 353 GLN cc_start: 0.6792 (pt0) cc_final: 0.5955 (pt0) REVERT: D 357 ASN cc_start: 0.7853 (p0) cc_final: 0.7579 (p0) REVERT: D 372 ILE cc_start: 0.8634 (mp) cc_final: 0.8427 (mm) REVERT: D 378 ASN cc_start: 0.7956 (m-40) cc_final: 0.7670 (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: 0.5935 (t70) REVERT: E 71 SER cc_start: 0.7650 (p) cc_final: 0.7444 (t) REVERT: E 93 ASP cc_start: 0.8214 (t0) cc_final: 0.7870 (t70) REVERT: E 103 LYS cc_start: 0.7259 (tttm) cc_final: 0.7028 (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: 0.6638 (mmmm) REVERT: E 200 GLN cc_start: 0.7650 (mm-40) cc_final: 0.7281 (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: 0.8474 (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: 0.7486 (ptm-80) REVERT: E 283 VAL cc_start: 0.8472 (t) cc_final: 0.8236 (m) REVERT: E 294 MET cc_start: 0.6658 (mmm) cc_final: 0.6170 (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: 0.6248 (mp) REVERT: F 196 GLN cc_start: 0.8219 (mm-40) cc_final: 0.7671 (mm-40) REVERT: F 206 VAL cc_start: 0.8300 (t) cc_final: 0.7825 (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: 0.7303 (ptp) REVERT: F 251 ASN cc_start: 0.7497 (m110) cc_final: 0.7288 (m-40) REVERT: F 273 THR cc_start: 0.8284 (m) cc_final: 0.7990 (t) REVERT: F 274 ILE cc_start: 0.8091 (mp) cc_final: 0.7874 (mm) REVERT: F 283 VAL cc_start: 0.7154 (p) cc_final: 0.6879 (m) REVERT: F 294 MET cc_start: 0.6057 (mtp) cc_final: 0.5803 (mtp) REVERT: F 373 SER cc_start: 0.8504 (t) cc_final: 0.8055 (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: 0.7503 (tt) REVERT: J 44 LEU cc_start: 0.7350 (mt) cc_final: 0.7115 (mt) REVERT: J 161 ILE cc_start: 0.7747 (mm) cc_final: 0.7494 (mm) REVERT: J 184 MET cc_start: 0.7470 (mtm) cc_final: 0.7105 (mtm) REVERT: J 219 MET cc_start: 0.7122 (tmt) cc_final: 0.6861 (tmt) REVERT: J 220 LEU cc_start: 0.7571 (mt) cc_final: 0.7208 (mm) REVERT: J 299 TYR cc_start: 0.7536 (m-80) cc_final: 0.7234 (m-80) REVERT: J 301 TYR cc_start: 0.7618 (m-80) cc_final: 0.7206 (m-80) REVERT: J 327 PHE cc_start: 0.6177 (t80) cc_final: 0.5749 (t80) REVERT: J 357 PRO cc_start: 0.8179 (Cg_exo) cc_final: 0.7698 (Cg_endo) REVERT: J 382 LEU cc_start: 0.7236 (tp) cc_final: 0.6928 (tt) REVERT: J 411 SER cc_start: 0.7821 (m) cc_final: 0.7491 (p) REVERT: J 447 TYR cc_start: 0.8329 (m-80) cc_final: 0.7846 (m-80) REVERT: J 458 GLN cc_start: 0.7542 (tt0) cc_final: 0.7298 (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: 0.6307 (tttm) REVERT: G 23 ASP cc_start: 0.6497 (m-30) cc_final: 0.6128 (m-30) REVERT: G 29 GLU cc_start: 0.5714 (tp30) cc_final: 0.5474 (tp30) REVERT: G 47 ASP cc_start: 0.5784 (p0) cc_final: 0.5446 (p0) REVERT: G 95 ASP cc_start: 0.7130 (t70) cc_final: 0.6794 (t0) REVERT: G 103 GLN cc_start: 0.7101 (mt0) cc_final: 0.6812 (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: 0.5960 (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: 0.6832 (mm) REVERT: G 242 ASP cc_start: 0.5771 (t0) cc_final: 0.5446 (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: 0.6741 (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: 0.7502 (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: 0.7515 (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: 0.7260 (t80) REVERT: H 29 GLU cc_start: 0.6751 (tp30) cc_final: 0.6476 (tp30) REVERT: H 237 ILE cc_start: 0.8208 (mt) cc_final: 0.7246 (mt) REVERT: H 248 LEU cc_start: 0.7170 (mt) cc_final: 0.6821 (mt) REVERT: H 302 VAL cc_start: 0.7725 (t) cc_final: 0.7144 (m) REVERT: H 337 SER cc_start: 0.8275 (m) cc_final: 0.7995 (p) REVERT: H 356 ASP cc_start: 0.7145 (t0) cc_final: 0.6883 (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: 0.7258 (mm-40) REVERT: I 29 GLU cc_start: 0.6321 (tp30) cc_final: 0.6059 (tp30) REVERT: I 42 LEU cc_start: 0.6720 (tt) cc_final: 0.5444 (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: 0.6388 (tt0) REVERT: I 212 LEU cc_start: 0.8543 (tp) cc_final: 0.8207 (tt) REVERT: I 215 GLU cc_start: 0.7189 (tp30) cc_final: 0.6907 (tp30) REVERT: I 223 LEU cc_start: 0.8331 (pp) cc_final: 0.7060 (mt) REVERT: I 224 LEU cc_start: 0.8137 (tp) cc_final: 0.7561 (mt) REVERT: I 225 GLN cc_start: 0.6867 (tm-30) cc_final: 0.6570 (tm-30) REVERT: I 232 LEU cc_start: 0.8146 (pp) cc_final: 0.7753 (pp) REVERT: I 235 GLU cc_start: 0.6956 (tp30) cc_final: 0.6708 (tp30) REVERT: I 394 LEU cc_start: 0.8494 (mt) cc_final: 0.8184 (mm) REVERT: I 395 ILE cc_start: 0.8591 (mm) cc_final: 0.8154 (mm) REVERT: I 398 LEU cc_start: 0.8311 (tp) cc_final: 0.8068 (tp) outliers start: 5 outliers final: 0 residues processed: 1325 average time/residue: 0.4493 time to fit residues: 907.7926 Evaluate side-chains 1094 residues out of total 3232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1094 time to evaluate : 3.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 322 optimal weight: 2.9990 chunk 289 optimal weight: 5.9990 chunk 160 optimal weight: 0.0050 chunk 98 optimal weight: 1.9990 chunk 195 optimal weight: 0.7980 chunk 154 optimal weight: 1.9990 chunk 299 optimal weight: 0.6980 chunk 115 optimal weight: 0.9980 chunk 182 optimal weight: 0.5980 chunk 222 optimal weight: 0.0870 chunk 346 optimal weight: 20.0000 overall best weight: 0.4372 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 GLN A 180 GLN A 200 GLN A 311 ASN A 327 GLN A 332 GLN B 162 HIS B 180 GLN B 265 ASN B 388 ASN C 61 GLN C 67 GLN C 124 GLN C 232 GLN D 182 ASN D 306 GLN D 388 ASN E 117 GLN E 124 GLN E 201 GLN E 236 GLN E 257 ASN F 67 GLN F 162 HIS F 179 GLN ** F 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 346 ASN J 166 HIS 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 315 GLN H 8 GLN H 14 ASN ** H 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 103 GLN H 173 ASN H 230 GLN H 244 HIS ** I 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 127 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: 44 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.124055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.106374 restraints weight = 59789.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.109439 restraints weight = 26502.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.111347 restraints weight = 14293.307| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 30315 Z= 0.169 Angle : 0.617 9.292 41246 Z= 0.324 Chirality : 0.042 0.248 4889 Planarity : 0.005 0.107 5392 Dihedral : 3.792 21.226 4179 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.57 % Allowed : 16.18 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.14), residues: 3860 helix: 3.28 (0.11), residues: 2011 sheet: -0.44 (0.23), residues: 503 loop : -0.95 (0.16), residues: 1346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP E 312 HIS 0.010 0.001 HIS J 166 PHE 0.024 0.002 PHE I 331 TYR 0.031 0.002 TYR G 307 ARG 0.010 0.001 ARG G 18 Details of bonding type rmsd hydrogen bonds : bond 0.07705 ( 1888) hydrogen bonds : angle 4.61130 ( 5523) covalent geometry : bond 0.00337 (30315) covalent geometry : angle 0.61728 (41246) *********************** 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 1255 residues out of total 3232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 1172 time to evaluate : 3.269 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: 0.6710 (mm-30) cc_final: 0.6439 (mm-30) REVERT: A 53 ASP cc_start: 0.6784 (t0) cc_final: 0.6277 (t0) REVERT: A 56 TYR cc_start: 0.6894 (m-80) cc_final: 0.5958 (m-80) REVERT: A 65 MET cc_start: 0.7349 (mtt) cc_final: 0.7070 (mtm) REVERT: A 79 ASN cc_start: 0.7452 (t0) cc_final: 0.7229 (t0) REVERT: A 123 LYS cc_start: 0.7680 (mttt) cc_final: 0.7237 (mtmm) REVERT: A 128 ASN cc_start: 0.7858 (t0) cc_final: 0.7495 (t0) REVERT: A 130 GLU cc_start: 0.6933 (mm-30) cc_final: 0.6161 (mm-30) REVERT: A 133 LYS cc_start: 0.8259 (mtpt) cc_final: 0.7967 (mtpp) REVERT: A 138 LYS cc_start: 0.7275 (mttt) cc_final: 0.6967 (ttmm) REVERT: A 146 ARG cc_start: 0.7533 (ttm-80) cc_final: 0.7250 (mtt90) REVERT: A 151 ASN cc_start: 0.7700 (m-40) cc_final: 0.7471 (m-40) REVERT: A 159 GLU cc_start: 0.7496 (mp0) cc_final: 0.7275 (mp0) REVERT: A 171 GLN cc_start: 0.8104 (tp40) cc_final: 0.7831 (tp40) REVERT: A 173 GLN cc_start: 0.7405 (mm-40) cc_final: 0.6951 (mm-40) REVERT: A 225 TYR cc_start: 0.8198 (m-80) cc_final: 0.7255 (m-80) REVERT: A 247 VAL cc_start: 0.8653 (t) cc_final: 0.8257 (m) REVERT: A 259 LYS cc_start: 0.8029 (mtmm) cc_final: 0.7616 (mtmm) REVERT: A 294 MET cc_start: 0.6226 (mmm) cc_final: 0.5683 (mmm) REVERT: A 371 GLU cc_start: 0.7278 (pm20) cc_final: 0.6905 (pm20) REVERT: B 50 GLU cc_start: 0.7121 (mm-30) cc_final: 0.6843 (mm-30) REVERT: B 66 SER cc_start: 0.7891 (t) cc_final: 0.7634 (p) REVERT: B 84 LYS cc_start: 0.7443 (mttp) cc_final: 0.7045 (mttp) REVERT: B 117 GLN cc_start: 0.7062 (OUTLIER) cc_final: 0.6648 (tt0) REVERT: B 133 LYS cc_start: 0.7624 (mtpp) cc_final: 0.7420 (mtpp) REVERT: B 142 ASP cc_start: 0.6522 (t0) cc_final: 0.5517 (t0) REVERT: B 143 TYR cc_start: 0.8285 (t80) cc_final: 0.7866 (t80) REVERT: B 146 ARG cc_start: 0.7494 (mtt-85) cc_final: 0.7048 (mtt-85) REVERT: B 154 LEU cc_start: 0.6927 (mt) cc_final: 0.6719 (tp) REVERT: B 157 ARG cc_start: 0.7280 (mtp-110) cc_final: 0.6869 (mtm110) REVERT: B 161 GLN cc_start: 0.8046 (tp40) cc_final: 0.7632 (tp-100) REVERT: B 164 ARG cc_start: 0.7411 (ttm-80) cc_final: 0.6995 (ttm-80) REVERT: B 179 GLN cc_start: 0.7533 (mm-40) cc_final: 0.7184 (tp40) REVERT: B 187 MET cc_start: 0.6930 (mmm) cc_final: 0.6722 (mtm) REVERT: B 244 MET cc_start: 0.7908 (ptp) cc_final: 0.7510 (ptp) REVERT: B 251 ASN cc_start: 0.7411 (p0) cc_final: 0.7143 (p0) REVERT: B 292 LEU cc_start: 0.7753 (mm) cc_final: 0.7440 (tp) REVERT: B 328 LYS cc_start: 0.7636 (mmpt) cc_final: 0.7018 (mmpt) REVERT: B 330 LEU cc_start: 0.7893 (tt) cc_final: 0.7569 (tp) REVERT: B 371 GLU cc_start: 0.6764 (mt-10) cc_final: 0.6436 (mt-10) REVERT: B 386 LYS cc_start: 0.7911 (tttt) cc_final: 0.7536 (tttt) REVERT: C 130 GLU cc_start: 0.7562 (tp30) cc_final: 0.7266 (tp30) REVERT: C 161 GLN cc_start: 0.7501 (tp40) cc_final: 0.6300 (tp40) REVERT: C 164 ARG cc_start: 0.7096 (ttp80) cc_final: 0.6238 (ttp80) REVERT: C 185 GLN cc_start: 0.7095 (tp40) cc_final: 0.6727 (tm-30) REVERT: C 200 GLN cc_start: 0.6972 (mt0) cc_final: 0.6517 (mt0) REVERT: C 207 ARG cc_start: 0.7824 (mtm-85) cc_final: 0.7527 (mtm-85) REVERT: C 294 MET cc_start: 0.7219 (mmm) cc_final: 0.6997 (mmm) REVERT: C 302 LEU cc_start: 0.8709 (tp) cc_final: 0.8451 (tt) REVERT: C 315 VAL cc_start: 0.8353 (p) cc_final: 0.8064 (m) REVERT: C 328 LYS cc_start: 0.8124 (mttt) cc_final: 0.7829 (mttt) REVERT: C 332 GLN cc_start: 0.6726 (tp40) cc_final: 0.6508 (tp40) REVERT: C 379 LYS cc_start: 0.7606 (ttmt) cc_final: 0.7349 (ttmt) REVERT: D 53 ASP cc_start: 0.7418 (p0) cc_final: 0.7177 (p0) REVERT: D 54 ASP cc_start: 0.6470 (t0) cc_final: 0.5967 (t0) REVERT: D 64 ILE cc_start: 0.8369 (mm) cc_final: 0.8140 (mm) REVERT: D 138 LYS cc_start: 0.7754 (tttt) cc_final: 0.6968 (tttt) REVERT: D 184 ASN cc_start: 0.7701 (t0) cc_final: 0.7435 (t0) REVERT: D 187 MET cc_start: 0.7364 (mmm) cc_final: 0.6723 (tpp) REVERT: D 218 ILE cc_start: 0.7951 (mt) cc_final: 0.7712 (mt) REVERT: D 219 ILE cc_start: 0.8282 (mm) cc_final: 0.7939 (mm) REVERT: D 247 VAL cc_start: 0.8880 (t) cc_final: 0.8488 (m) REVERT: D 252 MET cc_start: 0.6388 (mtt) cc_final: 0.6156 (mtt) REVERT: D 259 LYS cc_start: 0.7810 (mttt) cc_final: 0.7599 (mttm) REVERT: D 284 LYS cc_start: 0.6838 (mttp) cc_final: 0.6560 (mttp) REVERT: D 288 LYS cc_start: 0.8205 (ptpt) cc_final: 0.7518 (mtmm) REVERT: D 327 GLN cc_start: 0.7816 (mm-40) cc_final: 0.7165 (mm110) REVERT: D 331 GLU cc_start: 0.6947 (mp0) cc_final: 0.6304 (mp0) REVERT: D 345 VAL cc_start: 0.8347 (t) cc_final: 0.7964 (m) REVERT: D 353 GLN cc_start: 0.6728 (pt0) cc_final: 0.6184 (pt0) REVERT: D 378 ASN cc_start: 0.7947 (m-40) cc_final: 0.7552 (m-40) REVERT: E 65 MET cc_start: 0.7168 (mmm) cc_final: 0.6630 (mmm) REVERT: E 71 SER cc_start: 0.7576 (p) cc_final: 0.7352 (t) REVERT: E 103 LYS cc_start: 0.7152 (tttm) cc_final: 0.6756 (mtpp) REVERT: E 133 LYS cc_start: 0.8003 (ttmm) cc_final: 0.7752 (mtpp) REVERT: E 200 GLN cc_start: 0.7284 (mm-40) cc_final: 0.7032 (mm-40) REVERT: E 204 THR cc_start: 0.8545 (p) cc_final: 0.8315 (p) REVERT: E 210 TRP cc_start: 0.8272 (t60) cc_final: 0.7854 (t60) REVERT: E 211 LEU cc_start: 0.8509 (mt) cc_final: 0.8249 (mm) REVERT: E 229 ARG cc_start: 0.7859 (ttp80) cc_final: 0.7522 (ptm-80) REVERT: E 240 THR cc_start: 0.8060 (p) cc_final: 0.7716 (p) REVERT: E 251 ASN cc_start: 0.7252 (t0) cc_final: 0.6977 (t0) REVERT: E 260 GLU cc_start: 0.7255 (pt0) cc_final: 0.7001 (pt0) REVERT: E 283 VAL cc_start: 0.8587 (t) cc_final: 0.8185 (m) REVERT: E 294 MET cc_start: 0.6318 (mmm) cc_final: 0.5808 (mmm) REVERT: E 306 GLN cc_start: 0.6971 (mm-40) cc_final: 0.6629 (mp10) REVERT: E 312 TRP cc_start: 0.7959 (t60) cc_final: 0.7457 (t60) REVERT: E 339 LEU cc_start: 0.7346 (mt) cc_final: 0.7015 (mt) REVERT: E 346 ASN cc_start: 0.7692 (m-40) cc_final: 0.7366 (m-40) REVERT: F 78 ASP cc_start: 0.7038 (t0) cc_final: 0.6799 (t0) REVERT: F 128 ASN cc_start: 0.6971 (m-40) cc_final: 0.6655 (t0) REVERT: F 138 LYS cc_start: 0.7715 (ttpt) cc_final: 0.7488 (ttpp) REVERT: F 141 SER cc_start: 0.8184 (m) cc_final: 0.7579 (p) REVERT: F 154 LEU cc_start: 0.7293 (mt) cc_final: 0.6858 (mm) REVERT: F 158 GLU cc_start: 0.6852 (tp30) cc_final: 0.6392 (tp30) REVERT: F 196 GLN cc_start: 0.8196 (mm-40) cc_final: 0.7255 (mm-40) REVERT: F 217 ARG cc_start: 0.6874 (mtt180) cc_final: 0.6549 (ttm-80) REVERT: F 273 THR cc_start: 0.8200 (m) cc_final: 0.7739 (t) REVERT: F 275 THR cc_start: 0.7737 (m) cc_final: 0.7394 (p) REVERT: F 283 VAL cc_start: 0.7188 (p) cc_final: 0.6923 (m) REVERT: F 288 LYS cc_start: 0.8008 (OUTLIER) cc_final: 0.7735 (mtmt) REVERT: F 294 MET cc_start: 0.6097 (mtp) cc_final: 0.5825 (mtp) REVERT: F 314 LYS cc_start: 0.7925 (ttmm) cc_final: 0.7514 (tppt) REVERT: F 364 VAL cc_start: 0.8004 (t) cc_final: 0.7605 (p) REVERT: F 382 ASP cc_start: 0.7589 (t0) cc_final: 0.7373 (m-30) REVERT: F 383 ASP cc_start: 0.6878 (m-30) cc_final: 0.6413 (m-30) REVERT: J 21 LEU cc_start: 0.8027 (mt) cc_final: 0.7824 (mm) REVERT: J 32 ILE cc_start: 0.7757 (tt) cc_final: 0.7495 (tp) REVERT: J 40 ILE cc_start: 0.8111 (mt) cc_final: 0.7768 (pt) REVERT: J 87 ILE cc_start: 0.8484 (tt) cc_final: 0.8068 (pt) REVERT: J 122 LEU cc_start: 0.7860 (OUTLIER) cc_final: 0.7564 (mp) REVERT: J 161 ILE cc_start: 0.8019 (mm) cc_final: 0.7658 (tt) REVERT: J 184 MET cc_start: 0.7576 (mtm) cc_final: 0.7045 (mtm) REVERT: J 219 MET cc_start: 0.7151 (tmt) cc_final: 0.6907 (tmt) REVERT: J 251 TRP cc_start: 0.5797 (t-100) cc_final: 0.5282 (t-100) REVERT: J 268 ARG cc_start: 0.7634 (ttt90) cc_final: 0.7133 (mmm-85) REVERT: J 271 THR cc_start: 0.7945 (m) cc_final: 0.7538 (p) REVERT: J 301 TYR cc_start: 0.8127 (m-80) cc_final: 0.7918 (m-10) REVERT: J 327 PHE cc_start: 0.6539 (t80) cc_final: 0.5770 (t80) REVERT: J 333 MET cc_start: 0.7094 (mtm) cc_final: 0.6321 (ttm) REVERT: J 339 PHE cc_start: 0.7757 (t80) cc_final: 0.7501 (t80) REVERT: J 342 ILE cc_start: 0.7921 (mm) cc_final: 0.7688 (tp) REVERT: J 357 PRO cc_start: 0.8157 (Cg_exo) cc_final: 0.7934 (Cg_endo) REVERT: J 382 LEU cc_start: 0.7754 (tp) cc_final: 0.7503 (tt) REVERT: J 384 THR cc_start: 0.7402 (m) cc_final: 0.7169 (p) REVERT: J 406 ARG cc_start: 0.7410 (ttp80) cc_final: 0.7008 (ttp80) REVERT: J 411 SER cc_start: 0.7702 (m) cc_final: 0.7259 (p) REVERT: J 416 ILE cc_start: 0.7902 (mt) cc_final: 0.7593 (tp) REVERT: J 446 MET cc_start: 0.7434 (tpt) cc_final: 0.7230 (tpt) REVERT: J 458 GLN cc_start: 0.7661 (tt0) cc_final: 0.7323 (tt0) REVERT: J 491 LEU cc_start: 0.8138 (mt) cc_final: 0.7709 (pp) REVERT: G 3 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8442 (tp) REVERT: G 5 GLN cc_start: 0.8080 (mt0) cc_final: 0.7634 (mt0) REVERT: G 18 ARG cc_start: 0.7258 (OUTLIER) cc_final: 0.7055 (mtt-85) REVERT: G 29 GLU cc_start: 0.7003 (tp30) cc_final: 0.5923 (tp30) REVERT: G 30 LYS cc_start: 0.8485 (tttt) cc_final: 0.8280 (tttt) REVERT: G 32 ASN cc_start: 0.7869 (m-40) cc_final: 0.6611 (p0) REVERT: G 81 TRP cc_start: 0.7233 (m100) cc_final: 0.6999 (m100) REVERT: G 87 GLN cc_start: 0.8368 (tp40) cc_final: 0.7889 (tp40) REVERT: G 88 GLU cc_start: 0.8022 (pt0) cc_final: 0.7757 (pt0) REVERT: G 98 TYR cc_start: 0.8142 (t80) cc_final: 0.7881 (t80) REVERT: G 105 LEU cc_start: 0.9136 (tp) cc_final: 0.8934 (tt) REVERT: G 127 GLN cc_start: 0.7949 (tm-30) cc_final: 0.7617 (tm-30) REVERT: G 158 ARG cc_start: 0.7471 (tpt170) cc_final: 0.7238 (tpt170) REVERT: G 164 VAL cc_start: 0.8542 (m) cc_final: 0.8299 (p) REVERT: G 168 GLU cc_start: 0.8153 (tt0) cc_final: 0.7932 (tt0) REVERT: G 181 GLN cc_start: 0.8541 (mm-40) cc_final: 0.7665 (tm-30) REVERT: G 185 ILE cc_start: 0.8493 (tp) cc_final: 0.8259 (tt) REVERT: G 192 GLU cc_start: 0.7104 (tt0) cc_final: 0.6889 (tt0) REVERT: G 215 GLU cc_start: 0.7341 (tm-30) cc_final: 0.6602 (tm-30) REVERT: G 217 GLU cc_start: 0.7985 (tm-30) cc_final: 0.7684 (mm-30) REVERT: G 230 GLN cc_start: 0.8367 (pt0) cc_final: 0.7900 (pp30) REVERT: G 236 GLN cc_start: 0.8361 (mt0) cc_final: 0.7931 (mp10) REVERT: G 299 ASN cc_start: 0.8093 (m-40) cc_final: 0.7671 (m-40) REVERT: G 301 GLN cc_start: 0.7827 (mp10) cc_final: 0.7474 (mp10) REVERT: G 303 LYS cc_start: 0.8513 (mtpp) cc_final: 0.8241 (mtpp) REVERT: G 317 GLU cc_start: 0.7940 (tp30) cc_final: 0.7070 (tp30) REVERT: G 321 ARG cc_start: 0.8367 (mtt180) cc_final: 0.7710 (mtt180) REVERT: G 344 TYR cc_start: 0.8088 (m-80) cc_final: 0.7880 (m-80) REVERT: G 345 LYS cc_start: 0.8607 (ttmt) cc_final: 0.8339 (ttmm) REVERT: G 374 ASP cc_start: 0.7538 (t70) cc_final: 0.7104 (t0) REVERT: G 385 GLU cc_start: 0.7390 (mm-30) cc_final: 0.6806 (mm-30) REVERT: G 397 GLN cc_start: 0.7610 (OUTLIER) cc_final: 0.7393 (mt0) REVERT: G 401 LYS cc_start: 0.8519 (tptm) cc_final: 0.8046 (tppp) REVERT: H 14 ASN cc_start: 0.7598 (t0) cc_final: 0.7095 (t0) REVERT: H 18 ARG cc_start: 0.7178 (mtp85) cc_final: 0.6959 (mtp85) REVERT: H 24 ARG cc_start: 0.8307 (ttp80) cc_final: 0.8056 (ttp80) REVERT: H 29 GLU cc_start: 0.7727 (tp30) cc_final: 0.6845 (tp30) REVERT: H 30 LYS cc_start: 0.8467 (ttpt) cc_final: 0.7725 (ttpt) REVERT: H 87 GLN cc_start: 0.7667 (tp40) cc_final: 0.7003 (tp-100) REVERT: H 89 LYS cc_start: 0.8732 (mmmt) cc_final: 0.8300 (mmmt) REVERT: H 94 GLN cc_start: 0.7832 (tp40) cc_final: 0.7559 (tp40) REVERT: H 98 TYR cc_start: 0.8411 (t80) cc_final: 0.8178 (t80) REVERT: H 113 TYR cc_start: 0.7876 (t80) cc_final: 0.7289 (t80) REVERT: H 114 PHE cc_start: 0.8302 (m-80) cc_final: 0.8071 (m-80) REVERT: H 123 LEU cc_start: 0.8507 (tp) cc_final: 0.8159 (mt) REVERT: H 127 GLN cc_start: 0.7835 (mt0) cc_final: 0.7597 (mm110) REVERT: H 135 ARG cc_start: 0.7925 (ttm-80) cc_final: 0.7501 (mmm160) REVERT: H 139 GLN cc_start: 0.8082 (tt0) cc_final: 0.7728 (tm-30) REVERT: H 143 ARG cc_start: 0.7569 (ttp-110) cc_final: 0.6931 (ttp-170) REVERT: H 168 GLU cc_start: 0.8201 (tt0) cc_final: 0.7151 (tt0) REVERT: H 169 LEU cc_start: 0.8729 (tt) cc_final: 0.8406 (tp) REVERT: H 179 VAL cc_start: 0.8846 (t) cc_final: 0.8589 (m) REVERT: H 180 GLU cc_start: 0.8330 (mm-30) cc_final: 0.8110 (mm-30) REVERT: H 184 GLN cc_start: 0.8309 (OUTLIER) cc_final: 0.7305 (tp-100) REVERT: H 231 ASP cc_start: 0.7490 (t0) cc_final: 0.7283 (t0) REVERT: H 234 ARG cc_start: 0.7667 (mmm-85) cc_final: 0.7164 (mmm-85) REVERT: H 237 ILE cc_start: 0.8730 (mt) cc_final: 0.8409 (mt) REVERT: H 248 LEU cc_start: 0.8573 (mt) cc_final: 0.8357 (mm) REVERT: H 314 GLU cc_start: 0.7605 (mm-30) cc_final: 0.7287 (mm-30) REVERT: H 317 GLU cc_start: 0.7404 (tp30) cc_final: 0.7048 (tp30) REVERT: H 321 ARG cc_start: 0.8141 (mtt180) cc_final: 0.7722 (mtt180) REVERT: H 328 ARG cc_start: 0.7981 (mtt-85) cc_final: 0.7611 (mtt-85) REVERT: H 337 SER cc_start: 0.8702 (m) cc_final: 0.8167 (p) REVERT: H 356 ASP cc_start: 0.8104 (t0) cc_final: 0.7786 (t0) REVERT: H 358 MET cc_start: 0.7716 (tpp) cc_final: 0.7513 (mmm) REVERT: H 362 TYR cc_start: 0.8432 (t80) cc_final: 0.8180 (t80) REVERT: H 367 ARG cc_start: 0.8260 (tpp80) cc_final: 0.7673 (tpp80) REVERT: H 374 ASP cc_start: 0.7943 (t0) cc_final: 0.7570 (t0) REVERT: H 412 LEU cc_start: 0.8507 (tp) cc_final: 0.8152 (tp) REVERT: H 421 LYS cc_start: 0.8626 (mttt) cc_final: 0.8377 (mttt) REVERT: I 8 GLN cc_start: 0.8126 (mm-40) cc_final: 0.7514 (mm-40) REVERT: I 11 ARG cc_start: 0.7558 (ttp80) cc_final: 0.6310 (ttp80) REVERT: I 29 GLU cc_start: 0.7451 (tp30) cc_final: 0.6661 (tp30) REVERT: I 31 ILE cc_start: 0.9026 (mt) cc_final: 0.8812 (mm) REVERT: I 42 LEU cc_start: 0.7381 (tt) cc_final: 0.6498 (tp) REVERT: I 99 GLN cc_start: 0.8261 (mt0) cc_final: 0.8029 (mt0) REVERT: I 135 ARG cc_start: 0.7928 (tpp-160) cc_final: 0.7592 (tpp-160) REVERT: I 138 ASP cc_start: 0.8307 (t0) cc_final: 0.8092 (t0) REVERT: I 212 LEU cc_start: 0.9095 (tp) cc_final: 0.8812 (tt) REVERT: I 215 GLU cc_start: 0.7989 (tp30) cc_final: 0.7369 (tp30) REVERT: I 224 LEU cc_start: 0.8642 (tp) cc_final: 0.8399 (mp) REVERT: I 225 GLN cc_start: 0.7703 (tm-30) cc_final: 0.7177 (tm-30) REVERT: I 227 ARG cc_start: 0.7486 (mtm-85) cc_final: 0.7147 (mtt-85) REVERT: I 235 GLU cc_start: 0.7945 (tp30) cc_final: 0.7475 (tp30) REVERT: I 236 GLN cc_start: 0.8197 (mt0) cc_final: 0.7957 (mt0) REVERT: I 238 ARG cc_start: 0.7886 (mpt180) cc_final: 0.7409 (mpt180) REVERT: I 297 MET cc_start: 0.5634 (tmm) cc_final: 0.5405 (tmm) REVERT: I 306 GLN cc_start: 0.8381 (pt0) cc_final: 0.8020 (mt0) REVERT: I 325 GLN cc_start: 0.8334 (OUTLIER) cc_final: 0.8005 (pp30) REVERT: I 394 LEU cc_start: 0.8732 (mt) cc_final: 0.8401 (mm) REVERT: I 396 ASN cc_start: 0.8271 (m-40) cc_final: 0.7770 (m-40) REVERT: I 404 LEU cc_start: 0.9148 (tp) cc_final: 0.8931 (tp) outliers start: 83 outliers final: 45 residues processed: 1201 average time/residue: 0.4583 time to fit residues: 826.2422 Evaluate side-chains 1159 residues out of total 3232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 1106 time to evaluate : 3.424 ------------------------------------------------------------------------------- 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 263 ILE Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 288 LYS Chi-restraints excluded: chain A residue 330 LEU 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 C residue 187 MET 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 D residue 84 LYS Chi-restraints excluded: chain D residue 169 SER Chi-restraints excluded: chain D residue 337 ILE Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 149 LEU 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 296 THR Chi-restraints excluded: chain E residue 344 SER Chi-restraints excluded: chain E residue 386 LYS Chi-restraints excluded: chain F residue 162 HIS Chi-restraints excluded: chain F residue 194 GLU Chi-restraints excluded: chain F residue 288 LYS Chi-restraints excluded: chain F residue 386 LYS Chi-restraints excluded: chain J residue 122 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 35 ARG Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 183 ARG Chi-restraints excluded: chain G residue 197 ASN Chi-restraints excluded: chain G residue 232 LEU Chi-restraints excluded: chain G residue 279 MET Chi-restraints excluded: chain G residue 397 GLN Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 184 GLN 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 325 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 175 optimal weight: 0.6980 chunk 361 optimal weight: 0.6980 chunk 242 optimal weight: 0.0870 chunk 205 optimal weight: 4.9990 chunk 352 optimal weight: 5.9990 chunk 337 optimal weight: 2.9990 chunk 129 optimal weight: 0.0470 chunk 293 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 316 optimal weight: 0.6980 overall best weight: 0.4456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN A 200 GLN B 162 HIS C 117 GLN C 179 GLN ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 196 GLN E 201 GLN E 236 GLN E 311 ASN F 116 HIS F 179 GLN F 251 ASN F 346 ASN J 166 HIS J 368 GLN ** G 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 299 ASN ** H 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 294 GLN I 73 GLN ** I 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 320 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.121877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.103393 restraints weight = 59501.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.106527 restraints weight = 26380.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.108468 restraints weight = 14353.950| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.3704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 30315 Z= 0.148 Angle : 0.589 12.177 41246 Z= 0.303 Chirality : 0.042 0.207 4889 Planarity : 0.004 0.089 5392 Dihedral : 3.740 22.327 4179 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.37 % Allowed : 18.16 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.14), residues: 3860 helix: 3.30 (0.11), residues: 2029 sheet: -0.32 (0.23), residues: 507 loop : -0.83 (0.16), residues: 1324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP J 421 HIS 0.014 0.001 HIS F 162 PHE 0.024 0.002 PHE I 331 TYR 0.025 0.001 TYR G 293 ARG 0.011 0.001 ARG I 234 Details of bonding type rmsd hydrogen bonds : bond 0.06840 ( 1888) hydrogen bonds : angle 4.30513 ( 5523) covalent geometry : bond 0.00295 (30315) covalent geometry : angle 0.58904 (41246) *********************** 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 1263 residues out of total 3232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 1154 time to evaluate : 3.059 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 49 PHE cc_start: 0.7041 (m-80) cc_final: 0.6604 (m-10) REVERT: A 50 GLU cc_start: 0.6771 (mm-30) cc_final: 0.6414 (mm-30) REVERT: A 53 ASP cc_start: 0.6809 (t0) cc_final: 0.6188 (t0) REVERT: A 56 TYR cc_start: 0.6943 (m-80) cc_final: 0.5924 (m-80) REVERT: A 65 MET cc_start: 0.7426 (mtt) cc_final: 0.7174 (mtm) REVERT: A 79 ASN cc_start: 0.7527 (t0) cc_final: 0.7273 (t0) REVERT: A 122 SER cc_start: 0.7812 (m) cc_final: 0.7464 (t) REVERT: A 128 ASN cc_start: 0.8238 (t0) cc_final: 0.7850 (t0) REVERT: A 130 GLU cc_start: 0.7041 (mm-30) cc_final: 0.6269 (mm-30) REVERT: A 133 LYS cc_start: 0.8321 (mtpt) cc_final: 0.7987 (mtpp) REVERT: A 138 LYS cc_start: 0.7894 (mttt) cc_final: 0.7584 (tttp) REVERT: A 146 ARG cc_start: 0.7601 (ttm-80) cc_final: 0.6672 (mtt90) REVERT: A 151 ASN cc_start: 0.7794 (m-40) cc_final: 0.7495 (m-40) REVERT: A 158 GLU cc_start: 0.7818 (mm-30) cc_final: 0.7380 (tm-30) REVERT: A 173 GLN cc_start: 0.7483 (mm-40) cc_final: 0.7023 (mm-40) REVERT: A 184 ASN cc_start: 0.7263 (t0) cc_final: 0.6987 (t0) REVERT: A 225 TYR cc_start: 0.8199 (m-80) cc_final: 0.7261 (m-80) REVERT: A 247 VAL cc_start: 0.8711 (t) cc_final: 0.8340 (m) REVERT: A 259 LYS cc_start: 0.7999 (mtmm) cc_final: 0.7608 (mtmm) REVERT: A 296 THR cc_start: 0.8171 (p) cc_final: 0.7886 (t) REVERT: B 67 GLN cc_start: 0.8147 (mt0) cc_final: 0.7908 (mt0) REVERT: B 84 LYS cc_start: 0.7362 (mttp) cc_final: 0.7109 (mttp) REVERT: B 117 GLN cc_start: 0.7125 (OUTLIER) cc_final: 0.6718 (tt0) REVERT: B 133 LYS cc_start: 0.7785 (mtpp) cc_final: 0.7503 (mtpp) REVERT: B 138 LYS cc_start: 0.8379 (ttpp) cc_final: 0.8146 (ttpp) REVERT: B 142 ASP cc_start: 0.6738 (t0) cc_final: 0.5701 (t0) REVERT: B 143 TYR cc_start: 0.8390 (t80) cc_final: 0.8002 (t80) REVERT: B 146 ARG cc_start: 0.7535 (mtt-85) cc_final: 0.7044 (mtt-85) REVERT: B 154 LEU cc_start: 0.7151 (mt) cc_final: 0.6844 (mp) REVERT: B 157 ARG cc_start: 0.7089 (mtp-110) cc_final: 0.6787 (mtm110) REVERT: B 158 GLU cc_start: 0.7330 (tt0) cc_final: 0.6928 (tm-30) REVERT: B 161 GLN cc_start: 0.8113 (tp40) cc_final: 0.7248 (tm-30) REVERT: B 162 HIS cc_start: 0.7852 (m-70) cc_final: 0.7472 (m90) REVERT: B 171 GLN cc_start: 0.7932 (tp-100) cc_final: 0.7732 (tp-100) REVERT: B 207 ARG cc_start: 0.7195 (mtt-85) cc_final: 0.6956 (mtt-85) REVERT: B 244 MET cc_start: 0.7948 (ptp) cc_final: 0.7701 (ptp) REVERT: B 328 LYS cc_start: 0.7805 (mmpt) cc_final: 0.7264 (mmpt) REVERT: B 330 LEU cc_start: 0.7935 (tt) cc_final: 0.7623 (tp) REVERT: B 371 GLU cc_start: 0.6827 (mt-10) cc_final: 0.6494 (mt-10) REVERT: B 386 LYS cc_start: 0.7911 (tttt) cc_final: 0.7558 (tttt) REVERT: C 56 TYR cc_start: 0.7345 (m-80) cc_final: 0.6852 (m-80) REVERT: C 130 GLU cc_start: 0.7606 (tp30) cc_final: 0.7393 (tp30) REVERT: C 142 ASP cc_start: 0.7079 (t70) cc_final: 0.6338 (t0) REVERT: C 155 ILE cc_start: 0.7716 (mm) cc_final: 0.7477 (tp) REVERT: C 158 GLU cc_start: 0.7405 (tt0) cc_final: 0.7111 (tt0) REVERT: C 185 GLN cc_start: 0.7112 (tp40) cc_final: 0.6826 (tm-30) REVERT: C 196 GLN cc_start: 0.7830 (mm-40) cc_final: 0.7604 (mm-40) REVERT: C 200 GLN cc_start: 0.7003 (mt0) cc_final: 0.6528 (mt0) REVERT: C 231 VAL cc_start: 0.7968 (t) cc_final: 0.7545 (p) REVERT: C 302 LEU cc_start: 0.8650 (tp) cc_final: 0.8343 (tt) REVERT: C 328 LYS cc_start: 0.8240 (mttt) cc_final: 0.7949 (mttt) REVERT: C 373 SER cc_start: 0.8366 (t) cc_final: 0.8111 (p) REVERT: C 379 LYS cc_start: 0.7609 (ttmt) cc_final: 0.7350 (ttmt) REVERT: D 50 GLU cc_start: 0.6536 (tp30) cc_final: 0.6120 (tp30) REVERT: D 53 ASP cc_start: 0.7399 (p0) cc_final: 0.7165 (p0) REVERT: D 54 ASP cc_start: 0.6523 (t0) cc_final: 0.5904 (t0) REVERT: D 138 LYS cc_start: 0.7873 (tttt) cc_final: 0.7479 (tttt) REVERT: D 157 ARG cc_start: 0.7423 (mtm110) cc_final: 0.6942 (mtm110) REVERT: D 184 ASN cc_start: 0.7844 (t0) cc_final: 0.7603 (t0) REVERT: D 247 VAL cc_start: 0.8937 (t) cc_final: 0.8588 (m) REVERT: D 259 LYS cc_start: 0.7987 (mttt) cc_final: 0.7690 (mttm) REVERT: D 288 LYS cc_start: 0.8146 (ptpt) cc_final: 0.7596 (mtmm) REVERT: D 302 LEU cc_start: 0.7785 (mm) cc_final: 0.7568 (mm) REVERT: D 327 GLN cc_start: 0.7863 (mm-40) cc_final: 0.7500 (mm-40) REVERT: D 331 GLU cc_start: 0.7012 (mp0) cc_final: 0.6361 (mp0) REVERT: D 345 VAL cc_start: 0.8435 (t) cc_final: 0.8045 (m) REVERT: D 353 GLN cc_start: 0.6627 (pt0) cc_final: 0.6140 (pt0) REVERT: D 366 VAL cc_start: 0.8461 (t) cc_final: 0.8196 (p) REVERT: D 378 ASN cc_start: 0.7939 (m-40) cc_final: 0.7517 (m-40) REVERT: E 65 MET cc_start: 0.7266 (mmm) cc_final: 0.6707 (mmm) REVERT: E 71 SER cc_start: 0.7678 (p) cc_final: 0.7402 (t) REVERT: E 85 GLU cc_start: 0.6862 (mm-30) cc_final: 0.6468 (tm-30) REVERT: E 103 LYS cc_start: 0.7149 (tttm) cc_final: 0.6714 (mtpp) REVERT: E 133 LYS cc_start: 0.8061 (ttmm) cc_final: 0.7714 (mtpp) REVERT: E 160 LEU cc_start: 0.7716 (tp) cc_final: 0.7313 (tp) REVERT: E 165 ASP cc_start: 0.7371 (m-30) cc_final: 0.6878 (m-30) REVERT: E 168 THR cc_start: 0.7758 (m) cc_final: 0.7451 (p) REVERT: E 174 LEU cc_start: 0.8070 (tp) cc_final: 0.7479 (tt) REVERT: E 204 THR cc_start: 0.8521 (p) cc_final: 0.8253 (t) REVERT: E 210 TRP cc_start: 0.8276 (t60) cc_final: 0.7915 (t60) REVERT: E 211 LEU cc_start: 0.8479 (mt) cc_final: 0.8196 (mm) REVERT: E 229 ARG cc_start: 0.7941 (ttp80) cc_final: 0.7689 (ptm-80) REVERT: E 240 THR cc_start: 0.7964 (p) cc_final: 0.7533 (m) REVERT: E 251 ASN cc_start: 0.7186 (t0) cc_final: 0.6776 (t0) REVERT: E 260 GLU cc_start: 0.7346 (pt0) cc_final: 0.7057 (pt0) REVERT: E 294 MET cc_start: 0.6465 (mmm) cc_final: 0.6005 (mmm) REVERT: E 312 TRP cc_start: 0.8177 (t60) cc_final: 0.7668 (t60) REVERT: E 346 ASN cc_start: 0.7822 (m-40) cc_final: 0.7502 (m-40) REVERT: F 105 LYS cc_start: 0.7761 (mttt) cc_final: 0.7544 (mtmt) REVERT: F 108 LEU cc_start: 0.7823 (tp) cc_final: 0.7542 (tp) REVERT: F 120 ILE cc_start: 0.8253 (OUTLIER) cc_final: 0.8049 (mp) REVERT: F 138 LYS cc_start: 0.7973 (ttpt) cc_final: 0.7721 (ttpp) REVERT: F 141 SER cc_start: 0.8334 (m) cc_final: 0.8100 (m) REVERT: F 153 ASN cc_start: 0.6572 (m-40) cc_final: 0.6199 (m110) REVERT: F 154 LEU cc_start: 0.7704 (mt) cc_final: 0.7499 (mp) REVERT: F 158 GLU cc_start: 0.7025 (tp30) cc_final: 0.6459 (tp30) REVERT: F 162 HIS cc_start: 0.7634 (OUTLIER) cc_final: 0.7354 (m-70) REVERT: F 175 ASP cc_start: 0.7357 (m-30) cc_final: 0.7025 (m-30) REVERT: F 196 GLN cc_start: 0.8096 (mm-40) cc_final: 0.7820 (mm-40) REVERT: F 200 GLN cc_start: 0.7237 (mp10) cc_final: 0.6924 (mp10) REVERT: F 273 THR cc_start: 0.8128 (m) cc_final: 0.7912 (t) REVERT: F 288 LYS cc_start: 0.8209 (OUTLIER) cc_final: 0.7893 (mtmt) REVERT: F 294 MET cc_start: 0.6493 (mtp) cc_final: 0.6253 (mmm) REVERT: F 314 LYS cc_start: 0.8002 (ttmm) cc_final: 0.7680 (tppt) REVERT: F 364 VAL cc_start: 0.8031 (t) cc_final: 0.7699 (p) REVERT: F 379 LYS cc_start: 0.7442 (tptm) cc_final: 0.6799 (tptm) REVERT: F 382 ASP cc_start: 0.7646 (t0) cc_final: 0.7421 (m-30) REVERT: F 383 ASP cc_start: 0.6968 (m-30) cc_final: 0.6443 (m-30) REVERT: J 34 ASN cc_start: 0.8125 (p0) cc_final: 0.7824 (p0) REVERT: J 40 ILE cc_start: 0.8135 (mt) cc_final: 0.7884 (pt) REVERT: J 87 ILE cc_start: 0.8555 (tt) cc_final: 0.8174 (pt) REVERT: J 122 LEU cc_start: 0.7873 (OUTLIER) cc_final: 0.7504 (mp) REVERT: J 145 MET cc_start: 0.6674 (tmm) cc_final: 0.6131 (tmm) REVERT: J 152 ILE cc_start: 0.7322 (OUTLIER) cc_final: 0.7053 (tp) REVERT: J 161 ILE cc_start: 0.8068 (mm) cc_final: 0.7726 (tt) REVERT: J 184 MET cc_start: 0.7654 (mtm) cc_final: 0.7107 (mtm) REVERT: J 219 MET cc_start: 0.7189 (tmt) cc_final: 0.6961 (tmt) REVERT: J 220 LEU cc_start: 0.7805 (mt) cc_final: 0.7597 (mt) REVERT: J 268 ARG cc_start: 0.7712 (ttt90) cc_final: 0.7184 (mmm-85) REVERT: J 271 THR cc_start: 0.8117 (m) cc_final: 0.7762 (p) REVERT: J 301 TYR cc_start: 0.8277 (m-80) cc_final: 0.8032 (m-10) REVERT: J 320 LEU cc_start: 0.8032 (mt) cc_final: 0.7743 (mm) REVERT: J 326 ARG cc_start: 0.7218 (tpt170) cc_final: 0.7009 (tpt170) REVERT: J 327 PHE cc_start: 0.6536 (t80) cc_final: 0.5801 (t80) REVERT: J 333 MET cc_start: 0.7203 (mtm) cc_final: 0.6476 (mtm) REVERT: J 339 PHE cc_start: 0.7822 (t80) cc_final: 0.7603 (t80) REVERT: J 342 ILE cc_start: 0.7988 (mm) cc_final: 0.7725 (tp) REVERT: J 382 LEU cc_start: 0.7840 (tp) cc_final: 0.7584 (tt) REVERT: J 403 ASN cc_start: 0.8260 (m-40) cc_final: 0.7706 (m-40) REVERT: J 406 ARG cc_start: 0.7413 (ttp80) cc_final: 0.7014 (ttp80) REVERT: J 411 SER cc_start: 0.7934 (m) cc_final: 0.7319 (p) REVERT: J 416 ILE cc_start: 0.7960 (mt) cc_final: 0.7624 (tp) REVERT: J 421 TRP cc_start: 0.7853 (t60) cc_final: 0.7204 (t60) REVERT: J 424 ARG cc_start: 0.7660 (mmm160) cc_final: 0.6975 (mmm160) REVERT: J 447 TYR cc_start: 0.8364 (m-80) cc_final: 0.8073 (m-80) REVERT: J 457 GLN cc_start: 0.7379 (mm-40) cc_final: 0.7051 (mm-40) REVERT: J 458 GLN cc_start: 0.7743 (tt0) cc_final: 0.7347 (tt0) REVERT: J 479 GLU cc_start: 0.7176 (mm-30) cc_final: 0.6851 (mt-10) REVERT: J 491 LEU cc_start: 0.8017 (mt) cc_final: 0.7651 (pp) REVERT: G 3 LEU cc_start: 0.8846 (tt) cc_final: 0.8389 (tp) REVERT: G 5 GLN cc_start: 0.8153 (mt0) cc_final: 0.7662 (mt0) REVERT: G 9 GLN cc_start: 0.6859 (tm-30) cc_final: 0.6518 (pp30) REVERT: G 18 ARG cc_start: 0.7294 (OUTLIER) cc_final: 0.6983 (mtt-85) REVERT: G 29 GLU cc_start: 0.7304 (tp30) cc_final: 0.6159 (tp30) REVERT: G 30 LYS cc_start: 0.8541 (tttt) cc_final: 0.8182 (tttt) REVERT: G 32 ASN cc_start: 0.7907 (m-40) cc_final: 0.6571 (p0) REVERT: G 81 TRP cc_start: 0.7195 (m100) cc_final: 0.6960 (m100) REVERT: G 88 GLU cc_start: 0.8109 (pt0) cc_final: 0.7828 (pt0) REVERT: G 98 TYR cc_start: 0.8142 (t80) cc_final: 0.7855 (t80) REVERT: G 104 THR cc_start: 0.8725 (m) cc_final: 0.8391 (p) REVERT: G 121 ASP cc_start: 0.8397 (m-30) cc_final: 0.8111 (t0) REVERT: G 127 GLN cc_start: 0.7980 (tm-30) cc_final: 0.7746 (tm-30) REVERT: G 130 LYS cc_start: 0.8676 (tttt) cc_final: 0.8075 (ttpp) REVERT: G 138 ASP cc_start: 0.8044 (t0) cc_final: 0.7738 (t0) REVERT: G 156 ASN cc_start: 0.8060 (t0) cc_final: 0.7791 (t0) REVERT: G 168 GLU cc_start: 0.8167 (tt0) cc_final: 0.7855 (tt0) REVERT: G 169 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7795 (mm) REVERT: G 181 GLN cc_start: 0.8455 (mm-40) cc_final: 0.7781 (tm-30) REVERT: G 192 GLU cc_start: 0.7220 (tt0) cc_final: 0.6993 (tt0) REVERT: G 215 GLU cc_start: 0.7423 (tm-30) cc_final: 0.6646 (tm-30) REVERT: G 217 GLU cc_start: 0.7956 (tm-30) cc_final: 0.7540 (mm-30) REVERT: G 230 GLN cc_start: 0.8427 (OUTLIER) cc_final: 0.7843 (pp30) REVERT: G 236 GLN cc_start: 0.8355 (mt0) cc_final: 0.7876 (mp10) REVERT: G 239 GLN cc_start: 0.8467 (tm-30) cc_final: 0.7955 (tm-30) REVERT: G 299 ASN cc_start: 0.8119 (m110) cc_final: 0.7618 (m-40) REVERT: G 303 LYS cc_start: 0.8631 (mtpp) cc_final: 0.8315 (mtpp) REVERT: G 315 GLN cc_start: 0.8675 (tp40) cc_final: 0.8280 (tp-100) REVERT: G 317 GLU cc_start: 0.7933 (tp30) cc_final: 0.7040 (tp30) REVERT: G 321 ARG cc_start: 0.8372 (mtt180) cc_final: 0.7655 (mtt180) REVERT: G 344 TYR cc_start: 0.8121 (m-80) cc_final: 0.7869 (m-80) REVERT: G 385 GLU cc_start: 0.7490 (mm-30) cc_final: 0.6867 (mm-30) REVERT: G 401 LYS cc_start: 0.8396 (tptm) cc_final: 0.8068 (tppp) REVERT: G 411 ASP cc_start: 0.5312 (t0) cc_final: 0.4951 (t70) REVERT: H 4 MET cc_start: 0.8059 (tmm) cc_final: 0.7696 (tmm) REVERT: H 5 GLN cc_start: 0.8309 (mp10) cc_final: 0.7848 (mp10) REVERT: H 9 GLN cc_start: 0.8568 (tp-100) cc_final: 0.8210 (tp-100) REVERT: H 14 ASN cc_start: 0.7800 (t0) cc_final: 0.7137 (t0) REVERT: H 29 GLU cc_start: 0.7819 (tp30) cc_final: 0.7076 (tp30) REVERT: H 31 ILE cc_start: 0.8555 (OUTLIER) cc_final: 0.8130 (tp) REVERT: H 33 GLU cc_start: 0.7340 (pp20) cc_final: 0.7052 (pp20) REVERT: H 77 ASP cc_start: 0.7644 (t0) cc_final: 0.6889 (t0) REVERT: H 78 MET cc_start: 0.6922 (mtt) cc_final: 0.6042 (mtt) REVERT: H 89 LYS cc_start: 0.8765 (mmmt) cc_final: 0.8441 (mmmt) REVERT: H 94 GLN cc_start: 0.7900 (tp40) cc_final: 0.7660 (tp40) REVERT: H 98 TYR cc_start: 0.8466 (t80) cc_final: 0.8093 (t80) REVERT: H 123 LEU cc_start: 0.8602 (tp) cc_final: 0.8071 (tp) REVERT: H 130 LYS cc_start: 0.8937 (ttpp) cc_final: 0.8429 (ttpp) REVERT: H 135 ARG cc_start: 0.8051 (ttm-80) cc_final: 0.7436 (mmm160) REVERT: H 138 ASP cc_start: 0.7980 (OUTLIER) cc_final: 0.7176 (t0) REVERT: H 142 GLN cc_start: 0.8081 (mm-40) cc_final: 0.7809 (mm-40) REVERT: H 143 ARG cc_start: 0.7670 (ttp-110) cc_final: 0.7026 (ttp-170) REVERT: H 162 ASP cc_start: 0.7851 (m-30) cc_final: 0.7574 (m-30) REVERT: H 168 GLU cc_start: 0.8236 (tt0) cc_final: 0.7208 (tt0) REVERT: H 169 LEU cc_start: 0.8758 (tt) cc_final: 0.8447 (tp) REVERT: H 179 VAL cc_start: 0.8881 (t) cc_final: 0.8576 (m) REVERT: H 180 GLU cc_start: 0.8363 (mm-30) cc_final: 0.8124 (mm-30) REVERT: H 184 GLN cc_start: 0.8330 (OUTLIER) cc_final: 0.7364 (tp-100) REVERT: H 234 ARG cc_start: 0.7804 (mmm-85) cc_final: 0.6936 (mmm-85) REVERT: H 237 ILE cc_start: 0.8872 (mt) cc_final: 0.8007 (mt) REVERT: H 238 ARG cc_start: 0.8148 (mtt180) cc_final: 0.7863 (mtt180) REVERT: H 248 LEU cc_start: 0.8642 (mt) cc_final: 0.8407 (mm) REVERT: H 314 GLU cc_start: 0.7653 (mm-30) cc_final: 0.7233 (mm-30) REVERT: H 317 GLU cc_start: 0.7541 (tp30) cc_final: 0.7203 (tp30) REVERT: H 321 ARG cc_start: 0.8227 (mtt180) cc_final: 0.7740 (mtt180) REVERT: H 328 ARG cc_start: 0.8014 (mtt-85) cc_final: 0.7760 (mtt-85) REVERT: H 337 SER cc_start: 0.8726 (m) cc_final: 0.8050 (p) REVERT: H 340 SER cc_start: 0.8789 (m) cc_final: 0.8261 (p) REVERT: H 356 ASP cc_start: 0.8213 (t0) cc_final: 0.7946 (t0) REVERT: H 367 ARG cc_start: 0.8262 (tpp80) cc_final: 0.7832 (tpp80) REVERT: H 374 ASP cc_start: 0.7875 (t0) cc_final: 0.7549 (t0) REVERT: H 413 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8232 (pt) REVERT: H 421 LYS cc_start: 0.8681 (mttt) cc_final: 0.8406 (mttt) REVERT: I 8 GLN cc_start: 0.8183 (mm-40) cc_final: 0.7662 (mm-40) REVERT: I 9 GLN cc_start: 0.7924 (tt0) cc_final: 0.7404 (tt0) REVERT: I 11 ARG cc_start: 0.7864 (ttp80) cc_final: 0.7122 (ttp80) REVERT: I 25 ASP cc_start: 0.7727 (t0) cc_final: 0.7081 (t0) REVERT: I 29 GLU cc_start: 0.7503 (tp30) cc_final: 0.6525 (tp30) REVERT: I 31 ILE cc_start: 0.9052 (mt) cc_final: 0.8824 (mm) REVERT: I 42 LEU cc_start: 0.7498 (tt) cc_final: 0.7251 (tp) REVERT: I 76 PHE cc_start: 0.7253 (t80) cc_final: 0.6817 (t80) REVERT: I 82 ARG cc_start: 0.7688 (mmp80) cc_final: 0.6916 (mmp80) REVERT: I 89 LYS cc_start: 0.8452 (mmtp) cc_final: 0.8226 (mmtp) REVERT: I 99 GLN cc_start: 0.8309 (mt0) cc_final: 0.8038 (mt0) REVERT: I 103 GLN cc_start: 0.8433 (mt0) cc_final: 0.8168 (mm-40) REVERT: I 124 SER cc_start: 0.8513 (t) cc_final: 0.8284 (p) REVERT: I 138 ASP cc_start: 0.8360 (t0) cc_final: 0.8090 (t0) REVERT: I 212 LEU cc_start: 0.9127 (tp) cc_final: 0.8805 (tt) REVERT: I 215 GLU cc_start: 0.8020 (tp30) cc_final: 0.7397 (tp30) REVERT: I 224 LEU cc_start: 0.8639 (tp) cc_final: 0.8303 (mt) REVERT: I 225 GLN cc_start: 0.7763 (tm-30) cc_final: 0.7186 (tm-30) REVERT: I 227 ARG cc_start: 0.7608 (mtm-85) cc_final: 0.7184 (mtt-85) REVERT: I 235 GLU cc_start: 0.7965 (tp30) cc_final: 0.7711 (tp30) REVERT: I 236 GLN cc_start: 0.8273 (mt0) cc_final: 0.7979 (mt0) REVERT: I 238 ARG cc_start: 0.7952 (mpt180) cc_final: 0.7616 (mpt180) REVERT: I 259 THR cc_start: 0.3232 (OUTLIER) cc_final: 0.2944 (m) REVERT: I 297 MET cc_start: 0.5818 (tmm) cc_final: 0.5600 (tmm) REVERT: I 303 LYS cc_start: 0.8628 (mtpp) cc_final: 0.8273 (mtpp) REVERT: I 306 GLN cc_start: 0.8437 (pt0) cc_final: 0.8074 (mt0) REVERT: I 315 GLN cc_start: 0.8039 (mt0) cc_final: 0.7549 (mp10) REVERT: I 321 ARG cc_start: 0.8801 (ttm170) cc_final: 0.8182 (mtp180) REVERT: I 394 LEU cc_start: 0.8735 (mt) cc_final: 0.8504 (mm) REVERT: I 396 ASN cc_start: 0.8297 (m-40) cc_final: 0.7865 (m-40) outliers start: 109 outliers final: 56 residues processed: 1198 average time/residue: 0.4753 time to fit residues: 854.2298 Evaluate side-chains 1197 residues out of total 3232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 1127 time to evaluate : 3.467 ------------------------------------------------------------------------------- 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 254 VAL Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 273 THR 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 326 ASP Chi-restraints excluded: chain B residue 344 SER Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain C residue 187 MET Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 340 SER Chi-restraints excluded: chain D residue 84 LYS Chi-restraints excluded: chain D residue 115 THR 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 164 ARG Chi-restraints excluded: chain E residue 214 GLU 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 373 SER Chi-restraints excluded: chain E residue 386 LYS Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain F residue 162 HIS Chi-restraints excluded: chain F residue 237 ILE Chi-restraints excluded: chain F residue 288 LYS Chi-restraints excluded: chain F residue 372 ILE Chi-restraints excluded: chain J residue 122 LEU Chi-restraints excluded: chain J residue 152 ILE Chi-restraints excluded: chain J residue 290 LEU Chi-restraints excluded: chain J residue 293 GLN Chi-restraints excluded: chain J residue 319 ILE Chi-restraints excluded: chain J residue 371 GLN Chi-restraints excluded: chain J residue 466 GLN 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 203 THR Chi-restraints excluded: chain G residue 230 GLN Chi-restraints excluded: chain G residue 232 LEU Chi-restraints excluded: chain G residue 279 MET Chi-restraints excluded: chain G residue 398 LEU Chi-restraints excluded: chain H residue 19 LYS Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 138 ASP Chi-restraints excluded: chain H residue 184 GLN Chi-restraints excluded: chain H residue 221 LEU Chi-restraints excluded: chain H residue 250 LEU 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 19 LYS Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 203 THR Chi-restraints excluded: chain I residue 223 LEU Chi-restraints excluded: chain I residue 259 THR Chi-restraints excluded: chain I residue 272 THR Chi-restraints excluded: chain I residue 328 ARG Chi-restraints excluded: chain I residue 398 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 13 optimal weight: 0.7980 chunk 195 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 chunk 332 optimal weight: 2.9990 chunk 334 optimal weight: 3.9990 chunk 372 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 307 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 290 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 HIS A 126 GLN B 200 GLN ** B 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 ASN D 251 ASN E 201 GLN E 236 GLN F 162 HIS F 179 GLN F 251 ASN F 306 GLN F 346 ASN ** J 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 444 GLN J 459 GLN ** G 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 173 ASN ** H 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 294 GLN H 396 ASN I 32 ASN I 73 GLN I 87 GLN I 127 GLN I 320 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.115545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.097642 restraints weight = 59416.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.100622 restraints weight = 26141.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.102493 restraints weight = 14108.625| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.4896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 30315 Z= 0.205 Angle : 0.640 11.208 41246 Z= 0.340 Chirality : 0.044 0.187 4889 Planarity : 0.005 0.094 5392 Dihedral : 4.107 22.628 4179 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 4.92 % Allowed : 18.10 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.14), residues: 3860 helix: 2.99 (0.11), residues: 2024 sheet: -0.39 (0.22), residues: 503 loop : -0.90 (0.16), residues: 1333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP J 251 HIS 0.008 0.001 HIS F 162 PHE 0.028 0.002 PHE J 265 TYR 0.022 0.002 TYR G 113 ARG 0.023 0.001 ARG G 158 Details of bonding type rmsd hydrogen bonds : bond 0.06926 ( 1888) hydrogen bonds : angle 4.40688 ( 5523) covalent geometry : bond 0.00431 (30315) covalent geometry : angle 0.63969 (41246) *********************** 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 1417 residues out of total 3232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 1258 time to evaluate : 3.070 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 49 PHE cc_start: 0.7101 (m-80) cc_final: 0.6638 (m-80) REVERT: A 50 GLU cc_start: 0.6924 (mm-30) cc_final: 0.6432 (mm-30) REVERT: A 53 ASP cc_start: 0.7167 (t0) cc_final: 0.6862 (t70) REVERT: A 65 MET cc_start: 0.7244 (mtt) cc_final: 0.7018 (mtm) REVERT: A 79 ASN cc_start: 0.7658 (t0) cc_final: 0.7446 (t0) REVERT: A 138 LYS cc_start: 0.8189 (mttt) cc_final: 0.7756 (tttm) REVERT: A 143 TYR cc_start: 0.8111 (t80) cc_final: 0.7900 (t80) REVERT: A 146 ARG cc_start: 0.7688 (ttm-80) cc_final: 0.7110 (mtt90) REVERT: A 158 GLU cc_start: 0.7817 (mm-30) cc_final: 0.7383 (tm-30) REVERT: A 159 GLU cc_start: 0.7440 (mp0) cc_final: 0.7035 (mp0) REVERT: A 160 LEU cc_start: 0.8175 (mt) cc_final: 0.7684 (tt) REVERT: A 173 GLN cc_start: 0.7771 (mm-40) cc_final: 0.7414 (mm-40) REVERT: A 189 LEU cc_start: 0.8314 (mt) cc_final: 0.8109 (mt) REVERT: A 193 LEU cc_start: 0.8283 (tp) cc_final: 0.7994 (tp) REVERT: A 200 GLN cc_start: 0.7450 (mt0) cc_final: 0.7120 (mm-40) REVERT: A 225 TYR cc_start: 0.8133 (m-80) cc_final: 0.7195 (m-80) REVERT: A 247 VAL cc_start: 0.8750 (t) cc_final: 0.8401 (m) REVERT: A 259 LYS cc_start: 0.8267 (mtmm) cc_final: 0.7877 (mtmm) REVERT: A 284 LYS cc_start: 0.7501 (mtpp) cc_final: 0.7254 (mtpp) REVERT: A 293 ASP cc_start: 0.7506 (t0) cc_final: 0.7224 (t0) REVERT: A 296 THR cc_start: 0.8367 (p) cc_final: 0.8160 (t) REVERT: A 306 GLN cc_start: 0.6431 (tp-100) cc_final: 0.6024 (tp-100) REVERT: A 312 TRP cc_start: 0.7292 (t60) cc_final: 0.7033 (t60) REVERT: A 324 GLU cc_start: 0.6177 (tp30) cc_final: 0.5802 (tp30) REVERT: A 347 THR cc_start: 0.7285 (OUTLIER) cc_final: 0.6654 (p) REVERT: A 381 ILE cc_start: 0.8513 (mt) cc_final: 0.8261 (mp) REVERT: B 54 ASP cc_start: 0.7657 (t70) cc_final: 0.7389 (t70) REVERT: B 93 ASP cc_start: 0.7862 (t0) cc_final: 0.7566 (t70) REVERT: B 105 LYS cc_start: 0.7928 (mtmt) cc_final: 0.7712 (mmtp) REVERT: B 117 GLN cc_start: 0.7458 (OUTLIER) cc_final: 0.7062 (tt0) REVERT: B 130 GLU cc_start: 0.7171 (mm-30) cc_final: 0.6886 (tm-30) REVERT: B 138 LYS cc_start: 0.8566 (ttpp) cc_final: 0.8229 (ttpp) REVERT: B 143 TYR cc_start: 0.8467 (t80) cc_final: 0.8245 (t80) REVERT: B 145 ARG cc_start: 0.8136 (mtt-85) cc_final: 0.7852 (mtt90) REVERT: B 154 LEU cc_start: 0.7665 (mt) cc_final: 0.7448 (mm) REVERT: B 157 ARG cc_start: 0.6853 (mtp-110) cc_final: 0.6494 (mtm110) REVERT: B 160 LEU cc_start: 0.8856 (tp) cc_final: 0.8606 (tt) REVERT: B 161 GLN cc_start: 0.8117 (tp40) cc_final: 0.7331 (mm-40) REVERT: B 165 ASP cc_start: 0.7010 (m-30) cc_final: 0.6488 (m-30) REVERT: B 171 GLN cc_start: 0.8071 (tp-100) cc_final: 0.7683 (tp-100) REVERT: B 207 ARG cc_start: 0.7370 (mtt-85) cc_final: 0.6956 (mtt-85) REVERT: B 244 MET cc_start: 0.7969 (ptp) cc_final: 0.7634 (ptp) REVERT: B 259 LYS cc_start: 0.7748 (mtmt) cc_final: 0.7536 (mttt) REVERT: B 284 LYS cc_start: 0.8086 (mtpt) cc_final: 0.7800 (mtpt) REVERT: B 290 VAL cc_start: 0.8078 (t) cc_final: 0.7702 (t) REVERT: B 317 GLN cc_start: 0.7714 (mm-40) cc_final: 0.7453 (mm110) REVERT: B 328 LYS cc_start: 0.7948 (mmpt) cc_final: 0.7415 (mmpt) REVERT: B 330 LEU cc_start: 0.8153 (tt) cc_final: 0.7782 (tp) REVERT: B 368 THR cc_start: 0.7350 (t) cc_final: 0.7104 (p) REVERT: B 371 GLU cc_start: 0.6988 (mt-10) cc_final: 0.6733 (mt-10) REVERT: B 386 LYS cc_start: 0.8104 (tttt) cc_final: 0.7769 (tttt) REVERT: C 83 VAL cc_start: 0.7321 (m) cc_final: 0.7102 (p) REVERT: C 133 LYS cc_start: 0.8215 (mtpt) cc_final: 0.7903 (mtpt) REVERT: C 138 LYS cc_start: 0.7714 (ptmm) cc_final: 0.7469 (ptmm) REVERT: C 142 ASP cc_start: 0.7590 (t70) cc_final: 0.7021 (t0) REVERT: C 146 ARG cc_start: 0.8552 (mmt-90) cc_final: 0.8194 (mmt-90) REVERT: C 154 LEU cc_start: 0.8460 (mt) cc_final: 0.8136 (mt) REVERT: C 155 ILE cc_start: 0.8246 (OUTLIER) cc_final: 0.8031 (tp) REVERT: C 161 GLN cc_start: 0.7639 (tp40) cc_final: 0.7388 (tp40) REVERT: C 200 GLN cc_start: 0.7005 (mt0) cc_final: 0.6571 (mt0) REVERT: C 207 ARG cc_start: 0.7953 (mtm-85) cc_final: 0.7721 (mtm-85) REVERT: C 231 VAL cc_start: 0.8304 (OUTLIER) cc_final: 0.7914 (p) REVERT: C 284 LYS cc_start: 0.8220 (mmmt) cc_final: 0.7863 (mmmt) REVERT: C 302 LEU cc_start: 0.8604 (tp) cc_final: 0.8308 (tt) REVERT: D 50 GLU cc_start: 0.6725 (tp30) cc_final: 0.6333 (tp30) REVERT: D 54 ASP cc_start: 0.6907 (t0) cc_final: 0.6426 (t0) REVERT: D 73 THR cc_start: 0.8575 (m) cc_final: 0.8318 (m) REVERT: D 117 GLN cc_start: 0.7790 (tt0) cc_final: 0.7237 (tt0) REVERT: D 121 ASN cc_start: 0.7796 (m-40) cc_final: 0.7546 (m-40) REVERT: D 129 ILE cc_start: 0.8353 (mt) cc_final: 0.8093 (mm) REVERT: D 138 LYS cc_start: 0.8095 (tttt) cc_final: 0.7452 (tttt) REVERT: D 143 TYR cc_start: 0.8396 (t80) cc_final: 0.8132 (t80) REVERT: D 157 ARG cc_start: 0.7442 (mtm110) cc_final: 0.6992 (mtm110) REVERT: D 247 VAL cc_start: 0.8893 (t) cc_final: 0.8579 (m) REVERT: D 253 TRP cc_start: 0.8436 (p90) cc_final: 0.8199 (p90) REVERT: D 259 LYS cc_start: 0.8205 (mttt) cc_final: 0.7895 (mttm) REVERT: D 327 GLN cc_start: 0.7873 (mm-40) cc_final: 0.7593 (mm110) REVERT: D 331 GLU cc_start: 0.7043 (mp0) cc_final: 0.6502 (mp0) REVERT: D 332 GLN cc_start: 0.7420 (tp40) cc_final: 0.7181 (tp40) REVERT: D 366 VAL cc_start: 0.8614 (t) cc_final: 0.8342 (p) REVERT: D 378 ASN cc_start: 0.7969 (m-40) cc_final: 0.7152 (m-40) REVERT: D 382 ASP cc_start: 0.7277 (m-30) cc_final: 0.6910 (m-30) REVERT: E 65 MET cc_start: 0.7154 (mmm) cc_final: 0.6836 (mmm) REVERT: E 71 SER cc_start: 0.7780 (p) cc_final: 0.7427 (t) REVERT: E 125 LEU cc_start: 0.8114 (mt) cc_final: 0.7899 (mt) REVERT: E 126 GLN cc_start: 0.7753 (tm-30) cc_final: 0.7395 (tm-30) REVERT: E 144 ASN cc_start: 0.7870 (m-40) cc_final: 0.7653 (p0) REVERT: E 161 GLN cc_start: 0.7897 (tt0) cc_final: 0.7231 (tp-100) REVERT: E 168 THR cc_start: 0.7962 (m) cc_final: 0.7646 (p) REVERT: E 200 GLN cc_start: 0.7382 (mm-40) cc_final: 0.6957 (mt0) REVERT: E 204 THR cc_start: 0.8612 (p) cc_final: 0.8399 (t) REVERT: E 210 TRP cc_start: 0.8434 (t60) cc_final: 0.8057 (t60) REVERT: E 211 LEU cc_start: 0.8396 (mt) cc_final: 0.8149 (mt) REVERT: E 229 ARG cc_start: 0.7900 (ttp80) cc_final: 0.7689 (ptm-80) REVERT: E 251 ASN cc_start: 0.7062 (t0) cc_final: 0.6628 (t0) REVERT: E 252 MET cc_start: 0.7743 (mmm) cc_final: 0.7361 (mtp) REVERT: E 260 GLU cc_start: 0.7384 (pt0) cc_final: 0.7103 (pt0) REVERT: E 283 VAL cc_start: 0.8494 (t) cc_final: 0.8062 (m) REVERT: E 294 MET cc_start: 0.6787 (mmm) cc_final: 0.6423 (mmm) REVERT: E 312 TRP cc_start: 0.8316 (t60) cc_final: 0.7722 (t60) REVERT: E 346 ASN cc_start: 0.7859 (m-40) cc_final: 0.7599 (m-40) REVERT: F 49 PHE cc_start: 0.7813 (m-80) cc_final: 0.7557 (m-80) REVERT: F 74 LYS cc_start: 0.8033 (mttp) cc_final: 0.7808 (mttm) REVERT: F 105 LYS cc_start: 0.7999 (mttt) cc_final: 0.7785 (mtmm) REVERT: F 119 MET cc_start: 0.7845 (mtt) cc_final: 0.7440 (mtt) REVERT: F 120 ILE cc_start: 0.8386 (OUTLIER) cc_final: 0.8106 (mp) REVERT: F 122 SER cc_start: 0.8455 (m) cc_final: 0.8236 (p) REVERT: F 130 GLU cc_start: 0.7384 (tp30) cc_final: 0.7079 (tp30) REVERT: F 138 LYS cc_start: 0.8309 (ttpt) cc_final: 0.7996 (ttpp) REVERT: F 141 SER cc_start: 0.8449 (m) cc_final: 0.8185 (t) REVERT: F 144 ASN cc_start: 0.8534 (m-40) cc_final: 0.8320 (m-40) REVERT: F 153 ASN cc_start: 0.7423 (m-40) cc_final: 0.7194 (m-40) REVERT: F 158 GLU cc_start: 0.7035 (tp30) cc_final: 0.6511 (tp30) REVERT: F 192 LYS cc_start: 0.8119 (mttp) cc_final: 0.7727 (mttp) REVERT: F 200 GLN cc_start: 0.7287 (mp10) cc_final: 0.6866 (mp10) REVERT: F 214 GLU cc_start: 0.7541 (tp30) cc_final: 0.6741 (mp0) REVERT: F 217 ARG cc_start: 0.6691 (ttm110) cc_final: 0.6303 (ttm110) REVERT: F 272 VAL cc_start: 0.7857 (t) cc_final: 0.7576 (p) REVERT: F 273 THR cc_start: 0.8213 (m) cc_final: 0.7687 (t) REVERT: F 284 LYS cc_start: 0.7390 (mmtp) cc_final: 0.7101 (mmtp) REVERT: F 288 LYS cc_start: 0.8364 (OUTLIER) cc_final: 0.7950 (mtmt) REVERT: F 293 ASP cc_start: 0.7290 (t70) cc_final: 0.7078 (t0) REVERT: F 317 GLN cc_start: 0.7439 (mm-40) cc_final: 0.7176 (mp10) REVERT: F 332 GLN cc_start: 0.7559 (OUTLIER) cc_final: 0.7317 (mp10) REVERT: F 379 LYS cc_start: 0.7517 (tptm) cc_final: 0.6804 (tptm) REVERT: F 383 ASP cc_start: 0.7095 (m-30) cc_final: 0.6554 (m-30) REVERT: J 25 MET cc_start: 0.7445 (ptm) cc_final: 0.7236 (ptm) REVERT: J 40 ILE cc_start: 0.8229 (mt) cc_final: 0.7922 (pt) REVERT: J 87 ILE cc_start: 0.8648 (tt) cc_final: 0.8372 (pt) REVERT: J 122 LEU cc_start: 0.8122 (OUTLIER) cc_final: 0.7772 (mp) REVERT: J 131 TYR cc_start: 0.7135 (OUTLIER) cc_final: 0.6900 (t80) REVERT: J 136 ARG cc_start: 0.7223 (ttt-90) cc_final: 0.7022 (ttt-90) REVERT: J 145 MET cc_start: 0.6787 (tmm) cc_final: 0.6148 (tmm) REVERT: J 184 MET cc_start: 0.7632 (mtm) cc_final: 0.7266 (mtm) REVERT: J 216 LEU cc_start: 0.8325 (tp) cc_final: 0.7980 (tt) REVERT: J 217 GLN cc_start: 0.7885 (tp40) cc_final: 0.7590 (tp40) REVERT: J 219 MET cc_start: 0.7246 (tmt) cc_final: 0.6998 (tmt) REVERT: J 247 PHE cc_start: 0.7159 (t80) cc_final: 0.6917 (m-80) REVERT: J 268 ARG cc_start: 0.7915 (ttt90) cc_final: 0.7375 (mmm-85) REVERT: J 271 THR cc_start: 0.8307 (m) cc_final: 0.8015 (p) REVERT: J 282 MET cc_start: 0.7712 (ttt) cc_final: 0.7404 (ttm) REVERT: J 297 GLU cc_start: 0.7351 (tt0) cc_final: 0.7052 (tt0) REVERT: J 308 LEU cc_start: 0.7973 (mt) cc_final: 0.7572 (mt) REVERT: J 320 LEU cc_start: 0.8191 (mt) cc_final: 0.7986 (mm) REVERT: J 327 PHE cc_start: 0.6591 (t80) cc_final: 0.5874 (t80) REVERT: J 333 MET cc_start: 0.7145 (mtm) cc_final: 0.6871 (mtm) REVERT: J 334 ARG cc_start: 0.7932 (mtm180) cc_final: 0.7712 (mtm180) REVERT: J 339 PHE cc_start: 0.7902 (t80) cc_final: 0.7676 (t80) REVERT: J 342 ILE cc_start: 0.8221 (mm) cc_final: 0.7967 (tt) REVERT: J 351 ARG cc_start: 0.7912 (ttm-80) cc_final: 0.7706 (ttm-80) REVERT: J 356 GLU cc_start: 0.6638 (OUTLIER) cc_final: 0.6436 (tm-30) REVERT: J 403 ASN cc_start: 0.8290 (m-40) cc_final: 0.7725 (m-40) REVERT: J 421 TRP cc_start: 0.8019 (t60) cc_final: 0.7779 (t60) REVERT: J 424 ARG cc_start: 0.7729 (mmm160) cc_final: 0.6199 (mmm160) REVERT: J 427 MET cc_start: 0.7554 (ttp) cc_final: 0.7342 (ttp) REVERT: J 447 TYR cc_start: 0.8454 (m-80) cc_final: 0.8118 (m-80) REVERT: J 458 GLN cc_start: 0.8186 (tt0) cc_final: 0.7874 (tt0) REVERT: J 491 LEU cc_start: 0.7926 (mt) cc_final: 0.7607 (pp) REVERT: G 5 GLN cc_start: 0.8290 (mt0) cc_final: 0.7786 (mt0) REVERT: G 9 GLN cc_start: 0.6985 (tm-30) cc_final: 0.6540 (tm-30) REVERT: G 29 GLU cc_start: 0.7643 (tp30) cc_final: 0.6446 (tp30) REVERT: G 30 LYS cc_start: 0.8732 (tttt) cc_final: 0.8358 (tttt) REVERT: G 32 ASN cc_start: 0.8062 (m-40) cc_final: 0.6798 (p0) REVERT: G 77 ASP cc_start: 0.7898 (t0) cc_final: 0.3871 (p0) REVERT: G 87 GLN cc_start: 0.8353 (tp40) cc_final: 0.8041 (tp40) REVERT: G 98 TYR cc_start: 0.8229 (t80) cc_final: 0.7783 (t80) REVERT: G 99 GLN cc_start: 0.7732 (tm-30) cc_final: 0.6685 (tm-30) REVERT: G 103 GLN cc_start: 0.8261 (mt0) cc_final: 0.7665 (mm-40) REVERT: G 104 THR cc_start: 0.8695 (m) cc_final: 0.8457 (p) REVERT: G 130 LYS cc_start: 0.8734 (tttt) cc_final: 0.8230 (ttpp) REVERT: G 136 GLN cc_start: 0.8527 (tp40) cc_final: 0.7966 (tm-30) REVERT: G 156 ASN cc_start: 0.8012 (t0) cc_final: 0.7740 (t0) REVERT: G 158 ARG cc_start: 0.7786 (tpm170) cc_final: 0.7412 (tpm170) REVERT: G 169 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8072 (mm) REVERT: G 181 GLN cc_start: 0.8391 (mm-40) cc_final: 0.7787 (tm-30) REVERT: G 192 GLU cc_start: 0.7341 (tt0) cc_final: 0.7139 (tt0) REVERT: G 212 LEU cc_start: 0.9112 (mt) cc_final: 0.8869 (mp) REVERT: G 215 GLU cc_start: 0.7539 (tm-30) cc_final: 0.6759 (tm-30) REVERT: G 217 GLU cc_start: 0.7980 (tm-30) cc_final: 0.7529 (mm-30) REVERT: G 225 GLN cc_start: 0.8325 (tm-30) cc_final: 0.8118 (tm-30) REVERT: G 230 GLN cc_start: 0.8480 (OUTLIER) cc_final: 0.7920 (pp30) REVERT: G 232 LEU cc_start: 0.9240 (tt) cc_final: 0.8804 (tt) REVERT: G 236 GLN cc_start: 0.8363 (mt0) cc_final: 0.7829 (mm-40) REVERT: G 299 ASN cc_start: 0.8153 (m110) cc_final: 0.7688 (m-40) REVERT: G 303 LYS cc_start: 0.8552 (mtpp) cc_final: 0.8297 (mtpp) REVERT: G 315 GLN cc_start: 0.8630 (tp40) cc_final: 0.8216 (tp-100) REVERT: G 317 GLU cc_start: 0.7954 (tp30) cc_final: 0.7042 (tp30) REVERT: G 321 ARG cc_start: 0.8412 (mtt180) cc_final: 0.7728 (mtt180) REVERT: G 332 ASN cc_start: 0.8572 (m-40) cc_final: 0.8305 (m110) REVERT: G 344 TYR cc_start: 0.8119 (m-80) cc_final: 0.7876 (m-80) REVERT: G 384 GLN cc_start: 0.8153 (tm-30) cc_final: 0.7239 (tm-30) REVERT: G 385 GLU cc_start: 0.7525 (mm-30) cc_final: 0.6992 (mm-30) REVERT: G 401 LYS cc_start: 0.8555 (tptm) cc_final: 0.8212 (tppp) REVERT: H 4 MET cc_start: 0.8099 (tmm) cc_final: 0.7808 (tmm) REVERT: H 9 GLN cc_start: 0.8595 (tp-100) cc_final: 0.8229 (tp40) REVERT: H 14 ASN cc_start: 0.8128 (t0) cc_final: 0.7765 (t0) REVERT: H 17 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8607 (mp) REVERT: H 25 ASP cc_start: 0.7985 (m-30) cc_final: 0.7619 (t0) REVERT: H 29 GLU cc_start: 0.7808 (tp30) cc_final: 0.6734 (tp30) REVERT: H 30 LYS cc_start: 0.8911 (OUTLIER) cc_final: 0.7629 (ttpt) REVERT: H 77 ASP cc_start: 0.6943 (t0) cc_final: 0.6615 (p0) REVERT: H 94 GLN cc_start: 0.8030 (tp40) cc_final: 0.7763 (tp40) REVERT: H 98 TYR cc_start: 0.8574 (t80) cc_final: 0.8364 (t80) REVERT: H 129 GLN cc_start: 0.8366 (tt0) cc_final: 0.8146 (tt0) REVERT: H 131 GLU cc_start: 0.8047 (tp30) cc_final: 0.7588 (tp30) REVERT: H 135 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.7521 (mmm160) REVERT: H 138 ASP cc_start: 0.7846 (OUTLIER) cc_final: 0.6894 (t0) REVERT: H 142 GLN cc_start: 0.7971 (mm-40) cc_final: 0.7600 (mm-40) REVERT: H 162 ASP cc_start: 0.8094 (m-30) cc_final: 0.7754 (m-30) REVERT: H 179 VAL cc_start: 0.8923 (t) cc_final: 0.8570 (p) REVERT: H 180 GLU cc_start: 0.8398 (mm-30) cc_final: 0.7970 (tm-30) REVERT: H 181 GLN cc_start: 0.7952 (tm-30) cc_final: 0.7712 (tm-30) REVERT: H 184 GLN cc_start: 0.8355 (tt0) cc_final: 0.7532 (tp-100) REVERT: H 218 LYS cc_start: 0.8745 (mmtt) cc_final: 0.8362 (mmtt) REVERT: H 231 ASP cc_start: 0.7358 (t0) cc_final: 0.6835 (t70) REVERT: H 234 ARG cc_start: 0.7776 (mmm-85) cc_final: 0.7289 (mmm-85) REVERT: H 236 GLN cc_start: 0.7928 (pp30) cc_final: 0.7645 (pp30) REVERT: H 237 ILE cc_start: 0.8831 (mt) cc_final: 0.8456 (mt) REVERT: H 238 ARG cc_start: 0.8131 (mtt180) cc_final: 0.7868 (mtt180) REVERT: H 245 LEU cc_start: 0.8387 (mt) cc_final: 0.7764 (mt) REVERT: H 297 MET cc_start: 0.6095 (mtm) cc_final: 0.5565 (mtm) REVERT: H 306 GLN cc_start: 0.8334 (OUTLIER) cc_final: 0.8039 (mp10) REVERT: H 317 GLU cc_start: 0.7611 (tp30) cc_final: 0.7248 (tp30) REVERT: H 321 ARG cc_start: 0.8362 (mtt180) cc_final: 0.7710 (mtt180) REVERT: H 337 SER cc_start: 0.8802 (m) cc_final: 0.8369 (m) REVERT: H 340 SER cc_start: 0.8706 (m) cc_final: 0.8181 (p) REVERT: H 356 ASP cc_start: 0.8257 (t0) cc_final: 0.7919 (t0) REVERT: H 374 ASP cc_start: 0.7857 (t0) cc_final: 0.7522 (t0) REVERT: H 390 ARG cc_start: 0.8634 (mtt-85) cc_final: 0.8315 (ttm170) REVERT: H 392 ASN cc_start: 0.8359 (m-40) cc_final: 0.8032 (t0) REVERT: H 396 ASN cc_start: 0.8152 (m-40) cc_final: 0.7683 (m-40) REVERT: H 397 GLN cc_start: 0.8134 (tt0) cc_final: 0.7397 (tm-30) REVERT: H 421 LYS cc_start: 0.8691 (mttt) cc_final: 0.8459 (mttt) REVERT: I 11 ARG cc_start: 0.7969 (ttp80) cc_final: 0.7583 (ttp-110) REVERT: I 28 PHE cc_start: 0.8263 (m-80) cc_final: 0.8005 (m-80) REVERT: I 29 GLU cc_start: 0.7671 (tp30) cc_final: 0.6586 (tp30) REVERT: I 31 ILE cc_start: 0.9073 (mt) cc_final: 0.8795 (mm) REVERT: I 32 ASN cc_start: 0.8502 (m-40) cc_final: 0.7866 (m110) REVERT: I 42 LEU cc_start: 0.7566 (tt) cc_final: 0.7311 (tp) REVERT: I 76 PHE cc_start: 0.7605 (t80) cc_final: 0.7036 (t80) REVERT: I 86 LEU cc_start: 0.8906 (pp) cc_final: 0.8618 (mp) REVERT: I 89 LYS cc_start: 0.8436 (mmtp) cc_final: 0.8138 (mmtp) REVERT: I 99 GLN cc_start: 0.8280 (mt0) cc_final: 0.8069 (mt0) REVERT: I 118 ASN cc_start: 0.8378 (t0) cc_final: 0.8160 (t0) REVERT: I 124 SER cc_start: 0.8618 (t) cc_final: 0.8369 (p) REVERT: I 143 ARG cc_start: 0.7759 (ttm110) cc_final: 0.7354 (ttm110) REVERT: I 213 LEU cc_start: 0.9031 (mt) cc_final: 0.8603 (mt) REVERT: I 215 GLU cc_start: 0.7990 (tp30) cc_final: 0.7427 (tp30) REVERT: I 223 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8365 (mm) REVERT: I 224 LEU cc_start: 0.8770 (tp) cc_final: 0.7926 (mm) REVERT: I 225 GLN cc_start: 0.7865 (tm-30) cc_final: 0.7275 (tm-30) REVERT: I 227 ARG cc_start: 0.7668 (mtm-85) cc_final: 0.7149 (mtm-85) REVERT: I 230 GLN cc_start: 0.7970 (tm-30) cc_final: 0.7692 (tm-30) REVERT: I 236 GLN cc_start: 0.8316 (mt0) cc_final: 0.7925 (mt0) REVERT: I 238 ARG cc_start: 0.7943 (mpt180) cc_final: 0.7622 (mpt180) REVERT: I 259 THR cc_start: 0.3512 (OUTLIER) cc_final: 0.3292 (m) REVERT: I 297 MET cc_start: 0.6301 (tmm) cc_final: 0.5862 (tmm) REVERT: I 301 GLN cc_start: 0.8468 (tt0) cc_final: 0.8095 (mt0) REVERT: I 303 LYS cc_start: 0.8615 (mtpp) cc_final: 0.7527 (mtpp) REVERT: I 306 GLN cc_start: 0.8423 (pt0) cc_final: 0.8120 (pp30) REVERT: I 314 GLU cc_start: 0.7446 (mt-10) cc_final: 0.7144 (mt-10) REVERT: I 315 GLN cc_start: 0.8105 (mt0) cc_final: 0.7478 (mp10) REVERT: I 362 TYR cc_start: 0.8618 (t80) cc_final: 0.8377 (t80) REVERT: I 383 LYS cc_start: 0.8277 (mtpp) cc_final: 0.8060 (mttp) REVERT: I 384 GLN cc_start: 0.8065 (tm-30) cc_final: 0.7844 (tm-30) REVERT: I 395 ILE cc_start: 0.9136 (tt) cc_final: 0.8905 (tp) REVERT: I 396 ASN cc_start: 0.8288 (m-40) cc_final: 0.7839 (m-40) REVERT: I 404 LEU cc_start: 0.9123 (tp) cc_final: 0.8866 (tp) outliers start: 159 outliers final: 91 residues processed: 1327 average time/residue: 0.4823 time to fit residues: 972.5801 Evaluate side-chains 1316 residues out of total 3232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 1206 time to evaluate : 3.063 ------------------------------------------------------------------------------- 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 219 ILE 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 303 LEU Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain B residue 117 GLN Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 315 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 155 ILE Chi-restraints excluded: chain C residue 187 MET Chi-restraints excluded: chain C residue 231 VAL 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 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 344 SER Chi-restraints excluded: chain D residue 84 LYS Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 169 SER 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 167 VAL 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 371 GLU Chi-restraints excluded: chain E residue 373 SER Chi-restraints excluded: chain E residue 386 LYS Chi-restraints excluded: chain F residue 98 ARG 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 237 ILE Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 288 LYS Chi-restraints excluded: chain F residue 332 GLN Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain F residue 354 VAL 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 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 290 LEU Chi-restraints excluded: chain J residue 293 GLN Chi-restraints excluded: chain J residue 298 VAL Chi-restraints excluded: chain J residue 319 ILE Chi-restraints excluded: chain J residue 356 GLU Chi-restraints excluded: chain J residue 371 GLN Chi-restraints excluded: chain J residue 408 LEU Chi-restraints excluded: chain J residue 450 LEU Chi-restraints excluded: chain G residue 11 ARG Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 141 THR 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 244 HIS Chi-restraints excluded: chain G residue 245 LEU Chi-restraints excluded: chain G residue 272 THR Chi-restraints excluded: chain G residue 398 LEU Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 17 LEU Chi-restraints excluded: chain H residue 19 LYS Chi-restraints excluded: chain H residue 30 LYS Chi-restraints excluded: chain H residue 35 ARG Chi-restraints excluded: chain H residue 135 ARG Chi-restraints excluded: chain H residue 138 ASP Chi-restraints excluded: chain H residue 221 LEU Chi-restraints excluded: chain H residue 286 LEU Chi-restraints excluded: chain H residue 306 GLN 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 49 THR Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 203 THR Chi-restraints excluded: chain I residue 223 LEU Chi-restraints excluded: chain I residue 259 THR Chi-restraints excluded: chain I residue 272 THR Chi-restraints excluded: chain I residue 328 ARG Chi-restraints excluded: chain I residue 398 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 72 optimal weight: 2.9990 chunk 221 optimal weight: 1.9990 chunk 295 optimal weight: 2.9990 chunk 346 optimal weight: 9.9990 chunk 199 optimal weight: 1.9990 chunk 176 optimal weight: 2.9990 chunk 183 optimal weight: 0.6980 chunk 334 optimal weight: 3.9990 chunk 300 optimal weight: 2.9990 chunk 358 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 GLN A 124 GLN A 126 GLN A 144 ASN A 265 ASN ** B 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 349 ASN C 265 ASN ** D 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 200 GLN D 257 ASN D 306 GLN D 353 GLN E 63 GLN ** E 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 162 HIS F 208 ASN F 251 ASN F 306 GLN F 346 ASN J 34 ASN J 269 ASN J 457 GLN ** G 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 58 ASN I 188 ASN I 320 HIS Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.110975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.092806 restraints weight = 58979.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.095780 restraints weight = 26159.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.097646 restraints weight = 14200.216| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.5873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.086 30315 Z= 0.363 Angle : 0.752 11.601 41246 Z= 0.411 Chirality : 0.049 0.242 4889 Planarity : 0.006 0.082 5392 Dihedral : 4.764 24.146 4179 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 5.60 % Allowed : 20.30 % Favored : 74.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.13), residues: 3860 helix: 2.31 (0.11), residues: 2023 sheet: -0.44 (0.22), residues: 501 loop : -1.24 (0.16), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.003 TRP C 312 HIS 0.029 0.002 HIS F 162 PHE 0.023 0.002 PHE B 258 TYR 0.025 0.002 TYR D 56 ARG 0.010 0.001 ARG G 24 Details of bonding type rmsd hydrogen bonds : bond 0.07811 ( 1888) hydrogen bonds : angle 4.88481 ( 5523) covalent geometry : bond 0.00752 (30315) covalent geometry : angle 0.75154 (41246) *********************** 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 1470 residues out of total 3232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 181 poor density : 1289 time to evaluate : 3.166 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 49 PHE cc_start: 0.7122 (m-80) cc_final: 0.6616 (m-80) REVERT: A 50 GLU cc_start: 0.6956 (mm-30) cc_final: 0.6540 (mm-30) REVERT: A 56 TYR cc_start: 0.7607 (m-80) cc_final: 0.6605 (m-80) REVERT: A 57 VAL cc_start: 0.8537 (t) cc_final: 0.8257 (p) REVERT: A 79 ASN cc_start: 0.7855 (t0) cc_final: 0.7641 (t0) REVERT: A 126 GLN cc_start: 0.7672 (mm-40) cc_final: 0.7424 (tp-100) REVERT: A 143 TYR cc_start: 0.8282 (t80) cc_final: 0.7983 (t80) REVERT: A 158 GLU cc_start: 0.7792 (mm-30) cc_final: 0.7059 (tm-30) REVERT: A 173 GLN cc_start: 0.7891 (mm-40) cc_final: 0.7655 (mm-40) REVERT: A 175 ASP cc_start: 0.6941 (OUTLIER) cc_final: 0.6455 (m-30) REVERT: A 189 LEU cc_start: 0.8464 (mt) cc_final: 0.8248 (mt) REVERT: A 247 VAL cc_start: 0.8764 (t) cc_final: 0.8455 (m) REVERT: A 259 LYS cc_start: 0.8255 (mtmm) cc_final: 0.7906 (mtmm) REVERT: A 284 LYS cc_start: 0.7489 (mtpp) cc_final: 0.7234 (mtpp) REVERT: A 293 ASP cc_start: 0.7540 (t0) cc_final: 0.7313 (t0) REVERT: A 306 GLN cc_start: 0.7010 (tp-100) cc_final: 0.6788 (tp-100) REVERT: A 324 GLU cc_start: 0.6308 (tp30) cc_final: 0.5904 (tp30) REVERT: A 347 THR cc_start: 0.7352 (OUTLIER) cc_final: 0.6821 (p) REVERT: A 371 GLU cc_start: 0.7400 (pm20) cc_final: 0.7031 (pm20) REVERT: A 379 LYS cc_start: 0.7970 (tttt) cc_final: 0.7737 (tttt) REVERT: A 381 ILE cc_start: 0.8609 (mt) cc_final: 0.8338 (mt) REVERT: B 50 GLU cc_start: 0.7419 (mm-30) cc_final: 0.7099 (mm-30) REVERT: B 54 ASP cc_start: 0.7291 (t70) cc_final: 0.7074 (t70) REVERT: B 93 ASP cc_start: 0.7970 (t0) cc_final: 0.7683 (t70) REVERT: B 98 ARG cc_start: 0.7433 (tpp80) cc_final: 0.7175 (ttm-80) REVERT: B 117 GLN cc_start: 0.7623 (OUTLIER) cc_final: 0.7213 (tt0) REVERT: B 123 LYS cc_start: 0.7573 (mttp) cc_final: 0.7139 (mttp) REVERT: B 130 GLU cc_start: 0.7222 (mm-30) cc_final: 0.6829 (tm-30) REVERT: B 138 LYS cc_start: 0.8632 (ttpp) cc_final: 0.8263 (ttpp) REVERT: B 145 ARG cc_start: 0.8132 (mtt-85) cc_final: 0.7801 (mmm-85) REVERT: B 146 ARG cc_start: 0.7853 (tpp80) cc_final: 0.7632 (mpp80) REVERT: B 157 ARG cc_start: 0.6795 (mtp-110) cc_final: 0.6533 (mtp-110) REVERT: B 160 LEU cc_start: 0.8969 (tp) cc_final: 0.8741 (tt) REVERT: B 161 GLN cc_start: 0.8116 (tp40) cc_final: 0.7806 (mm-40) REVERT: B 162 HIS cc_start: 0.7884 (m-70) cc_final: 0.7628 (m90) REVERT: B 165 ASP cc_start: 0.7070 (m-30) cc_final: 0.6849 (m-30) REVERT: B 171 GLN cc_start: 0.8124 (tp-100) cc_final: 0.7865 (tp40) REVERT: B 259 LYS cc_start: 0.7927 (mtmt) cc_final: 0.7593 (mtmt) REVERT: B 284 LYS cc_start: 0.8025 (mtpt) cc_final: 0.7726 (mtpt) REVERT: B 319 LEU cc_start: 0.8021 (tp) cc_final: 0.7815 (tt) REVERT: B 328 LYS cc_start: 0.8280 (mmpt) cc_final: 0.7767 (mmpt) REVERT: B 330 LEU cc_start: 0.8244 (tt) cc_final: 0.7896 (tp) REVERT: B 371 GLU cc_start: 0.7063 (mt-10) cc_final: 0.6792 (mt-10) REVERT: B 386 LYS cc_start: 0.8333 (tttt) cc_final: 0.7983 (tttt) REVERT: C 53 ASP cc_start: 0.6875 (t0) cc_final: 0.6628 (t0) REVERT: C 54 ASP cc_start: 0.7517 (t0) cc_final: 0.7093 (t0) REVERT: C 103 LYS cc_start: 0.7986 (tttt) cc_final: 0.7563 (ttmm) REVERT: C 117 GLN cc_start: 0.7473 (mt0) cc_final: 0.6799 (mt0) REVERT: C 121 ASN cc_start: 0.7244 (m-40) cc_final: 0.6784 (m-40) REVERT: C 142 ASP cc_start: 0.7672 (t70) cc_final: 0.6638 (t0) REVERT: C 146 ARG cc_start: 0.8459 (mmt-90) cc_final: 0.7756 (mmt-90) REVERT: C 179 GLN cc_start: 0.8249 (mm-40) cc_final: 0.7993 (mm-40) REVERT: C 200 GLN cc_start: 0.6989 (mt0) cc_final: 0.6542 (mt0) REVERT: C 231 VAL cc_start: 0.8453 (OUTLIER) cc_final: 0.8252 (p) REVERT: C 265 ASN cc_start: 0.8112 (OUTLIER) cc_final: 0.7724 (t0) REVERT: C 272 VAL cc_start: 0.7995 (t) cc_final: 0.7795 (p) REVERT: C 274 ILE cc_start: 0.8485 (mt) cc_final: 0.8189 (mp) REVERT: C 284 LYS cc_start: 0.8350 (mmmt) cc_final: 0.7873 (mtmt) REVERT: C 296 THR cc_start: 0.7514 (p) cc_final: 0.7060 (t) REVERT: C 302 LEU cc_start: 0.8553 (tp) cc_final: 0.8303 (tp) REVERT: C 353 GLN cc_start: 0.5871 (tm-30) cc_final: 0.5641 (tm-30) REVERT: C 355 LEU cc_start: 0.8634 (mt) cc_final: 0.8429 (mt) REVERT: C 384 ILE cc_start: 0.8431 (tp) cc_final: 0.8186 (tp) REVERT: D 50 GLU cc_start: 0.6837 (OUTLIER) cc_final: 0.6402 (tp30) REVERT: D 54 ASP cc_start: 0.6864 (t0) cc_final: 0.6308 (t0) REVERT: D 73 THR cc_start: 0.8534 (m) cc_final: 0.8265 (m) REVERT: D 110 SER cc_start: 0.8503 (t) cc_final: 0.8269 (m) REVERT: D 117 GLN cc_start: 0.7996 (tt0) cc_final: 0.7404 (tt0) REVERT: D 120 ILE cc_start: 0.8307 (mm) cc_final: 0.8079 (mt) REVERT: D 121 ASN cc_start: 0.7998 (m-40) cc_final: 0.7573 (m-40) REVERT: D 129 ILE cc_start: 0.8342 (mt) cc_final: 0.8086 (mm) REVERT: D 138 LYS cc_start: 0.8110 (tttt) cc_final: 0.7775 (tttt) REVERT: D 154 LEU cc_start: 0.7289 (mp) cc_final: 0.6794 (mp) REVERT: D 157 ARG cc_start: 0.7477 (mtm110) cc_final: 0.7242 (mtm110) REVERT: D 247 VAL cc_start: 0.8910 (t) cc_final: 0.8591 (m) REVERT: D 259 LYS cc_start: 0.8211 (mttt) cc_final: 0.7906 (mttm) REVERT: D 319 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8537 (tp) REVERT: D 324 GLU cc_start: 0.6828 (tm-30) cc_final: 0.6508 (tm-30) REVERT: D 327 GLN cc_start: 0.7886 (mm-40) cc_final: 0.7611 (mm-40) REVERT: D 331 GLU cc_start: 0.7033 (mp0) cc_final: 0.6644 (mp0) REVERT: D 332 GLN cc_start: 0.7454 (tp40) cc_final: 0.6999 (tp40) REVERT: D 366 VAL cc_start: 0.8712 (t) cc_final: 0.8472 (p) REVERT: D 378 ASN cc_start: 0.7996 (m-40) cc_final: 0.7220 (m-40) REVERT: D 382 ASP cc_start: 0.7321 (m-30) cc_final: 0.6965 (m-30) REVERT: E 53 ASP cc_start: 0.7170 (t0) cc_final: 0.6897 (t0) REVERT: E 61 GLN cc_start: 0.7643 (mp10) cc_final: 0.7253 (mp10) REVERT: E 65 MET cc_start: 0.7161 (mmm) cc_final: 0.6926 (mmm) REVERT: E 71 SER cc_start: 0.7801 (p) cc_final: 0.7476 (t) REVERT: E 85 GLU cc_start: 0.6936 (mm-30) cc_final: 0.6552 (tm-30) REVERT: E 125 LEU cc_start: 0.8180 (mt) cc_final: 0.7957 (mt) REVERT: E 142 ASP cc_start: 0.7393 (m-30) cc_final: 0.6986 (m-30) REVERT: E 153 ASN cc_start: 0.7615 (t0) cc_final: 0.7035 (p0) REVERT: E 154 LEU cc_start: 0.7704 (pp) cc_final: 0.7210 (mt) REVERT: E 160 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8379 (mt) REVERT: E 161 GLN cc_start: 0.7695 (tt0) cc_final: 0.7009 (tp-100) REVERT: E 165 ASP cc_start: 0.7467 (m-30) cc_final: 0.6836 (m-30) REVERT: E 168 THR cc_start: 0.8072 (m) cc_final: 0.7862 (p) REVERT: E 179 GLN cc_start: 0.8105 (mm-40) cc_final: 0.7681 (mm-40) REVERT: E 181 TYR cc_start: 0.8232 (t80) cc_final: 0.7987 (t80) REVERT: E 196 GLN cc_start: 0.7867 (OUTLIER) cc_final: 0.7143 (mp10) REVERT: E 210 TRP cc_start: 0.8411 (t60) cc_final: 0.8116 (t60) REVERT: E 211 LEU cc_start: 0.8371 (mt) cc_final: 0.8142 (mt) REVERT: E 251 ASN cc_start: 0.7274 (t0) cc_final: 0.6884 (t0) REVERT: E 252 MET cc_start: 0.7750 (mmm) cc_final: 0.7431 (mtt) REVERT: E 283 VAL cc_start: 0.8468 (t) cc_final: 0.8071 (m) REVERT: E 294 MET cc_start: 0.6788 (mmm) cc_final: 0.6373 (tpp) REVERT: E 312 TRP cc_start: 0.8248 (t60) cc_final: 0.7907 (t60) REVERT: E 346 ASN cc_start: 0.7948 (m-40) cc_final: 0.7707 (m-40) REVERT: F 105 LYS cc_start: 0.8192 (mttt) cc_final: 0.7865 (mtmm) REVERT: F 120 ILE cc_start: 0.8400 (OUTLIER) cc_final: 0.8198 (mp) REVERT: F 122 SER cc_start: 0.8483 (m) cc_final: 0.8168 (p) REVERT: F 133 LYS cc_start: 0.7978 (mttt) cc_final: 0.7773 (mttt) REVERT: F 138 LYS cc_start: 0.8447 (ttpt) cc_final: 0.8211 (ttpp) REVERT: F 140 GLN cc_start: 0.7982 (mt0) cc_final: 0.7631 (mt0) REVERT: F 141 SER cc_start: 0.8562 (m) cc_final: 0.8135 (t) REVERT: F 158 GLU cc_start: 0.7220 (tp30) cc_final: 0.6549 (tp30) REVERT: F 161 GLN cc_start: 0.7498 (tp40) cc_final: 0.6352 (tp-100) REVERT: F 162 HIS cc_start: 0.7874 (OUTLIER) cc_final: 0.7209 (m-70) REVERT: F 164 ARG cc_start: 0.7690 (ttm-80) cc_final: 0.7392 (ttm-80) REVERT: F 192 LYS cc_start: 0.8077 (mttp) cc_final: 0.7686 (mttp) REVERT: F 200 GLN cc_start: 0.7245 (mp10) cc_final: 0.6563 (mp10) REVERT: F 214 GLU cc_start: 0.7624 (tp30) cc_final: 0.6863 (mp0) REVERT: F 217 ARG cc_start: 0.6714 (ttm110) cc_final: 0.6489 (ttm110) REVERT: F 284 LYS cc_start: 0.7888 (mmtp) cc_final: 0.7657 (mmtp) REVERT: F 288 LYS cc_start: 0.8348 (OUTLIER) cc_final: 0.7865 (mtmt) REVERT: F 293 ASP cc_start: 0.7273 (t70) cc_final: 0.7067 (t70) REVERT: F 317 GLN cc_start: 0.7450 (mm-40) cc_final: 0.7088 (mp10) REVERT: F 332 GLN cc_start: 0.7514 (OUTLIER) cc_final: 0.7225 (mp10) REVERT: F 337 ILE cc_start: 0.8025 (OUTLIER) cc_final: 0.7823 (mp) REVERT: F 372 ILE cc_start: 0.8611 (OUTLIER) cc_final: 0.8372 (mm) REVERT: F 379 LYS cc_start: 0.7698 (tptm) cc_final: 0.7177 (tptm) REVERT: F 382 ASP cc_start: 0.7783 (OUTLIER) cc_final: 0.7558 (m-30) REVERT: F 383 ASP cc_start: 0.7105 (m-30) cc_final: 0.6690 (m-30) REVERT: J 25 MET cc_start: 0.7545 (ptm) cc_final: 0.7343 (ptm) REVERT: J 40 ILE cc_start: 0.8265 (mt) cc_final: 0.7874 (pt) REVERT: J 66 ILE cc_start: 0.8640 (mm) cc_final: 0.8276 (mm) REVERT: J 87 ILE cc_start: 0.8724 (tt) cc_final: 0.8425 (pt) REVERT: J 110 VAL cc_start: 0.7658 (m) cc_final: 0.7224 (p) REVERT: J 114 ILE cc_start: 0.8273 (mm) cc_final: 0.8060 (mm) REVERT: J 122 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.7822 (mp) REVERT: J 131 TYR cc_start: 0.7358 (OUTLIER) cc_final: 0.6908 (t80) REVERT: J 136 ARG cc_start: 0.7372 (ttt-90) cc_final: 0.7171 (ttt-90) REVERT: J 145 MET cc_start: 0.6816 (tmm) cc_final: 0.6224 (tmm) REVERT: J 161 ILE cc_start: 0.8324 (mm) cc_final: 0.7958 (mp) REVERT: J 184 MET cc_start: 0.7673 (mtm) cc_final: 0.7464 (mtm) REVERT: J 213 ILE cc_start: 0.8302 (OUTLIER) cc_final: 0.8003 (mt) REVERT: J 216 LEU cc_start: 0.8511 (tp) cc_final: 0.8200 (tt) REVERT: J 217 GLN cc_start: 0.7871 (tp40) cc_final: 0.7535 (tp40) REVERT: J 264 LEU cc_start: 0.7550 (mt) cc_final: 0.7341 (mt) REVERT: J 268 ARG cc_start: 0.7933 (ttt90) cc_final: 0.7474 (mmm-85) REVERT: J 271 THR cc_start: 0.8412 (m) cc_final: 0.8150 (p) REVERT: J 282 MET cc_start: 0.7907 (ttt) cc_final: 0.7572 (ttm) REVERT: J 297 GLU cc_start: 0.7362 (tt0) cc_final: 0.7107 (tt0) REVERT: J 308 LEU cc_start: 0.8018 (mt) cc_final: 0.7662 (mt) REVERT: J 327 PHE cc_start: 0.6777 (t80) cc_final: 0.5996 (t80) REVERT: J 334 ARG cc_start: 0.7860 (mtm180) cc_final: 0.7535 (mtm180) REVERT: J 339 PHE cc_start: 0.7979 (t80) cc_final: 0.7591 (t80) REVERT: J 342 ILE cc_start: 0.8380 (mm) cc_final: 0.8131 (tp) REVERT: J 395 LEU cc_start: 0.7941 (mt) cc_final: 0.7535 (mt) REVERT: J 403 ASN cc_start: 0.8460 (m-40) cc_final: 0.7794 (m-40) REVERT: J 406 ARG cc_start: 0.7432 (ttp80) cc_final: 0.7140 (ttp80) REVERT: J 408 LEU cc_start: 0.7625 (OUTLIER) cc_final: 0.7335 (tt) REVERT: J 447 TYR cc_start: 0.8516 (m-80) cc_final: 0.8238 (m-80) REVERT: J 458 GLN cc_start: 0.8367 (tt0) cc_final: 0.8008 (tt0) REVERT: J 467 GLN cc_start: 0.8129 (mm-40) cc_final: 0.7894 (mm110) REVERT: J 471 GLN cc_start: 0.7834 (mm-40) cc_final: 0.7294 (mm-40) REVERT: J 479 GLU cc_start: 0.7622 (mt-10) cc_final: 0.7420 (mt-10) REVERT: J 489 LEU cc_start: 0.8429 (mt) cc_final: 0.8164 (mt) REVERT: J 491 LEU cc_start: 0.7965 (mt) cc_final: 0.7649 (pp) REVERT: J 494 LEU cc_start: 0.8338 (pp) cc_final: 0.8138 (pp) REVERT: G 5 GLN cc_start: 0.8432 (mt0) cc_final: 0.7806 (mt0) REVERT: G 9 GLN cc_start: 0.7046 (tm-30) cc_final: 0.6644 (tm-30) REVERT: G 17 LEU cc_start: 0.8587 (mp) cc_final: 0.8118 (tt) REVERT: G 29 GLU cc_start: 0.7886 (tp30) cc_final: 0.6815 (tp30) REVERT: G 30 LYS cc_start: 0.8744 (tttt) cc_final: 0.8306 (tttt) REVERT: G 32 ASN cc_start: 0.8240 (m-40) cc_final: 0.6983 (p0) REVERT: G 42 LEU cc_start: 0.8401 (mp) cc_final: 0.8200 (mm) REVERT: G 76 PHE cc_start: 0.7367 (t80) cc_final: 0.7132 (t80) REVERT: G 77 ASP cc_start: 0.8733 (t0) cc_final: 0.5300 (p0) REVERT: G 87 GLN cc_start: 0.8503 (tp40) cc_final: 0.8206 (tp40) REVERT: G 103 GLN cc_start: 0.8328 (mt0) cc_final: 0.7929 (mm-40) REVERT: G 104 THR cc_start: 0.8729 (m) cc_final: 0.8474 (p) REVERT: G 130 LYS cc_start: 0.8778 (tttt) cc_final: 0.8113 (ttpp) REVERT: G 142 GLN cc_start: 0.7801 (mm-40) cc_final: 0.7258 (mm-40) REVERT: G 156 ASN cc_start: 0.8090 (t0) cc_final: 0.7713 (t0) REVERT: G 168 GLU cc_start: 0.8407 (tt0) cc_final: 0.8112 (tt0) REVERT: G 169 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8250 (mm) REVERT: G 181 GLN cc_start: 0.8435 (mm-40) cc_final: 0.7789 (tm-30) REVERT: G 215 GLU cc_start: 0.7641 (tm-30) cc_final: 0.6841 (tm-30) REVERT: G 217 GLU cc_start: 0.8064 (tm-30) cc_final: 0.7679 (mm-30) REVERT: G 230 GLN cc_start: 0.8540 (OUTLIER) cc_final: 0.7916 (pp30) REVERT: G 231 ASP cc_start: 0.8231 (m-30) cc_final: 0.7648 (m-30) REVERT: G 232 LEU cc_start: 0.9280 (tt) cc_final: 0.9040 (tt) REVERT: G 236 GLN cc_start: 0.8518 (mt0) cc_final: 0.8181 (mt0) REVERT: G 279 MET cc_start: 0.3878 (tpt) cc_final: 0.3412 (tpt) REVERT: G 297 MET cc_start: 0.7067 (ttt) cc_final: 0.6651 (ttm) REVERT: G 299 ASN cc_start: 0.8352 (m110) cc_final: 0.7966 (m-40) REVERT: G 301 GLN cc_start: 0.8043 (mp10) cc_final: 0.7734 (mp10) REVERT: G 303 LYS cc_start: 0.8713 (mtpp) cc_final: 0.7855 (mtpp) REVERT: G 307 TYR cc_start: 0.8022 (m-80) cc_final: 0.7646 (m-80) REVERT: G 314 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7465 (mm-30) REVERT: G 315 GLN cc_start: 0.8685 (tp40) cc_final: 0.8271 (tp-100) REVERT: G 317 GLU cc_start: 0.8042 (tp30) cc_final: 0.7210 (tp30) REVERT: G 321 ARG cc_start: 0.8476 (mtt180) cc_final: 0.8026 (mtt180) REVERT: G 344 TYR cc_start: 0.8157 (m-80) cc_final: 0.7917 (m-80) REVERT: G 401 LYS cc_start: 0.8575 (tptm) cc_final: 0.8198 (tppp) REVERT: G 411 ASP cc_start: 0.5755 (t0) cc_final: 0.5462 (t0) REVERT: H 9 GLN cc_start: 0.8659 (tp-100) cc_final: 0.8199 (tp40) REVERT: H 14 ASN cc_start: 0.8278 (t0) cc_final: 0.8043 (t0) REVERT: H 19 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.7925 (tttt) REVERT: H 25 ASP cc_start: 0.7982 (m-30) cc_final: 0.7595 (t0) REVERT: H 29 GLU cc_start: 0.7874 (tp30) cc_final: 0.7216 (tp30) REVERT: H 30 LYS cc_start: 0.8895 (ttpt) cc_final: 0.8140 (ttpt) REVERT: H 89 LYS cc_start: 0.8778 (mmmt) cc_final: 0.8254 (mmmt) REVERT: H 94 GLN cc_start: 0.8176 (tp40) cc_final: 0.7965 (tp40) REVERT: H 120 ILE cc_start: 0.8949 (mt) cc_final: 0.8677 (mm) REVERT: H 131 GLU cc_start: 0.8054 (tp30) cc_final: 0.7693 (tp30) REVERT: H 135 ARG cc_start: 0.8147 (ttm-80) cc_final: 0.7490 (mmm160) REVERT: H 138 ASP cc_start: 0.8039 (OUTLIER) cc_final: 0.6975 (t0) REVERT: H 142 GLN cc_start: 0.7930 (mm-40) cc_final: 0.7698 (mm-40) REVERT: H 143 ARG cc_start: 0.7655 (ttp-170) cc_final: 0.7381 (ttp-170) REVERT: H 162 ASP cc_start: 0.8233 (m-30) cc_final: 0.7949 (m-30) REVERT: H 173 ASN cc_start: 0.8504 (m-40) cc_final: 0.8220 (m-40) REVERT: H 179 VAL cc_start: 0.8964 (t) cc_final: 0.8691 (p) REVERT: H 180 GLU cc_start: 0.8553 (mm-30) cc_final: 0.8039 (tm-30) REVERT: H 181 GLN cc_start: 0.7973 (tm-30) cc_final: 0.7731 (tm-30) REVERT: H 184 GLN cc_start: 0.8464 (tt0) cc_final: 0.7612 (tp-100) REVERT: H 218 LYS cc_start: 0.8783 (mmtt) cc_final: 0.8463 (mmtt) REVERT: H 231 ASP cc_start: 0.7657 (t0) cc_final: 0.7345 (t70) REVERT: H 234 ARG cc_start: 0.7978 (mmm-85) cc_final: 0.7493 (mmm-85) REVERT: H 236 GLN cc_start: 0.7906 (pp30) cc_final: 0.7567 (pp30) REVERT: H 237 ILE cc_start: 0.8808 (mt) cc_final: 0.8283 (mt) REVERT: H 301 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.7958 (pm20) REVERT: H 303 LYS cc_start: 0.8455 (mttt) cc_final: 0.7938 (mttt) REVERT: H 317 GLU cc_start: 0.7703 (tp30) cc_final: 0.7213 (tp30) REVERT: H 321 ARG cc_start: 0.8413 (mtt180) cc_final: 0.7670 (mtt180) REVERT: H 331 PHE cc_start: 0.9078 (t80) cc_final: 0.8791 (t80) REVERT: H 340 SER cc_start: 0.8744 (m) cc_final: 0.8229 (p) REVERT: H 341 ILE cc_start: 0.8919 (OUTLIER) cc_final: 0.8684 (tt) REVERT: H 356 ASP cc_start: 0.8359 (t0) cc_final: 0.8155 (t0) REVERT: H 362 TYR cc_start: 0.8715 (t80) cc_final: 0.8418 (t80) REVERT: H 367 ARG cc_start: 0.8051 (tpp80) cc_final: 0.7662 (mtm-85) REVERT: H 374 ASP cc_start: 0.7918 (t0) cc_final: 0.7568 (t0) REVERT: H 390 ARG cc_start: 0.8655 (mtt-85) cc_final: 0.8440 (ttm170) REVERT: H 392 ASN cc_start: 0.8432 (m-40) cc_final: 0.7910 (t0) REVERT: H 396 ASN cc_start: 0.8225 (m-40) cc_final: 0.7757 (m110) REVERT: H 397 GLN cc_start: 0.8154 (tt0) cc_final: 0.7422 (tm-30) REVERT: I 16 GLU cc_start: 0.7989 (mp0) cc_final: 0.7531 (mp0) REVERT: I 19 LYS cc_start: 0.8456 (OUTLIER) cc_final: 0.8231 (tttt) REVERT: I 28 PHE cc_start: 0.8300 (m-80) cc_final: 0.7939 (m-80) REVERT: I 29 GLU cc_start: 0.7882 (tp30) cc_final: 0.7016 (tp30) REVERT: I 32 ASN cc_start: 0.8656 (m-40) cc_final: 0.7943 (m110) REVERT: I 42 LEU cc_start: 0.7575 (tt) cc_final: 0.7365 (tp) REVERT: I 76 PHE cc_start: 0.7715 (t80) cc_final: 0.6959 (t80) REVERT: I 86 LEU cc_start: 0.8971 (pp) cc_final: 0.8702 (mp) REVERT: I 89 LYS cc_start: 0.8539 (mmtp) cc_final: 0.8306 (mmtp) REVERT: I 95 ASP cc_start: 0.8281 (t0) cc_final: 0.7285 (t0) REVERT: I 99 GLN cc_start: 0.8370 (mt0) cc_final: 0.7859 (mt0) REVERT: I 124 SER cc_start: 0.8634 (t) cc_final: 0.8412 (p) REVERT: I 135 ARG cc_start: 0.8166 (tpp-160) cc_final: 0.7791 (tpp-160) REVERT: I 143 ARG cc_start: 0.7790 (ttm110) cc_final: 0.7427 (ttm110) REVERT: I 215 GLU cc_start: 0.8170 (tp30) cc_final: 0.7636 (tp30) REVERT: I 223 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8558 (mm) REVERT: I 224 LEU cc_start: 0.8922 (tp) cc_final: 0.7874 (mm) REVERT: I 225 GLN cc_start: 0.8035 (tm-30) cc_final: 0.7408 (tm-30) REVERT: I 227 ARG cc_start: 0.7816 (mtm-85) cc_final: 0.7261 (mtm-85) REVERT: I 230 GLN cc_start: 0.8035 (tm-30) cc_final: 0.7750 (tm-30) REVERT: I 236 GLN cc_start: 0.8436 (mt0) cc_final: 0.7931 (mt0) REVERT: I 238 ARG cc_start: 0.8219 (mpt180) cc_final: 0.7977 (mpt180) REVERT: I 259 THR cc_start: 0.3738 (OUTLIER) cc_final: 0.3523 (m) REVERT: I 297 MET cc_start: 0.6708 (tmm) cc_final: 0.6342 (tmm) REVERT: I 301 GLN cc_start: 0.8468 (tt0) cc_final: 0.7839 (mt0) REVERT: I 314 GLU cc_start: 0.7492 (mt-10) cc_final: 0.7093 (mt-10) REVERT: I 396 ASN cc_start: 0.8296 (m-40) cc_final: 0.7798 (m-40) outliers start: 181 outliers final: 111 residues processed: 1370 average time/residue: 0.4811 time to fit residues: 1000.2986 Evaluate side-chains 1387 residues out of total 3232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 1247 time to evaluate : 3.138 ------------------------------------------------------------------------------- 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 93 ASP 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 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 277 ASP Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 326 ASP 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 117 GLN Chi-restraints excluded: chain B residue 140 GLN Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 272 VAL 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 335 LEU Chi-restraints excluded: chain B residue 344 SER Chi-restraints excluded: chain B residue 348 THR 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 187 MET Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 265 ASN 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 330 LEU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 340 SER Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain D residue 84 LYS Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 167 VAL 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 319 LEU 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 103 LYS Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 160 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 325 LEU Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 342 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 313 ILE Chi-restraints excluded: chain F residue 332 GLN Chi-restraints excluded: chain F residue 337 ILE Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain F residue 372 ILE Chi-restraints excluded: chain F residue 382 ASP 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 52 THR 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 213 ILE Chi-restraints excluded: chain J residue 253 LEU Chi-restraints excluded: chain J residue 290 LEU Chi-restraints excluded: chain J residue 293 GLN Chi-restraints excluded: chain J residue 298 VAL Chi-restraints excluded: chain J residue 408 LEU Chi-restraints excluded: chain J residue 448 SER Chi-restraints excluded: chain G residue 11 ARG Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 69 LEU 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 245 LEU Chi-restraints excluded: chain G residue 272 THR Chi-restraints excluded: chain H residue 19 LYS Chi-restraints excluded: chain H residue 138 ASP Chi-restraints excluded: chain H residue 163 THR Chi-restraints excluded: chain H residue 168 GLU Chi-restraints excluded: chain H residue 221 LEU Chi-restraints excluded: chain H residue 286 LEU Chi-restraints excluded: chain H residue 301 GLN Chi-restraints excluded: chain H residue 320 HIS 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 12 LEU Chi-restraints excluded: chain I residue 19 LYS Chi-restraints excluded: chain I residue 58 ASN Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 203 THR Chi-restraints excluded: chain I residue 223 LEU Chi-restraints excluded: chain I residue 244 HIS Chi-restraints excluded: chain I residue 250 LEU 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 302 VAL Chi-restraints excluded: chain I residue 398 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 230 optimal weight: 0.7980 chunk 160 optimal weight: 0.0970 chunk 259 optimal weight: 0.9980 chunk 134 optimal weight: 1.9990 chunk 326 optimal weight: 8.9990 chunk 336 optimal weight: 3.9990 chunk 137 optimal weight: 1.9990 chunk 379 optimal weight: 3.9990 chunk 348 optimal weight: 3.9990 chunk 185 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN B 144 ASN B 173 GLN ** B 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 251 ASN C 265 ASN D 184 ASN D 306 GLN E 185 GLN ** E 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 251 ASN F 306 GLN F 327 GLN F 346 ASN J 34 ASN ** J 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 478 ASN ** G 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 220 ASN ** H 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 320 HIS ** I 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.112891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.095097 restraints weight = 58887.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.098067 restraints weight = 25862.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.099908 restraints weight = 13916.471| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.6104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 30315 Z= 0.194 Angle : 0.643 11.001 41246 Z= 0.339 Chirality : 0.043 0.207 4889 Planarity : 0.005 0.075 5392 Dihedral : 4.338 22.177 4179 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 5.01 % Allowed : 23.36 % Favored : 71.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.14), residues: 3860 helix: 2.78 (0.11), residues: 2017 sheet: -0.33 (0.22), residues: 500 loop : -1.15 (0.16), residues: 1343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 312 HIS 0.008 0.001 HIS H 320 PHE 0.025 0.002 PHE H 309 TYR 0.024 0.002 TYR D 143 ARG 0.007 0.001 ARG G 24 Details of bonding type rmsd hydrogen bonds : bond 0.06882 ( 1888) hydrogen bonds : angle 4.47463 ( 5523) covalent geometry : bond 0.00407 (30315) covalent geometry : angle 0.64296 (41246) *********************** 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 1454 residues out of total 3232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 1292 time to evaluate : 3.236 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: A 49 PHE cc_start: 0.7158 (m-80) cc_final: 0.6745 (m-80) REVERT: A 50 GLU cc_start: 0.6960 (mm-30) cc_final: 0.6742 (mm-30) REVERT: A 56 TYR cc_start: 0.7485 (m-80) cc_final: 0.6432 (m-80) REVERT: A 79 ASN cc_start: 0.7714 (t0) cc_final: 0.7393 (t0) REVERT: A 138 LYS cc_start: 0.8276 (mttt) cc_final: 0.7857 (tttm) REVERT: A 143 TYR cc_start: 0.8224 (t80) cc_final: 0.7828 (t80) REVERT: A 158 GLU cc_start: 0.7591 (mm-30) cc_final: 0.6851 (tm-30) REVERT: A 162 HIS cc_start: 0.8107 (m-70) cc_final: 0.7236 (m-70) REVERT: A 173 GLN cc_start: 0.7856 (mm-40) cc_final: 0.7589 (mm110) REVERT: A 175 ASP cc_start: 0.6878 (OUTLIER) cc_final: 0.6394 (m-30) REVERT: A 189 LEU cc_start: 0.8427 (mt) cc_final: 0.8219 (mt) REVERT: A 200 GLN cc_start: 0.7601 (mt0) cc_final: 0.7357 (mm-40) REVERT: A 225 TYR cc_start: 0.7951 (m-80) cc_final: 0.7472 (m-80) REVERT: A 247 VAL cc_start: 0.8756 (t) cc_final: 0.8521 (m) REVERT: A 259 LYS cc_start: 0.8236 (mtmm) cc_final: 0.7860 (mtmm) REVERT: A 284 LYS cc_start: 0.7454 (mtpp) cc_final: 0.7153 (mtpp) REVERT: A 306 GLN cc_start: 0.6921 (tp-100) cc_final: 0.6422 (tp-100) REVERT: A 324 GLU cc_start: 0.6280 (tp30) cc_final: 0.5986 (tp30) REVERT: A 347 THR cc_start: 0.7394 (OUTLIER) cc_final: 0.6850 (p) REVERT: A 371 GLU cc_start: 0.7369 (pm20) cc_final: 0.6844 (pm20) REVERT: A 379 LYS cc_start: 0.7929 (tttt) cc_final: 0.7696 (tttt) REVERT: A 381 ILE cc_start: 0.8602 (mt) cc_final: 0.8280 (mt) REVERT: B 50 GLU cc_start: 0.7404 (mm-30) cc_final: 0.7044 (mm-30) REVERT: B 54 ASP cc_start: 0.7567 (t70) cc_final: 0.7329 (t70) REVERT: B 93 ASP cc_start: 0.7921 (t0) cc_final: 0.7591 (t70) REVERT: B 98 ARG cc_start: 0.7261 (tpp80) cc_final: 0.7004 (ttm-80) REVERT: B 117 GLN cc_start: 0.7565 (OUTLIER) cc_final: 0.7093 (tt0) REVERT: B 123 LYS cc_start: 0.7547 (mttp) cc_final: 0.6945 (mttp) REVERT: B 130 GLU cc_start: 0.7229 (mm-30) cc_final: 0.6714 (tm-30) REVERT: B 134 ILE cc_start: 0.8445 (mt) cc_final: 0.8154 (mp) REVERT: B 138 LYS cc_start: 0.8646 (ttpp) cc_final: 0.8245 (ttpp) REVERT: B 146 ARG cc_start: 0.7832 (tpp80) cc_final: 0.7474 (mpp80) REVERT: B 160 LEU cc_start: 0.8923 (tp) cc_final: 0.8682 (tt) REVERT: B 161 GLN cc_start: 0.7959 (tp40) cc_final: 0.7531 (mm-40) REVERT: B 162 HIS cc_start: 0.7832 (m-70) cc_final: 0.7578 (m90) REVERT: B 165 ASP cc_start: 0.6976 (m-30) cc_final: 0.6690 (m-30) REVERT: B 171 GLN cc_start: 0.8080 (tp-100) cc_final: 0.7790 (tp40) REVERT: B 184 ASN cc_start: 0.8031 (t0) cc_final: 0.7759 (t0) REVERT: B 259 LYS cc_start: 0.7919 (mtmt) cc_final: 0.7619 (mtmt) REVERT: B 284 LYS cc_start: 0.7808 (mtpt) cc_final: 0.7575 (mtpt) REVERT: B 303 LEU cc_start: 0.8011 (mt) cc_final: 0.7797 (mp) REVERT: B 318 ARG cc_start: 0.8157 (ptp-110) cc_final: 0.7870 (ptp90) REVERT: B 328 LYS cc_start: 0.8226 (mmpt) cc_final: 0.7723 (mmpt) REVERT: B 330 LEU cc_start: 0.8282 (tt) cc_final: 0.7905 (tp) REVERT: B 332 GLN cc_start: 0.7572 (mm-40) cc_final: 0.6917 (tp40) REVERT: B 386 LYS cc_start: 0.8239 (tttt) cc_final: 0.7891 (tttt) REVERT: C 53 ASP cc_start: 0.6804 (t0) cc_final: 0.6564 (t0) REVERT: C 54 ASP cc_start: 0.7465 (t0) cc_final: 0.7078 (t0) REVERT: C 103 LYS cc_start: 0.8006 (tttt) cc_final: 0.7600 (ttmm) REVERT: C 117 GLN cc_start: 0.7400 (mt0) cc_final: 0.6898 (mt0) REVERT: C 121 ASN cc_start: 0.7235 (m-40) cc_final: 0.6833 (m-40) REVERT: C 142 ASP cc_start: 0.7594 (OUTLIER) cc_final: 0.7380 (t0) REVERT: C 179 GLN cc_start: 0.8234 (mm-40) cc_final: 0.7968 (mm-40) REVERT: C 200 GLN cc_start: 0.6956 (mt0) cc_final: 0.6489 (mt0) REVERT: C 231 VAL cc_start: 0.8346 (OUTLIER) cc_final: 0.8052 (p) REVERT: C 259 LYS cc_start: 0.7797 (mtmm) cc_final: 0.7520 (mttm) REVERT: C 265 ASN cc_start: 0.8213 (OUTLIER) cc_final: 0.7858 (t0) REVERT: C 274 ILE cc_start: 0.8523 (mt) cc_final: 0.8194 (mp) REVERT: C 284 LYS cc_start: 0.8344 (mmmt) cc_final: 0.7910 (mtmt) REVERT: C 296 THR cc_start: 0.7458 (p) cc_final: 0.7013 (t) REVERT: C 302 LEU cc_start: 0.8556 (tp) cc_final: 0.8234 (tt) REVERT: C 379 LYS cc_start: 0.7751 (ttmt) cc_final: 0.7491 (ttmt) REVERT: D 50 GLU cc_start: 0.6781 (OUTLIER) cc_final: 0.6369 (tp30) REVERT: D 54 ASP cc_start: 0.6902 (t0) cc_final: 0.6205 (t0) REVERT: D 73 THR cc_start: 0.8576 (m) cc_final: 0.8305 (m) REVERT: D 110 SER cc_start: 0.8532 (t) cc_final: 0.8306 (m) REVERT: D 117 GLN cc_start: 0.7877 (tt0) cc_final: 0.7118 (tt0) REVERT: D 120 ILE cc_start: 0.8319 (mm) cc_final: 0.8105 (mp) REVERT: D 121 ASN cc_start: 0.7905 (m-40) cc_final: 0.7453 (m-40) REVERT: D 129 ILE cc_start: 0.8324 (mt) cc_final: 0.8054 (mm) REVERT: D 138 LYS cc_start: 0.8021 (tttt) cc_final: 0.7424 (tttt) REVERT: D 142 ASP cc_start: 0.6937 (m-30) cc_final: 0.6692 (m-30) REVERT: D 147 VAL cc_start: 0.8834 (t) cc_final: 0.8614 (t) REVERT: D 157 ARG cc_start: 0.7484 (mtm110) cc_final: 0.7163 (mtm110) REVERT: D 247 VAL cc_start: 0.8881 (t) cc_final: 0.8545 (m) REVERT: D 327 GLN cc_start: 0.7900 (mm-40) cc_final: 0.7547 (mm110) REVERT: D 331 GLU cc_start: 0.7045 (mp0) cc_final: 0.6564 (mp0) REVERT: D 332 GLN cc_start: 0.7448 (tp40) cc_final: 0.6856 (tp40) REVERT: D 333 TYR cc_start: 0.7607 (m-80) cc_final: 0.6977 (m-80) REVERT: D 366 VAL cc_start: 0.8638 (t) cc_final: 0.8412 (p) REVERT: D 378 ASN cc_start: 0.7867 (m-40) cc_final: 0.7036 (m-40) REVERT: D 382 ASP cc_start: 0.7310 (m-30) cc_final: 0.6769 (m-30) REVERT: D 385 VAL cc_start: 0.8499 (t) cc_final: 0.8162 (p) REVERT: E 53 ASP cc_start: 0.7100 (t0) cc_final: 0.6865 (t0) REVERT: E 61 GLN cc_start: 0.7612 (mp10) cc_final: 0.7192 (mp10) REVERT: E 65 MET cc_start: 0.7150 (mmm) cc_final: 0.6883 (mmm) REVERT: E 71 SER cc_start: 0.7777 (p) cc_final: 0.7241 (t) REVERT: E 85 GLU cc_start: 0.6911 (OUTLIER) cc_final: 0.6555 (tm-30) REVERT: E 142 ASP cc_start: 0.7392 (m-30) cc_final: 0.7003 (m-30) REVERT: E 153 ASN cc_start: 0.7580 (t0) cc_final: 0.7011 (p0) REVERT: E 154 LEU cc_start: 0.7635 (pp) cc_final: 0.7195 (mt) REVERT: E 165 ASP cc_start: 0.7527 (m-30) cc_final: 0.7205 (m-30) REVERT: E 168 THR cc_start: 0.8027 (m) cc_final: 0.7810 (p) REVERT: E 178 ILE cc_start: 0.8056 (mt) cc_final: 0.7825 (mm) REVERT: E 181 TYR cc_start: 0.8304 (t80) cc_final: 0.7968 (t80) REVERT: E 192 LYS cc_start: 0.7623 (mmmm) cc_final: 0.7132 (mmmm) REVERT: E 196 GLN cc_start: 0.7832 (OUTLIER) cc_final: 0.7127 (mp10) REVERT: E 200 GLN cc_start: 0.7432 (mm-40) cc_final: 0.7013 (mt0) REVERT: E 210 TRP cc_start: 0.8375 (t60) cc_final: 0.8053 (t60) REVERT: E 211 LEU cc_start: 0.8350 (mt) cc_final: 0.8120 (mt) REVERT: E 236 GLN cc_start: 0.7336 (mm-40) cc_final: 0.6854 (tp40) REVERT: E 251 ASN cc_start: 0.7215 (t0) cc_final: 0.6827 (t0) REVERT: E 252 MET cc_start: 0.7710 (mmm) cc_final: 0.7430 (mtt) REVERT: E 283 VAL cc_start: 0.8472 (t) cc_final: 0.8066 (m) REVERT: E 294 MET cc_start: 0.6665 (mmm) cc_final: 0.6264 (mmm) REVERT: E 306 GLN cc_start: 0.7021 (mp10) cc_final: 0.6698 (mp10) REVERT: E 346 ASN cc_start: 0.7897 (m-40) cc_final: 0.7647 (m-40) REVERT: F 50 GLU cc_start: 0.7812 (mm-30) cc_final: 0.7574 (mm-30) REVERT: F 65 MET cc_start: 0.7538 (mmm) cc_final: 0.7324 (mmm) REVERT: F 80 THR cc_start: 0.8047 (t) cc_final: 0.7718 (p) REVERT: F 105 LYS cc_start: 0.8057 (mttt) cc_final: 0.7834 (mtmm) REVERT: F 120 ILE cc_start: 0.8453 (OUTLIER) cc_final: 0.8232 (mp) REVERT: F 122 SER cc_start: 0.8453 (m) cc_final: 0.8125 (p) REVERT: F 133 LYS cc_start: 0.7907 (mttt) cc_final: 0.7678 (mttt) REVERT: F 138 LYS cc_start: 0.8515 (ttpt) cc_final: 0.8225 (ttpp) REVERT: F 141 SER cc_start: 0.8406 (m) cc_final: 0.8108 (t) REVERT: F 143 TYR cc_start: 0.7876 (t80) cc_final: 0.7669 (t80) REVERT: F 157 ARG cc_start: 0.7368 (mtm-85) cc_final: 0.7113 (ttm110) REVERT: F 158 GLU cc_start: 0.7211 (tp30) cc_final: 0.6557 (tp30) REVERT: F 161 GLN cc_start: 0.7407 (tp40) cc_final: 0.6719 (tp40) REVERT: F 164 ARG cc_start: 0.7638 (ttm-80) cc_final: 0.7250 (ttm110) REVERT: F 165 ASP cc_start: 0.7397 (m-30) cc_final: 0.7059 (m-30) REVERT: F 192 LYS cc_start: 0.8066 (mttp) cc_final: 0.7699 (mttp) REVERT: F 200 GLN cc_start: 0.7106 (mp10) cc_final: 0.6442 (mp10) REVERT: F 214 GLU cc_start: 0.7623 (tp30) cc_final: 0.6867 (mp0) REVERT: F 276 THR cc_start: 0.8397 (t) cc_final: 0.8122 (p) REVERT: F 284 LYS cc_start: 0.7724 (mmtp) cc_final: 0.7479 (mmtp) REVERT: F 288 LYS cc_start: 0.8313 (OUTLIER) cc_final: 0.7824 (mtmt) REVERT: F 317 GLN cc_start: 0.7422 (mm-40) cc_final: 0.6953 (mp10) REVERT: F 332 GLN cc_start: 0.7507 (OUTLIER) cc_final: 0.7255 (mp10) REVERT: F 337 ILE cc_start: 0.8107 (OUTLIER) cc_final: 0.7865 (mp) REVERT: F 372 ILE cc_start: 0.8619 (OUTLIER) cc_final: 0.8392 (mm) REVERT: F 379 LYS cc_start: 0.7670 (tptm) cc_final: 0.7140 (tptm) REVERT: F 380 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7972 (mp) REVERT: F 382 ASP cc_start: 0.7705 (t0) cc_final: 0.7457 (m-30) REVERT: F 383 ASP cc_start: 0.7082 (m-30) cc_final: 0.6702 (m-30) REVERT: J 40 ILE cc_start: 0.8303 (mt) cc_final: 0.8079 (pt) REVERT: J 66 ILE cc_start: 0.8638 (mm) cc_final: 0.8279 (mm) REVERT: J 87 ILE cc_start: 0.8635 (tt) cc_final: 0.8361 (pt) REVERT: J 106 ILE cc_start: 0.8173 (mt) cc_final: 0.7953 (tt) REVERT: J 110 VAL cc_start: 0.7614 (m) cc_final: 0.7133 (p) REVERT: J 114 ILE cc_start: 0.8221 (mm) cc_final: 0.7963 (mm) REVERT: J 120 ILE cc_start: 0.8088 (mt) cc_final: 0.7763 (mm) REVERT: J 122 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.7732 (mp) REVERT: J 131 TYR cc_start: 0.7293 (OUTLIER) cc_final: 0.6832 (t80) REVERT: J 145 MET cc_start: 0.6777 (tmm) cc_final: 0.6164 (tmm) REVERT: J 161 ILE cc_start: 0.8333 (mm) cc_final: 0.7983 (mp) REVERT: J 184 MET cc_start: 0.7631 (mtm) cc_final: 0.7385 (mtm) REVERT: J 213 ILE cc_start: 0.8258 (OUTLIER) cc_final: 0.7998 (mt) REVERT: J 216 LEU cc_start: 0.8413 (tp) cc_final: 0.8200 (tt) REVERT: J 217 GLN cc_start: 0.7847 (tp40) cc_final: 0.7553 (tp40) REVERT: J 268 ARG cc_start: 0.7831 (ttt90) cc_final: 0.7268 (mmm-85) REVERT: J 271 THR cc_start: 0.8355 (m) cc_final: 0.8117 (p) REVERT: J 282 MET cc_start: 0.7839 (ttt) cc_final: 0.7517 (ttm) REVERT: J 297 GLU cc_start: 0.7342 (tt0) cc_final: 0.7075 (tt0) REVERT: J 308 LEU cc_start: 0.8034 (mt) cc_final: 0.7784 (mm) REVERT: J 327 PHE cc_start: 0.6813 (t80) cc_final: 0.6005 (t80) REVERT: J 334 ARG cc_start: 0.7820 (mtm180) cc_final: 0.7505 (mtm180) REVERT: J 339 PHE cc_start: 0.7816 (t80) cc_final: 0.7560 (t80) REVERT: J 342 ILE cc_start: 0.8255 (mm) cc_final: 0.7980 (tt) REVERT: J 395 LEU cc_start: 0.7876 (mt) cc_final: 0.7481 (mt) REVERT: J 402 SER cc_start: 0.8084 (t) cc_final: 0.7819 (m) REVERT: J 403 ASN cc_start: 0.8332 (m-40) cc_final: 0.7743 (m110) REVERT: J 406 ARG cc_start: 0.7364 (ttp80) cc_final: 0.7091 (ttp80) REVERT: J 408 LEU cc_start: 0.7495 (OUTLIER) cc_final: 0.7154 (tt) REVERT: J 447 TYR cc_start: 0.8460 (m-80) cc_final: 0.8122 (m-80) REVERT: J 458 GLN cc_start: 0.8180 (tt0) cc_final: 0.7933 (tt0) REVERT: J 467 GLN cc_start: 0.7995 (mm-40) cc_final: 0.7615 (mm110) REVERT: J 471 GLN cc_start: 0.7743 (mm-40) cc_final: 0.7179 (mm-40) REVERT: J 489 LEU cc_start: 0.8394 (mt) cc_final: 0.8139 (mt) REVERT: J 491 LEU cc_start: 0.7775 (mt) cc_final: 0.7440 (pp) REVERT: G 3 LEU cc_start: 0.8737 (tt) cc_final: 0.8338 (tp) REVERT: G 5 GLN cc_start: 0.8379 (mt0) cc_final: 0.7759 (mt0) REVERT: G 9 GLN cc_start: 0.6966 (tm-30) cc_final: 0.6640 (tm-30) REVERT: G 17 LEU cc_start: 0.8580 (mp) cc_final: 0.8132 (tp) REVERT: G 24 ARG cc_start: 0.7888 (tpt170) cc_final: 0.7651 (tpm170) REVERT: G 29 GLU cc_start: 0.7725 (tp30) cc_final: 0.6675 (tp30) REVERT: G 30 LYS cc_start: 0.8596 (tttt) cc_final: 0.8218 (tttt) REVERT: G 32 ASN cc_start: 0.8141 (m-40) cc_final: 0.6964 (p0) REVERT: G 42 LEU cc_start: 0.8313 (mp) cc_final: 0.8103 (mm) REVERT: G 76 PHE cc_start: 0.7249 (t80) cc_final: 0.7039 (t80) REVERT: G 77 ASP cc_start: 0.8617 (t0) cc_final: 0.5387 (p0) REVERT: G 87 GLN cc_start: 0.8466 (tp40) cc_final: 0.7988 (tp40) REVERT: G 103 GLN cc_start: 0.8309 (mt0) cc_final: 0.7883 (mm-40) REVERT: G 104 THR cc_start: 0.8623 (m) cc_final: 0.8358 (p) REVERT: G 117 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8654 (mp) REVERT: G 130 LYS cc_start: 0.8740 (tttt) cc_final: 0.8014 (ttpp) REVERT: G 133 ILE cc_start: 0.8670 (OUTLIER) cc_final: 0.8286 (tt) REVERT: G 168 GLU cc_start: 0.8373 (tt0) cc_final: 0.8157 (tt0) REVERT: G 169 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8318 (mm) REVERT: G 181 GLN cc_start: 0.8409 (mm-40) cc_final: 0.7776 (tm-30) REVERT: G 215 GLU cc_start: 0.7593 (tm-30) cc_final: 0.6643 (tm-30) REVERT: G 217 GLU cc_start: 0.8030 (tm-30) cc_final: 0.7638 (mm-30) REVERT: G 230 GLN cc_start: 0.8474 (OUTLIER) cc_final: 0.7929 (pp30) REVERT: G 231 ASP cc_start: 0.8162 (m-30) cc_final: 0.7610 (m-30) REVERT: G 232 LEU cc_start: 0.9226 (tt) cc_final: 0.8882 (tt) REVERT: G 236 GLN cc_start: 0.8396 (mt0) cc_final: 0.8099 (mt0) REVERT: G 279 MET cc_start: 0.3867 (tpt) cc_final: 0.3218 (tpt) REVERT: G 299 ASN cc_start: 0.8212 (m110) cc_final: 0.7899 (m-40) REVERT: G 303 LYS cc_start: 0.8675 (mtpp) cc_final: 0.7850 (mtpp) REVERT: G 307 TYR cc_start: 0.7930 (m-80) cc_final: 0.7574 (m-80) REVERT: G 314 GLU cc_start: 0.7931 (mm-30) cc_final: 0.7305 (mm-30) REVERT: G 315 GLN cc_start: 0.8638 (tp40) cc_final: 0.8216 (tp-100) REVERT: G 317 GLU cc_start: 0.7980 (tp30) cc_final: 0.7117 (tp30) REVERT: G 321 ARG cc_start: 0.8430 (mtt180) cc_final: 0.7912 (mtt180) REVERT: G 344 TYR cc_start: 0.8116 (m-80) cc_final: 0.7832 (m-80) REVERT: G 385 GLU cc_start: 0.7653 (mm-30) cc_final: 0.7117 (mm-30) REVERT: G 401 LYS cc_start: 0.8594 (tptm) cc_final: 0.8267 (tppp) REVERT: G 404 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8647 (tp) REVERT: G 411 ASP cc_start: 0.5970 (t0) cc_final: 0.5427 (t0) REVERT: H 5 GLN cc_start: 0.8396 (mp10) cc_final: 0.8141 (mp10) REVERT: H 9 GLN cc_start: 0.8617 (tp-100) cc_final: 0.8168 (tp40) REVERT: H 14 ASN cc_start: 0.8125 (t0) cc_final: 0.7770 (t0) REVERT: H 19 LYS cc_start: 0.8220 (OUTLIER) cc_final: 0.7804 (tttt) REVERT: H 25 ASP cc_start: 0.7913 (m-30) cc_final: 0.7492 (t0) REVERT: H 29 GLU cc_start: 0.7891 (tp30) cc_final: 0.6789 (tp30) REVERT: H 87 GLN cc_start: 0.8137 (pt0) cc_final: 0.7925 (pt0) REVERT: H 89 LYS cc_start: 0.8688 (mmmt) cc_final: 0.8158 (mmmt) REVERT: H 94 GLN cc_start: 0.8055 (tp40) cc_final: 0.7778 (tp40) REVERT: H 129 GLN cc_start: 0.8471 (tt0) cc_final: 0.8120 (tt0) REVERT: H 131 GLU cc_start: 0.8039 (tp30) cc_final: 0.7726 (tp30) REVERT: H 135 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.7495 (mmm160) REVERT: H 136 GLN cc_start: 0.8313 (tp-100) cc_final: 0.7926 (tp40) REVERT: H 138 ASP cc_start: 0.7988 (OUTLIER) cc_final: 0.6985 (t0) REVERT: H 142 GLN cc_start: 0.7947 (mm-40) cc_final: 0.7631 (mm-40) REVERT: H 143 ARG cc_start: 0.7612 (ttp-170) cc_final: 0.7356 (ttp-170) REVERT: H 162 ASP cc_start: 0.8217 (m-30) cc_final: 0.7805 (m-30) REVERT: H 180 GLU cc_start: 0.8473 (mm-30) cc_final: 0.7958 (tm-30) REVERT: H 181 GLN cc_start: 0.7942 (tm-30) cc_final: 0.7649 (tm-30) REVERT: H 184 GLN cc_start: 0.8417 (tt0) cc_final: 0.7585 (tp-100) REVERT: H 218 LYS cc_start: 0.8743 (mmtt) cc_final: 0.8430 (mmtt) REVERT: H 231 ASP cc_start: 0.7576 (t0) cc_final: 0.7255 (t70) REVERT: H 234 ARG cc_start: 0.7927 (mmm-85) cc_final: 0.7308 (mmm-85) REVERT: H 236 GLN cc_start: 0.7830 (pp30) cc_final: 0.7302 (pp30) REVERT: H 237 ILE cc_start: 0.8722 (mt) cc_final: 0.8244 (mt) REVERT: H 239 GLN cc_start: 0.8580 (pp30) cc_final: 0.8245 (pp30) REVERT: H 301 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.7929 (pm20) REVERT: H 303 LYS cc_start: 0.8372 (mttt) cc_final: 0.7869 (mttt) REVERT: H 314 GLU cc_start: 0.7448 (mm-30) cc_final: 0.7056 (mm-30) REVERT: H 317 GLU cc_start: 0.7654 (tp30) cc_final: 0.7147 (tp30) REVERT: H 321 ARG cc_start: 0.8350 (mtt180) cc_final: 0.7587 (mtt180) REVERT: H 331 PHE cc_start: 0.9065 (t80) cc_final: 0.8824 (t80) REVERT: H 340 SER cc_start: 0.8751 (m) cc_final: 0.8207 (p) REVERT: H 356 ASP cc_start: 0.8346 (t0) cc_final: 0.8105 (t0) REVERT: H 362 TYR cc_start: 0.8729 (t80) cc_final: 0.8470 (t80) REVERT: H 367 ARG cc_start: 0.7979 (tpp80) cc_final: 0.7757 (mtm-85) REVERT: H 374 ASP cc_start: 0.7914 (t0) cc_final: 0.7344 (t0) REVERT: H 390 ARG cc_start: 0.8650 (mtt-85) cc_final: 0.8384 (ttm170) REVERT: H 392 ASN cc_start: 0.8430 (m-40) cc_final: 0.7882 (t0) REVERT: H 396 ASN cc_start: 0.8194 (m-40) cc_final: 0.7710 (m110) REVERT: H 397 GLN cc_start: 0.8133 (tt0) cc_final: 0.7418 (tm-30) REVERT: I 4 MET cc_start: 0.7932 (mmm) cc_final: 0.7559 (tmm) REVERT: I 8 GLN cc_start: 0.8568 (mm-40) cc_final: 0.7250 (tp-100) REVERT: I 11 ARG cc_start: 0.7907 (ttp80) cc_final: 0.6880 (ttp80) REVERT: I 16 GLU cc_start: 0.7963 (mp0) cc_final: 0.7469 (mp0) REVERT: I 29 GLU cc_start: 0.7792 (tp30) cc_final: 0.7031 (tp30) REVERT: I 31 ILE cc_start: 0.9127 (mt) cc_final: 0.8783 (mm) REVERT: I 32 ASN cc_start: 0.8658 (m-40) cc_final: 0.8049 (m110) REVERT: I 76 PHE cc_start: 0.7668 (t80) cc_final: 0.6929 (t80) REVERT: I 86 LEU cc_start: 0.8906 (pp) cc_final: 0.8697 (mt) REVERT: I 99 GLN cc_start: 0.8331 (mt0) cc_final: 0.8041 (mt0) REVERT: I 124 SER cc_start: 0.8592 (t) cc_final: 0.8384 (p) REVERT: I 127 GLN cc_start: 0.7833 (mm-40) cc_final: 0.7522 (mp10) REVERT: I 135 ARG cc_start: 0.8101 (tpp-160) cc_final: 0.7733 (tpp-160) REVERT: I 143 ARG cc_start: 0.7831 (ttm110) cc_final: 0.7401 (ttm110) REVERT: I 185 ILE cc_start: 0.9233 (mt) cc_final: 0.8960 (tt) REVERT: I 213 LEU cc_start: 0.8969 (mt) cc_final: 0.8699 (mt) REVERT: I 215 GLU cc_start: 0.8051 (tp30) cc_final: 0.7520 (tp30) REVERT: I 223 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8500 (mm) REVERT: I 224 LEU cc_start: 0.8870 (tp) cc_final: 0.7994 (mm) REVERT: I 225 GLN cc_start: 0.7957 (tm-30) cc_final: 0.7306 (tm-30) REVERT: I 227 ARG cc_start: 0.7736 (mtm-85) cc_final: 0.7200 (mtm-85) REVERT: I 230 GLN cc_start: 0.8025 (tm-30) cc_final: 0.7731 (tm-30) REVERT: I 235 GLU cc_start: 0.7800 (tp30) cc_final: 0.7409 (tp30) REVERT: I 236 GLN cc_start: 0.8360 (mt0) cc_final: 0.7999 (mt0) REVERT: I 238 ARG cc_start: 0.8133 (mpt180) cc_final: 0.7817 (mpt180) REVERT: I 259 THR cc_start: 0.3775 (OUTLIER) cc_final: 0.3574 (m) REVERT: I 297 MET cc_start: 0.6513 (tmm) cc_final: 0.6155 (tmm) REVERT: I 301 GLN cc_start: 0.8321 (tt0) cc_final: 0.8057 (mt0) REVERT: I 325 GLN cc_start: 0.8363 (pp30) cc_final: 0.7912 (pp30) REVERT: I 396 ASN cc_start: 0.8287 (m-40) cc_final: 0.7791 (m-40) outliers start: 162 outliers final: 100 residues processed: 1355 average time/residue: 0.4674 time to fit residues: 954.2652 Evaluate side-chains 1388 residues out of total 3232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 1258 time to evaluate : 3.052 ------------------------------------------------------------------------------- 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 175 ASP Chi-restraints excluded: chain A residue 194 GLU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 251 ASN 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 347 THR Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 117 GLN Chi-restraints excluded: chain B residue 140 GLN 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 313 ILE Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 335 LEU 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 142 ASP Chi-restraints excluded: chain C residue 187 MET Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 265 ASN 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 344 SER Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain D residue 84 LYS Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 115 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 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 85 GLU Chi-restraints excluded: chain E residue 103 LYS Chi-restraints excluded: chain E residue 196 GLN Chi-restraints excluded: chain E residue 214 GLU 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 325 LEU Chi-restraints excluded: chain E residue 335 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 153 ASN 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 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 332 GLN Chi-restraints excluded: chain F residue 337 ILE Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain F residue 353 GLN 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 122 LEU Chi-restraints excluded: chain J residue 131 TYR Chi-restraints excluded: chain J residue 213 ILE Chi-restraints excluded: chain J residue 253 LEU Chi-restraints excluded: chain J residue 290 LEU Chi-restraints excluded: chain J residue 293 GLN Chi-restraints excluded: chain J residue 298 VAL Chi-restraints excluded: chain J residue 408 LEU Chi-restraints excluded: chain G residue 11 ARG Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 50 TYR Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 133 ILE 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 398 LEU Chi-restraints excluded: chain G residue 404 LEU Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 19 LYS 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 138 ASP 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 249 ASP Chi-restraints excluded: chain H residue 286 LEU Chi-restraints excluded: chain H residue 298 VAL Chi-restraints excluded: chain H residue 301 GLN 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 12 LEU Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 203 THR Chi-restraints excluded: chain I residue 223 LEU Chi-restraints excluded: chain I residue 232 LEU Chi-restraints excluded: chain I residue 250 LEU 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 328 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 158 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 170 optimal weight: 0.8980 chunk 173 optimal weight: 2.9990 chunk 185 optimal weight: 1.9990 chunk 328 optimal weight: 2.9990 chunk 304 optimal weight: 6.9990 chunk 284 optimal weight: 3.9990 chunk 327 optimal weight: 0.9990 chunk 112 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 251 ASN C 265 ASN D 388 ASN E 236 GLN F 251 ASN F 346 ASN J 34 ASN J 449 GLN ** J 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 478 ASN ** G 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 426 ASN ** H 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 58 ASN I 102 GLN ** I 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 320 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.112170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.094012 restraints weight = 58602.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.097010 restraints weight = 25849.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.098896 restraints weight = 13991.458| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.6383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 30315 Z= 0.214 Angle : 0.667 12.731 41246 Z= 0.351 Chirality : 0.044 0.214 4889 Planarity : 0.005 0.071 5392 Dihedral : 4.323 20.750 4179 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 5.51 % Allowed : 23.98 % Favored : 70.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.14), residues: 3860 helix: 2.76 (0.11), residues: 2020 sheet: -0.36 (0.22), residues: 501 loop : -1.16 (0.16), residues: 1339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP E 312 HIS 0.012 0.001 HIS I 320 PHE 0.031 0.002 PHE H 309 TYR 0.029 0.002 TYR G 293 ARG 0.014 0.001 ARG I 35 Details of bonding type rmsd hydrogen bonds : bond 0.06773 ( 1888) hydrogen bonds : angle 4.47166 ( 5523) covalent geometry : bond 0.00449 (30315) covalent geometry : angle 0.66668 (41246) *********************** 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 1440 residues out of total 3232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 178 poor density : 1262 time to evaluate : 3.450 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: 0.7024 (mm-30) cc_final: 0.6815 (mm-30) REVERT: A 56 TYR cc_start: 0.7526 (m-80) cc_final: 0.6671 (m-80) REVERT: A 79 ASN cc_start: 0.7713 (t0) cc_final: 0.7394 (t0) REVERT: A 138 LYS cc_start: 0.8252 (tttt) cc_final: 0.7840 (tttm) REVERT: A 143 TYR cc_start: 0.8259 (t80) cc_final: 0.7829 (t80) REVERT: A 158 GLU cc_start: 0.7699 (mm-30) cc_final: 0.7029 (tm-30) REVERT: A 162 HIS cc_start: 0.8092 (m-70) cc_final: 0.7224 (m-70) REVERT: A 173 GLN cc_start: 0.7881 (mm-40) cc_final: 0.7663 (mm-40) REVERT: A 175 ASP cc_start: 0.6874 (OUTLIER) cc_final: 0.6391 (m-30) REVERT: A 189 LEU cc_start: 0.8429 (mt) cc_final: 0.8217 (mt) REVERT: A 200 GLN cc_start: 0.7614 (mt0) cc_final: 0.7361 (mm-40) REVERT: A 214 GLU cc_start: 0.7648 (mm-30) cc_final: 0.7213 (mm-30) REVERT: A 225 TYR cc_start: 0.7989 (m-80) cc_final: 0.7695 (m-80) REVERT: A 228 ARG cc_start: 0.7702 (mtm-85) cc_final: 0.7334 (mtm-85) REVERT: A 247 VAL cc_start: 0.8794 (t) cc_final: 0.8498 (m) REVERT: A 259 LYS cc_start: 0.8182 (mtmm) cc_final: 0.7779 (mtmm) REVERT: A 284 LYS cc_start: 0.7513 (mtpp) cc_final: 0.7214 (mtpp) REVERT: A 306 GLN cc_start: 0.6890 (tp-100) cc_final: 0.6328 (tp-100) REVERT: A 324 GLU cc_start: 0.6294 (tp30) cc_final: 0.5959 (tp30) REVERT: A 347 THR cc_start: 0.7364 (OUTLIER) cc_final: 0.6836 (p) REVERT: A 371 GLU cc_start: 0.7392 (pm20) cc_final: 0.6894 (pm20) REVERT: A 379 LYS cc_start: 0.7968 (tttt) cc_final: 0.7701 (tttt) REVERT: A 381 ILE cc_start: 0.8579 (mt) cc_final: 0.8274 (mt) REVERT: B 50 GLU cc_start: 0.7553 (mm-30) cc_final: 0.7168 (mm-30) REVERT: B 66 SER cc_start: 0.7793 (t) cc_final: 0.7545 (p) REVERT: B 93 ASP cc_start: 0.7930 (t0) cc_final: 0.7607 (t70) REVERT: B 98 ARG cc_start: 0.7265 (tpp80) cc_final: 0.7001 (ttm-80) REVERT: B 117 GLN cc_start: 0.7609 (OUTLIER) cc_final: 0.7269 (tt0) REVERT: B 123 LYS cc_start: 0.7594 (mttp) cc_final: 0.7006 (mttp) REVERT: B 130 GLU cc_start: 0.7231 (mm-30) cc_final: 0.6684 (tm-30) REVERT: B 134 ILE cc_start: 0.8439 (mt) cc_final: 0.8170 (mp) REVERT: B 138 LYS cc_start: 0.8644 (ttpp) cc_final: 0.8393 (ttpp) REVERT: B 161 GLN cc_start: 0.7981 (tp40) cc_final: 0.7570 (mm110) REVERT: B 162 HIS cc_start: 0.7893 (m-70) cc_final: 0.7635 (m90) REVERT: B 171 GLN cc_start: 0.8065 (tp-100) cc_final: 0.7782 (tp40) REVERT: B 184 ASN cc_start: 0.8056 (t0) cc_final: 0.7786 (t0) REVERT: B 244 MET cc_start: 0.8035 (ptp) cc_final: 0.7683 (ptp) REVERT: B 259 LYS cc_start: 0.8088 (mtmt) cc_final: 0.7603 (mtmt) REVERT: B 284 LYS cc_start: 0.7869 (mtpt) cc_final: 0.7628 (mtpt) REVERT: B 294 MET cc_start: 0.7185 (OUTLIER) cc_final: 0.6869 (mtp) REVERT: B 303 LEU cc_start: 0.8084 (mt) cc_final: 0.7799 (mp) REVERT: B 318 ARG cc_start: 0.8158 (ptp-110) cc_final: 0.7848 (mtp85) REVERT: B 328 LYS cc_start: 0.8264 (mmpt) cc_final: 0.7801 (mmpt) REVERT: B 330 LEU cc_start: 0.8256 (tt) cc_final: 0.7898 (tp) REVERT: B 332 GLN cc_start: 0.7624 (mm-40) cc_final: 0.7347 (mm-40) REVERT: B 386 LYS cc_start: 0.8277 (tttt) cc_final: 0.7947 (tttt) REVERT: C 53 ASP cc_start: 0.6782 (t0) cc_final: 0.6554 (t0) REVERT: C 54 ASP cc_start: 0.7493 (t0) cc_final: 0.7204 (t0) REVERT: C 78 ASP cc_start: 0.6625 (p0) cc_final: 0.6385 (p0) REVERT: C 117 GLN cc_start: 0.7273 (mt0) cc_final: 0.6798 (mt0) REVERT: C 121 ASN cc_start: 0.7295 (m-40) cc_final: 0.6953 (m-40) REVERT: C 133 LYS cc_start: 0.8244 (mtpt) cc_final: 0.7946 (mtpt) REVERT: C 179 GLN cc_start: 0.8234 (mm-40) cc_final: 0.7995 (mm-40) REVERT: C 231 VAL cc_start: 0.8341 (OUTLIER) cc_final: 0.8061 (p) REVERT: C 259 LYS cc_start: 0.7808 (mtmm) cc_final: 0.7575 (mttm) REVERT: C 265 ASN cc_start: 0.8237 (OUTLIER) cc_final: 0.7897 (t0) REVERT: C 274 ILE cc_start: 0.8566 (mt) cc_final: 0.8232 (mp) REVERT: C 284 LYS cc_start: 0.8320 (mmmt) cc_final: 0.7851 (mtmt) REVERT: C 296 THR cc_start: 0.7489 (p) cc_final: 0.7047 (t) REVERT: C 302 LEU cc_start: 0.8577 (tp) cc_final: 0.8246 (tt) REVERT: C 340 SER cc_start: 0.8369 (OUTLIER) cc_final: 0.8097 (p) REVERT: C 379 LYS cc_start: 0.7822 (ttmt) cc_final: 0.7565 (ttmt) REVERT: D 50 GLU cc_start: 0.6746 (OUTLIER) cc_final: 0.6321 (tp30) REVERT: D 54 ASP cc_start: 0.6846 (t0) cc_final: 0.5961 (t0) REVERT: D 73 THR cc_start: 0.8592 (m) cc_final: 0.8300 (m) REVERT: D 110 SER cc_start: 0.8525 (t) cc_final: 0.8309 (m) REVERT: D 117 GLN cc_start: 0.7899 (tt0) cc_final: 0.7274 (tt0) REVERT: D 120 ILE cc_start: 0.8351 (mm) cc_final: 0.8106 (mp) REVERT: D 121 ASN cc_start: 0.7891 (m-40) cc_final: 0.7422 (m-40) REVERT: D 129 ILE cc_start: 0.8319 (mt) cc_final: 0.8043 (mm) REVERT: D 138 LYS cc_start: 0.8046 (tttt) cc_final: 0.7673 (tttt) REVERT: D 145 ARG cc_start: 0.8028 (mtt90) cc_final: 0.7479 (mtm180) REVERT: D 157 ARG cc_start: 0.7463 (mtm110) cc_final: 0.7151 (mtm110) REVERT: D 187 MET cc_start: 0.7382 (mmm) cc_final: 0.6944 (mtp) REVERT: D 251 ASN cc_start: 0.7524 (p0) cc_final: 0.7193 (p0) REVERT: D 314 LYS cc_start: 0.7423 (tptm) cc_final: 0.7092 (tptm) REVERT: D 319 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8498 (tp) REVERT: D 327 GLN cc_start: 0.7921 (mm-40) cc_final: 0.7685 (mm-40) REVERT: D 331 GLU cc_start: 0.7072 (mp0) cc_final: 0.6575 (mp0) REVERT: D 332 GLN cc_start: 0.7465 (tp40) cc_final: 0.7114 (tp40) REVERT: D 366 VAL cc_start: 0.8633 (t) cc_final: 0.8399 (p) REVERT: D 378 ASN cc_start: 0.7894 (m-40) cc_final: 0.7053 (m-40) REVERT: D 382 ASP cc_start: 0.7310 (m-30) cc_final: 0.6770 (m-30) REVERT: D 385 VAL cc_start: 0.8534 (t) cc_final: 0.8208 (p) REVERT: E 53 ASP cc_start: 0.7078 (t0) cc_final: 0.6603 (t0) REVERT: E 61 GLN cc_start: 0.7658 (mp10) cc_final: 0.7304 (mp10) REVERT: E 71 SER cc_start: 0.7775 (p) cc_final: 0.7448 (t) REVERT: E 85 GLU cc_start: 0.6860 (OUTLIER) cc_final: 0.6512 (tm-30) REVERT: E 125 LEU cc_start: 0.8205 (mt) cc_final: 0.7917 (mp) REVERT: E 142 ASP cc_start: 0.7413 (m-30) cc_final: 0.7014 (m-30) REVERT: E 153 ASN cc_start: 0.7732 (t0) cc_final: 0.7237 (p0) REVERT: E 154 LEU cc_start: 0.7757 (pp) cc_final: 0.7363 (mt) REVERT: E 157 ARG cc_start: 0.7171 (mtp180) cc_final: 0.6778 (mtp180) REVERT: E 160 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8204 (mm) REVERT: E 181 TYR cc_start: 0.8291 (t80) cc_final: 0.8022 (t80) REVERT: E 192 LYS cc_start: 0.7600 (mmmm) cc_final: 0.7138 (mmmm) REVERT: E 196 GLN cc_start: 0.7867 (OUTLIER) cc_final: 0.7181 (mp10) REVERT: E 200 GLN cc_start: 0.7463 (mm-40) cc_final: 0.7020 (mt0) REVERT: E 211 LEU cc_start: 0.8345 (mt) cc_final: 0.8097 (mt) REVERT: E 228 ARG cc_start: 0.7228 (mtm-85) cc_final: 0.6858 (mtt180) REVERT: E 251 ASN cc_start: 0.7253 (t0) cc_final: 0.6875 (t0) REVERT: E 252 MET cc_start: 0.7675 (mmm) cc_final: 0.7433 (mtt) REVERT: E 283 VAL cc_start: 0.8474 (t) cc_final: 0.8079 (m) REVERT: E 294 MET cc_start: 0.6685 (mmm) cc_final: 0.6299 (mmm) REVERT: E 306 GLN cc_start: 0.7053 (mp10) cc_final: 0.6666 (mp10) REVERT: E 312 TRP cc_start: 0.8053 (t60) cc_final: 0.7767 (t60) REVERT: E 346 ASN cc_start: 0.7865 (m-40) cc_final: 0.7657 (m-40) REVERT: F 50 GLU cc_start: 0.7829 (mm-30) cc_final: 0.7568 (mm-30) REVERT: F 65 MET cc_start: 0.7502 (mmm) cc_final: 0.7300 (mmm) REVERT: F 80 THR cc_start: 0.8057 (t) cc_final: 0.7668 (p) REVERT: F 98 ARG cc_start: 0.6892 (mtm110) cc_final: 0.6389 (mtm180) REVERT: F 105 LYS cc_start: 0.8080 (mttt) cc_final: 0.7782 (mtmm) REVERT: F 122 SER cc_start: 0.8505 (m) cc_final: 0.8136 (p) REVERT: F 124 GLN cc_start: 0.7246 (tp40) cc_final: 0.7000 (tp40) REVERT: F 133 LYS cc_start: 0.7942 (mttt) cc_final: 0.7708 (mttt) REVERT: F 138 LYS cc_start: 0.8565 (ttpt) cc_final: 0.8184 (tttp) REVERT: F 141 SER cc_start: 0.8360 (m) cc_final: 0.8100 (t) REVERT: F 145 ARG cc_start: 0.7303 (OUTLIER) cc_final: 0.7037 (ttm-80) REVERT: F 157 ARG cc_start: 0.7295 (mtm-85) cc_final: 0.7013 (ttm110) REVERT: F 158 GLU cc_start: 0.7268 (tp30) cc_final: 0.6442 (tp30) REVERT: F 161 GLN cc_start: 0.7420 (tp40) cc_final: 0.6716 (tp40) REVERT: F 164 ARG cc_start: 0.7686 (ttm-80) cc_final: 0.7358 (ttm110) REVERT: F 165 ASP cc_start: 0.7546 (m-30) cc_final: 0.7210 (m-30) REVERT: F 192 LYS cc_start: 0.8048 (mttp) cc_final: 0.7691 (mttp) REVERT: F 200 GLN cc_start: 0.7102 (mp10) cc_final: 0.6440 (mp10) REVERT: F 214 GLU cc_start: 0.7612 (tp30) cc_final: 0.6789 (mp0) REVERT: F 217 ARG cc_start: 0.6726 (ttm110) cc_final: 0.6367 (ptp-110) REVERT: F 284 LYS cc_start: 0.7852 (mmtp) cc_final: 0.7584 (mmtp) REVERT: F 288 LYS cc_start: 0.8333 (OUTLIER) cc_final: 0.7833 (mtmt) REVERT: F 317 GLN cc_start: 0.7377 (mm-40) cc_final: 0.6937 (mp10) REVERT: F 332 GLN cc_start: 0.7505 (OUTLIER) cc_final: 0.7251 (mp10) REVERT: F 337 ILE cc_start: 0.8102 (OUTLIER) cc_final: 0.7901 (mp) REVERT: F 371 GLU cc_start: 0.6257 (tp30) cc_final: 0.5770 (tp30) REVERT: F 372 ILE cc_start: 0.8662 (OUTLIER) cc_final: 0.7944 (mm) REVERT: F 379 LYS cc_start: 0.7729 (tptm) cc_final: 0.7162 (tptm) REVERT: F 380 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7958 (mp) REVERT: F 382 ASP cc_start: 0.7729 (t0) cc_final: 0.7476 (m-30) REVERT: F 383 ASP cc_start: 0.7113 (m-30) cc_final: 0.6743 (m-30) REVERT: J 40 ILE cc_start: 0.8338 (mt) cc_final: 0.8007 (pt) REVERT: J 66 ILE cc_start: 0.8683 (mm) cc_final: 0.8303 (mm) REVERT: J 87 ILE cc_start: 0.8638 (tt) cc_final: 0.8384 (pt) REVERT: J 114 ILE cc_start: 0.8195 (mm) cc_final: 0.7951 (mm) REVERT: J 120 ILE cc_start: 0.8065 (mt) cc_final: 0.7745 (mm) REVERT: J 122 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.7630 (mp) REVERT: J 131 TYR cc_start: 0.7287 (OUTLIER) cc_final: 0.6788 (t80) REVERT: J 145 MET cc_start: 0.6763 (tmm) cc_final: 0.6159 (tmm) REVERT: J 161 ILE cc_start: 0.8364 (mm) cc_final: 0.8041 (mp) REVERT: J 181 VAL cc_start: 0.8675 (t) cc_final: 0.8384 (p) REVERT: J 184 MET cc_start: 0.7675 (mtm) cc_final: 0.7452 (mtm) REVERT: J 213 ILE cc_start: 0.8281 (OUTLIER) cc_final: 0.8027 (mt) REVERT: J 217 GLN cc_start: 0.7890 (tp40) cc_final: 0.7543 (tp40) REVERT: J 220 LEU cc_start: 0.8117 (mt) cc_final: 0.7880 (mt) REVERT: J 268 ARG cc_start: 0.7851 (ttt90) cc_final: 0.7373 (mmm-85) REVERT: J 271 THR cc_start: 0.8408 (m) cc_final: 0.8167 (p) REVERT: J 282 MET cc_start: 0.7837 (ttt) cc_final: 0.7544 (ttm) REVERT: J 297 GLU cc_start: 0.7363 (tt0) cc_final: 0.7100 (tt0) REVERT: J 308 LEU cc_start: 0.8003 (mt) cc_final: 0.7753 (mm) REVERT: J 327 PHE cc_start: 0.6848 (t80) cc_final: 0.6024 (t80) REVERT: J 334 ARG cc_start: 0.7728 (mtm180) cc_final: 0.7432 (mtm180) REVERT: J 342 ILE cc_start: 0.8238 (mm) cc_final: 0.7920 (tp) REVERT: J 356 GLU cc_start: 0.7011 (OUTLIER) cc_final: 0.6780 (tt0) REVERT: J 395 LEU cc_start: 0.7922 (mt) cc_final: 0.7536 (mt) REVERT: J 402 SER cc_start: 0.8103 (t) cc_final: 0.7851 (m) REVERT: J 403 ASN cc_start: 0.8299 (m-40) cc_final: 0.7794 (m110) REVERT: J 406 ARG cc_start: 0.7332 (ttp80) cc_final: 0.7030 (ttp80) REVERT: J 408 LEU cc_start: 0.7475 (OUTLIER) cc_final: 0.7143 (tt) REVERT: J 420 MET cc_start: 0.7426 (ttt) cc_final: 0.7146 (ttt) REVERT: J 447 TYR cc_start: 0.8458 (m-80) cc_final: 0.8112 (m-80) REVERT: J 455 MET cc_start: 0.7225 (OUTLIER) cc_final: 0.6877 (ptp) REVERT: J 458 GLN cc_start: 0.8103 (tt0) cc_final: 0.7860 (tt0) REVERT: J 471 GLN cc_start: 0.7817 (mm-40) cc_final: 0.7258 (mm-40) REVERT: J 482 TRP cc_start: 0.7695 (OUTLIER) cc_final: 0.7128 (t60) REVERT: J 489 LEU cc_start: 0.8400 (mt) cc_final: 0.8173 (mt) REVERT: J 491 LEU cc_start: 0.7709 (mt) cc_final: 0.7419 (pp) REVERT: G 5 GLN cc_start: 0.8389 (mt0) cc_final: 0.7687 (mt0) REVERT: G 9 GLN cc_start: 0.7020 (tm-30) cc_final: 0.6654 (tm-30) REVERT: G 17 LEU cc_start: 0.8649 (mp) cc_final: 0.8191 (tp) REVERT: G 29 GLU cc_start: 0.7810 (tp30) cc_final: 0.6644 (tp30) REVERT: G 32 ASN cc_start: 0.8246 (m-40) cc_final: 0.6928 (p0) REVERT: G 76 PHE cc_start: 0.7330 (t80) cc_final: 0.7062 (t80) REVERT: G 87 GLN cc_start: 0.8527 (tp40) cc_final: 0.8109 (tp40) REVERT: G 103 GLN cc_start: 0.8321 (mt0) cc_final: 0.7902 (mm-40) REVERT: G 104 THR cc_start: 0.8587 (m) cc_final: 0.8340 (p) REVERT: G 117 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8699 (mp) REVERT: G 130 LYS cc_start: 0.8719 (tttt) cc_final: 0.8122 (ttpp) REVERT: G 133 ILE cc_start: 0.8679 (OUTLIER) cc_final: 0.8283 (tt) REVERT: G 169 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8361 (mm) REVERT: G 181 GLN cc_start: 0.8397 (mm-40) cc_final: 0.7813 (tm-30) REVERT: G 215 GLU cc_start: 0.7626 (tm-30) cc_final: 0.6711 (tm-30) REVERT: G 217 GLU cc_start: 0.8054 (tm-30) cc_final: 0.7653 (tm-30) REVERT: G 230 GLN cc_start: 0.8526 (OUTLIER) cc_final: 0.7951 (pp30) REVERT: G 231 ASP cc_start: 0.8211 (m-30) cc_final: 0.7680 (m-30) REVERT: G 232 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8884 (tp) REVERT: G 236 GLN cc_start: 0.8490 (mt0) cc_final: 0.8247 (mt0) REVERT: G 279 MET cc_start: 0.4209 (tpt) cc_final: 0.3658 (tpt) REVERT: G 299 ASN cc_start: 0.8388 (m110) cc_final: 0.7986 (m110) REVERT: G 301 GLN cc_start: 0.8465 (mt0) cc_final: 0.7925 (mp10) REVERT: G 303 LYS cc_start: 0.8711 (mtpp) cc_final: 0.7912 (mtpp) REVERT: G 307 TYR cc_start: 0.7985 (m-80) cc_final: 0.7679 (m-80) REVERT: G 315 GLN cc_start: 0.8648 (tp40) cc_final: 0.8222 (tp-100) REVERT: G 317 GLU cc_start: 0.8000 (tp30) cc_final: 0.7130 (tp30) REVERT: G 321 ARG cc_start: 0.8424 (mtt180) cc_final: 0.7926 (mtt180) REVERT: G 333 ASN cc_start: 0.8636 (m-40) cc_final: 0.8365 (m-40) REVERT: G 344 TYR cc_start: 0.8091 (m-80) cc_final: 0.7795 (m-80) REVERT: G 385 GLU cc_start: 0.7676 (mm-30) cc_final: 0.7180 (mm-30) REVERT: G 401 LYS cc_start: 0.8611 (tptm) cc_final: 0.8266 (tppp) REVERT: G 404 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8665 (tp) REVERT: H 14 ASN cc_start: 0.8136 (t0) cc_final: 0.7711 (t0) REVERT: H 19 LYS cc_start: 0.8242 (OUTLIER) cc_final: 0.7604 (tttt) REVERT: H 29 GLU cc_start: 0.7945 (tp30) cc_final: 0.7207 (tp30) REVERT: H 33 GLU cc_start: 0.7285 (pm20) cc_final: 0.7019 (pm20) REVERT: H 89 LYS cc_start: 0.8704 (mmmt) cc_final: 0.8172 (mmmt) REVERT: H 94 GLN cc_start: 0.8115 (tp40) cc_final: 0.7834 (tp40) REVERT: H 129 GLN cc_start: 0.8451 (tt0) cc_final: 0.8249 (tt0) REVERT: H 131 GLU cc_start: 0.8065 (tp30) cc_final: 0.7719 (tp30) REVERT: H 135 ARG cc_start: 0.8132 (OUTLIER) cc_final: 0.7467 (mmm160) REVERT: H 138 ASP cc_start: 0.8006 (OUTLIER) cc_final: 0.7459 (t0) REVERT: H 143 ARG cc_start: 0.7626 (ttp-170) cc_final: 0.7408 (ttp-170) REVERT: H 162 ASP cc_start: 0.8228 (m-30) cc_final: 0.7830 (m-30) REVERT: H 173 ASN cc_start: 0.8464 (m-40) cc_final: 0.7985 (m-40) REVERT: H 180 GLU cc_start: 0.8563 (mm-30) cc_final: 0.7969 (tm-30) REVERT: H 184 GLN cc_start: 0.8454 (tt0) cc_final: 0.7849 (tm-30) REVERT: H 218 LYS cc_start: 0.8773 (mmtt) cc_final: 0.8486 (mmtt) REVERT: H 231 ASP cc_start: 0.7657 (t0) cc_final: 0.7338 (t70) REVERT: H 234 ARG cc_start: 0.7994 (mmm-85) cc_final: 0.7249 (mmm-85) REVERT: H 236 GLN cc_start: 0.7821 (pp30) cc_final: 0.7338 (pp30) REVERT: H 237 ILE cc_start: 0.8708 (mt) cc_final: 0.8167 (mt) REVERT: H 239 GLN cc_start: 0.8560 (pp30) cc_final: 0.8232 (pp30) REVERT: H 301 GLN cc_start: 0.8436 (OUTLIER) cc_final: 0.7914 (pm20) REVERT: H 303 LYS cc_start: 0.8406 (mttt) cc_final: 0.7889 (mttt) REVERT: H 314 GLU cc_start: 0.7493 (mm-30) cc_final: 0.7068 (mm-30) REVERT: H 317 GLU cc_start: 0.7701 (tp30) cc_final: 0.7250 (tp30) REVERT: H 331 PHE cc_start: 0.9046 (t80) cc_final: 0.8845 (t80) REVERT: H 340 SER cc_start: 0.8768 (m) cc_final: 0.8219 (p) REVERT: H 341 ILE cc_start: 0.8924 (OUTLIER) cc_final: 0.8653 (tt) REVERT: H 356 ASP cc_start: 0.8380 (t0) cc_final: 0.8084 (t0) REVERT: H 362 TYR cc_start: 0.8775 (t80) cc_final: 0.8491 (t80) REVERT: H 374 ASP cc_start: 0.7816 (t0) cc_final: 0.7434 (t0) REVERT: H 390 ARG cc_start: 0.8665 (mtt-85) cc_final: 0.8438 (ttm170) REVERT: H 392 ASN cc_start: 0.8417 (m-40) cc_final: 0.7903 (t0) REVERT: H 396 ASN cc_start: 0.8203 (m-40) cc_final: 0.7738 (m-40) REVERT: H 397 GLN cc_start: 0.8153 (tt0) cc_final: 0.7442 (tm-30) REVERT: I 4 MET cc_start: 0.7939 (mmm) cc_final: 0.7552 (tmm) REVERT: I 8 GLN cc_start: 0.8601 (mm-40) cc_final: 0.8294 (tp-100) REVERT: I 16 GLU cc_start: 0.8007 (mp0) cc_final: 0.7486 (mp0) REVERT: I 24 ARG cc_start: 0.8044 (ttp-170) cc_final: 0.7579 (ttp-110) REVERT: I 28 PHE cc_start: 0.8241 (m-80) cc_final: 0.8015 (m-80) REVERT: I 29 GLU cc_start: 0.7800 (tp30) cc_final: 0.7069 (tp30) REVERT: I 31 ILE cc_start: 0.9090 (mt) cc_final: 0.8814 (mm) REVERT: I 32 ASN cc_start: 0.8620 (m-40) cc_final: 0.7956 (m110) REVERT: I 76 PHE cc_start: 0.7664 (t80) cc_final: 0.6873 (t80) REVERT: I 89 LYS cc_start: 0.8495 (mmtp) cc_final: 0.8236 (mmtp) REVERT: I 95 ASP cc_start: 0.8340 (t0) cc_final: 0.7457 (t0) REVERT: I 99 GLN cc_start: 0.8311 (mt0) cc_final: 0.7896 (mt0) REVERT: I 124 SER cc_start: 0.8603 (t) cc_final: 0.8395 (p) REVERT: I 127 GLN cc_start: 0.7881 (mm-40) cc_final: 0.7568 (mp10) REVERT: I 135 ARG cc_start: 0.8100 (tpp-160) cc_final: 0.7748 (tpp-160) REVERT: I 143 ARG cc_start: 0.7925 (ttm110) cc_final: 0.7407 (ttm110) REVERT: I 160 GLN cc_start: 0.8264 (mm-40) cc_final: 0.8008 (mm-40) REVERT: I 185 ILE cc_start: 0.9217 (mt) cc_final: 0.8945 (tt) REVERT: I 213 LEU cc_start: 0.8969 (mt) cc_final: 0.8715 (mt) REVERT: I 215 GLU cc_start: 0.8034 (tp30) cc_final: 0.7540 (tp30) REVERT: I 223 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8475 (mm) REVERT: I 224 LEU cc_start: 0.8876 (tp) cc_final: 0.7884 (mm) REVERT: I 225 GLN cc_start: 0.7958 (tm-30) cc_final: 0.7288 (tm-30) REVERT: I 227 ARG cc_start: 0.7797 (mtm-85) cc_final: 0.7201 (mtm-85) REVERT: I 230 GLN cc_start: 0.8036 (tm-30) cc_final: 0.7731 (tm-30) REVERT: I 235 GLU cc_start: 0.7862 (tp30) cc_final: 0.7458 (tp30) REVERT: I 236 GLN cc_start: 0.8396 (mt0) cc_final: 0.8010 (mt0) REVERT: I 238 ARG cc_start: 0.8125 (mpt180) cc_final: 0.7765 (mpt180) REVERT: I 297 MET cc_start: 0.6608 (tmm) cc_final: 0.6178 (tmm) REVERT: I 301 GLN cc_start: 0.8417 (tt0) cc_final: 0.8093 (mt0) REVERT: I 306 GLN cc_start: 0.8441 (mp10) cc_final: 0.8099 (pm20) REVERT: I 314 GLU cc_start: 0.7293 (mt-10) cc_final: 0.6836 (mt-10) REVERT: I 396 ASN cc_start: 0.8318 (m-40) cc_final: 0.7782 (m-40) REVERT: I 398 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8675 (mt) outliers start: 178 outliers final: 113 residues processed: 1338 average time/residue: 0.4577 time to fit residues: 920.3211 Evaluate side-chains 1391 residues out of total 3232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 1240 time to evaluate : 3.051 ------------------------------------------------------------------------------- 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 147 VAL 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 250 THR Chi-restraints excluded: chain A residue 251 ASN Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 278 ILE 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 117 GLN Chi-restraints excluded: chain B residue 140 GLN 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 313 ILE Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 344 SER Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 379 LYS Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 124 GLN Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 265 ASN 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 344 SER Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain D residue 84 LYS Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 115 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 306 GLN Chi-restraints excluded: chain D residue 319 LEU 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 85 GLU Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 196 GLN 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 309 THR Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 342 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 145 ARG Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 153 ASN 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 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 332 GLN Chi-restraints excluded: chain F residue 337 ILE Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain F residue 353 GLN 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 48 LEU 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 131 TYR Chi-restraints excluded: chain J residue 213 ILE Chi-restraints excluded: chain J residue 237 LEU Chi-restraints excluded: chain J residue 253 LEU Chi-restraints excluded: chain J residue 275 LEU Chi-restraints excluded: chain J residue 290 LEU Chi-restraints excluded: chain J residue 293 GLN Chi-restraints excluded: chain J residue 298 VAL Chi-restraints excluded: chain J residue 356 GLU Chi-restraints excluded: chain J residue 408 LEU Chi-restraints excluded: chain J residue 455 MET Chi-restraints excluded: chain J residue 482 TRP Chi-restraints excluded: chain J residue 494 LEU Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 133 ILE Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain G residue 196 LEU 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 245 LEU Chi-restraints excluded: chain G residue 272 THR Chi-restraints excluded: chain G residue 300 SER Chi-restraints excluded: chain G residue 318 SER Chi-restraints excluded: chain G residue 334 ILE Chi-restraints excluded: chain G residue 398 LEU Chi-restraints excluded: chain G residue 404 LEU Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 17 LEU Chi-restraints excluded: chain H residue 19 LYS Chi-restraints excluded: chain H residue 35 ARG Chi-restraints excluded: chain H residue 135 ARG Chi-restraints excluded: chain H residue 138 ASP Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 205 LYS Chi-restraints excluded: chain H residue 215 GLU Chi-restraints excluded: chain H residue 221 LEU Chi-restraints excluded: chain H residue 286 LEU Chi-restraints excluded: chain H residue 298 VAL Chi-restraints excluded: chain H residue 301 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 12 LEU Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 203 THR Chi-restraints excluded: chain I residue 223 LEU Chi-restraints excluded: chain I residue 232 LEU 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 398 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 287 optimal weight: 0.8980 chunk 220 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 189 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 338 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 293 optimal weight: 2.9990 chunk 301 optimal weight: 0.2980 chunk 133 optimal weight: 2.9990 chunk 193 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 61 GLN C 251 ASN C 265 ASN E 185 GLN ** E 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 251 ASN F 306 GLN F 346 ASN J 34 ASN J 112 GLN J 130 ASN J 457 GLN J 478 ASN ** G 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 87 GLN G 156 ASN ** G 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 320 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.113407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.095533 restraints weight = 58837.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.098515 restraints weight = 25845.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.100357 restraints weight = 13954.495| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.6512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 30315 Z= 0.171 Angle : 0.651 11.873 41246 Z= 0.338 Chirality : 0.043 0.385 4889 Planarity : 0.005 0.069 5392 Dihedral : 4.160 20.353 4179 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 4.89 % Allowed : 25.34 % Favored : 69.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.14), residues: 3860 helix: 2.86 (0.11), residues: 2020 sheet: -0.22 (0.23), residues: 498 loop : -1.16 (0.16), residues: 1342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP E 312 HIS 0.012 0.001 HIS I 320 PHE 0.032 0.002 PHE H 309 TYR 0.026 0.002 TYR D 143 ARG 0.012 0.001 ARG I 35 Details of bonding type rmsd hydrogen bonds : bond 0.06382 ( 1888) hydrogen bonds : angle 4.32769 ( 5523) covalent geometry : bond 0.00362 (30315) covalent geometry : angle 0.65109 (41246) *********************** 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 1419 residues out of total 3232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 1261 time to evaluate : 3.299 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: 0.7020 (mm-30) cc_final: 0.6772 (mm-30) REVERT: A 54 ASP cc_start: 0.7655 (t0) cc_final: 0.7171 (t70) REVERT: A 56 TYR cc_start: 0.7485 (m-80) cc_final: 0.6821 (m-80) REVERT: A 79 ASN cc_start: 0.7649 (t0) cc_final: 0.7312 (t0) REVERT: A 138 LYS cc_start: 0.8224 (tttt) cc_final: 0.7861 (tttm) REVERT: A 143 TYR cc_start: 0.8237 (t80) cc_final: 0.7787 (t80) REVERT: A 158 GLU cc_start: 0.7751 (mm-30) cc_final: 0.6676 (tm-30) REVERT: A 159 GLU cc_start: 0.7280 (pm20) cc_final: 0.7054 (pm20) REVERT: A 162 HIS cc_start: 0.8035 (m-70) cc_final: 0.7246 (m-70) REVERT: A 173 GLN cc_start: 0.7860 (mm-40) cc_final: 0.7646 (mm-40) REVERT: A 175 ASP cc_start: 0.6867 (OUTLIER) cc_final: 0.6361 (m-30) REVERT: A 189 LEU cc_start: 0.8390 (mt) cc_final: 0.8170 (mt) REVERT: A 200 GLN cc_start: 0.7544 (mt0) cc_final: 0.7309 (mm-40) REVERT: A 214 GLU cc_start: 0.7683 (mm-30) cc_final: 0.7274 (mm-30) REVERT: A 228 ARG cc_start: 0.7560 (mtm-85) cc_final: 0.7176 (mtm-85) REVERT: A 247 VAL cc_start: 0.8751 (t) cc_final: 0.8533 (m) REVERT: A 259 LYS cc_start: 0.8174 (mtmm) cc_final: 0.7745 (mtmm) REVERT: A 284 LYS cc_start: 0.7477 (mtpp) cc_final: 0.7205 (mtpp) REVERT: A 312 TRP cc_start: 0.7808 (t-100) cc_final: 0.7394 (t60) REVERT: A 317 GLN cc_start: 0.7636 (mm-40) cc_final: 0.7299 (mm-40) REVERT: A 324 GLU cc_start: 0.6255 (tp30) cc_final: 0.5967 (tp30) REVERT: A 347 THR cc_start: 0.7317 (OUTLIER) cc_final: 0.6785 (p) REVERT: A 371 GLU cc_start: 0.7391 (pm20) cc_final: 0.6905 (pm20) REVERT: A 379 LYS cc_start: 0.7951 (tttt) cc_final: 0.7687 (tttt) REVERT: A 381 ILE cc_start: 0.8587 (mt) cc_final: 0.8297 (mt) REVERT: B 50 GLU cc_start: 0.7542 (mm-30) cc_final: 0.7096 (mm-30) REVERT: B 66 SER cc_start: 0.7761 (t) cc_final: 0.7512 (p) REVERT: B 93 ASP cc_start: 0.7925 (t0) cc_final: 0.7595 (t70) REVERT: B 117 GLN cc_start: 0.7593 (OUTLIER) cc_final: 0.7115 (tt0) REVERT: B 123 LYS cc_start: 0.7483 (mttp) cc_final: 0.6887 (mttp) REVERT: B 130 GLU cc_start: 0.7236 (mm-30) cc_final: 0.6682 (tm-30) REVERT: B 134 ILE cc_start: 0.8447 (mt) cc_final: 0.8179 (mp) REVERT: B 138 LYS cc_start: 0.8666 (ttpp) cc_final: 0.8385 (ttpp) REVERT: B 146 ARG cc_start: 0.7578 (tpp80) cc_final: 0.7110 (mpp80) REVERT: B 161 GLN cc_start: 0.7809 (tp40) cc_final: 0.7407 (mm-40) REVERT: B 162 HIS cc_start: 0.7860 (m-70) cc_final: 0.7542 (m90) REVERT: B 171 GLN cc_start: 0.8041 (tp-100) cc_final: 0.7741 (tp40) REVERT: B 184 ASN cc_start: 0.8002 (t0) cc_final: 0.7692 (t0) REVERT: B 259 LYS cc_start: 0.7906 (mtmt) cc_final: 0.7454 (mttt) REVERT: B 284 LYS cc_start: 0.7815 (mtpt) cc_final: 0.7574 (mtpt) REVERT: B 294 MET cc_start: 0.7173 (OUTLIER) cc_final: 0.6889 (mtp) REVERT: B 318 ARG cc_start: 0.8173 (ptp-110) cc_final: 0.7597 (mtp85) REVERT: B 328 LYS cc_start: 0.8228 (mmpt) cc_final: 0.7777 (mmpt) REVERT: B 332 GLN cc_start: 0.7614 (mm-40) cc_final: 0.7322 (mm-40) REVERT: B 386 LYS cc_start: 0.8188 (tttt) cc_final: 0.7860 (tttt) REVERT: C 53 ASP cc_start: 0.6750 (t0) cc_final: 0.6522 (t0) REVERT: C 54 ASP cc_start: 0.7436 (t0) cc_final: 0.7179 (t0) REVERT: C 78 ASP cc_start: 0.6521 (p0) cc_final: 0.6312 (p0) REVERT: C 121 ASN cc_start: 0.7302 (m-40) cc_final: 0.6976 (m-40) REVERT: C 130 GLU cc_start: 0.7969 (tp30) cc_final: 0.7758 (tp30) REVERT: C 133 LYS cc_start: 0.8263 (mtpt) cc_final: 0.7948 (mtpt) REVERT: C 231 VAL cc_start: 0.8324 (OUTLIER) cc_final: 0.8014 (p) REVERT: C 259 LYS cc_start: 0.7841 (mtmm) cc_final: 0.7586 (mttm) REVERT: C 265 ASN cc_start: 0.8197 (OUTLIER) cc_final: 0.7812 (t0) REVERT: C 274 ILE cc_start: 0.8554 (mt) cc_final: 0.8250 (mp) REVERT: C 284 LYS cc_start: 0.8245 (mmmt) cc_final: 0.7847 (mtmt) REVERT: C 296 THR cc_start: 0.7472 (p) cc_final: 0.7043 (t) REVERT: C 302 LEU cc_start: 0.8529 (tp) cc_final: 0.8242 (tp) REVERT: C 317 GLN cc_start: 0.7925 (mm-40) cc_final: 0.7641 (mm-40) REVERT: C 332 GLN cc_start: 0.7198 (tm-30) cc_final: 0.6835 (tp40) REVERT: C 340 SER cc_start: 0.8369 (OUTLIER) cc_final: 0.8064 (p) REVERT: C 379 LYS cc_start: 0.7822 (ttmt) cc_final: 0.7557 (ttmt) REVERT: D 50 GLU cc_start: 0.6658 (OUTLIER) cc_final: 0.6245 (tp30) REVERT: D 54 ASP cc_start: 0.6832 (t0) cc_final: 0.5919 (t0) REVERT: D 73 THR cc_start: 0.8609 (m) cc_final: 0.8292 (m) REVERT: D 92 LEU cc_start: 0.8034 (mt) cc_final: 0.7801 (mp) REVERT: D 110 SER cc_start: 0.8498 (t) cc_final: 0.8260 (m) REVERT: D 117 GLN cc_start: 0.7912 (tt0) cc_final: 0.7090 (tt0) REVERT: D 120 ILE cc_start: 0.8296 (mm) cc_final: 0.8082 (mp) REVERT: D 121 ASN cc_start: 0.7779 (m-40) cc_final: 0.7366 (m-40) REVERT: D 129 ILE cc_start: 0.8309 (mt) cc_final: 0.8090 (mm) REVERT: D 138 LYS cc_start: 0.8026 (tttt) cc_final: 0.7786 (tttt) REVERT: D 145 ARG cc_start: 0.7945 (mtt90) cc_final: 0.7458 (mtm180) REVERT: D 157 ARG cc_start: 0.7442 (mtm110) cc_final: 0.7241 (mtm110) REVERT: D 187 MET cc_start: 0.7298 (mmm) cc_final: 0.6978 (mtp) REVERT: D 251 ASN cc_start: 0.7519 (p0) cc_final: 0.7214 (p0) REVERT: D 314 LYS cc_start: 0.7413 (tptm) cc_final: 0.7047 (tptm) REVERT: D 327 GLN cc_start: 0.7883 (mm-40) cc_final: 0.7637 (mm-40) REVERT: D 331 GLU cc_start: 0.7070 (mp0) cc_final: 0.6601 (mp0) REVERT: D 332 GLN cc_start: 0.7450 (tp40) cc_final: 0.7147 (tp40) REVERT: D 366 VAL cc_start: 0.8602 (t) cc_final: 0.8328 (p) REVERT: D 378 ASN cc_start: 0.7855 (m-40) cc_final: 0.7012 (m-40) REVERT: D 382 ASP cc_start: 0.7307 (m-30) cc_final: 0.6747 (m-30) REVERT: D 385 VAL cc_start: 0.8535 (t) cc_final: 0.8210 (p) REVERT: E 53 ASP cc_start: 0.7062 (t0) cc_final: 0.6574 (t0) REVERT: E 61 GLN cc_start: 0.7626 (mp10) cc_final: 0.7253 (mp10) REVERT: E 71 SER cc_start: 0.7709 (p) cc_final: 0.7394 (t) REVERT: E 85 GLU cc_start: 0.6880 (OUTLIER) cc_final: 0.6533 (tm-30) REVERT: E 125 LEU cc_start: 0.8201 (mt) cc_final: 0.7931 (mp) REVERT: E 142 ASP cc_start: 0.7360 (m-30) cc_final: 0.7023 (m-30) REVERT: E 153 ASN cc_start: 0.7721 (t0) cc_final: 0.7271 (p0) REVERT: E 154 LEU cc_start: 0.7664 (pp) cc_final: 0.7326 (mt) REVERT: E 157 ARG cc_start: 0.7049 (mtp180) cc_final: 0.6664 (mtp180) REVERT: E 160 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.8041 (mt) REVERT: E 178 ILE cc_start: 0.7995 (mt) cc_final: 0.7787 (mm) REVERT: E 181 TYR cc_start: 0.8301 (t80) cc_final: 0.7999 (t80) REVERT: E 200 GLN cc_start: 0.7429 (mm-40) cc_final: 0.6977 (mt0) REVERT: E 222 MET cc_start: 0.6316 (tpp) cc_final: 0.5914 (mpp) REVERT: E 228 ARG cc_start: 0.7083 (mtm-85) cc_final: 0.6756 (mtt180) REVERT: E 251 ASN cc_start: 0.7253 (t0) cc_final: 0.6919 (t0) REVERT: E 252 MET cc_start: 0.7645 (mmm) cc_final: 0.7436 (mtt) REVERT: E 283 VAL cc_start: 0.8474 (t) cc_final: 0.8027 (m) REVERT: E 294 MET cc_start: 0.6659 (mmm) cc_final: 0.6222 (mmm) REVERT: E 306 GLN cc_start: 0.7066 (mp10) cc_final: 0.6648 (mp10) REVERT: E 312 TRP cc_start: 0.7994 (t60) cc_final: 0.7746 (t60) REVERT: F 50 GLU cc_start: 0.7844 (mm-30) cc_final: 0.7302 (mm-30) REVERT: F 65 MET cc_start: 0.7484 (mmm) cc_final: 0.7269 (mmm) REVERT: F 80 THR cc_start: 0.8037 (t) cc_final: 0.7660 (p) REVERT: F 105 LYS cc_start: 0.8007 (mttt) cc_final: 0.7524 (mttp) REVERT: F 122 SER cc_start: 0.8507 (m) cc_final: 0.8179 (p) REVERT: F 124 GLN cc_start: 0.7243 (tp40) cc_final: 0.6964 (tp40) REVERT: F 133 LYS cc_start: 0.7857 (mttt) cc_final: 0.7384 (mttt) REVERT: F 136 LEU cc_start: 0.7522 (OUTLIER) cc_final: 0.7273 (pp) REVERT: F 138 LYS cc_start: 0.8425 (ttpt) cc_final: 0.8086 (tttp) REVERT: F 141 SER cc_start: 0.8348 (m) cc_final: 0.8073 (t) REVERT: F 145 ARG cc_start: 0.7286 (OUTLIER) cc_final: 0.7058 (ttm-80) REVERT: F 157 ARG cc_start: 0.7334 (mtm-85) cc_final: 0.6965 (ttm110) REVERT: F 158 GLU cc_start: 0.7225 (tp30) cc_final: 0.6355 (tp30) REVERT: F 161 GLN cc_start: 0.7345 (tp40) cc_final: 0.6659 (tp40) REVERT: F 164 ARG cc_start: 0.7552 (ttm-80) cc_final: 0.7232 (ttm110) REVERT: F 165 ASP cc_start: 0.7462 (m-30) cc_final: 0.7108 (m-30) REVERT: F 178 ILE cc_start: 0.8135 (mm) cc_final: 0.7915 (mm) REVERT: F 192 LYS cc_start: 0.8023 (mttp) cc_final: 0.7697 (mttp) REVERT: F 200 GLN cc_start: 0.7069 (OUTLIER) cc_final: 0.6406 (mp10) REVERT: F 214 GLU cc_start: 0.7580 (tp30) cc_final: 0.7286 (mm-30) REVERT: F 217 ARG cc_start: 0.6716 (ttm110) cc_final: 0.6354 (ptp-110) REVERT: F 277 ASP cc_start: 0.7684 (m-30) cc_final: 0.7340 (m-30) REVERT: F 284 LYS cc_start: 0.7820 (mmtp) cc_final: 0.7571 (mmtp) REVERT: F 288 LYS cc_start: 0.8325 (OUTLIER) cc_final: 0.7852 (mtmt) REVERT: F 317 GLN cc_start: 0.7392 (mm-40) cc_final: 0.6944 (mp10) REVERT: F 332 GLN cc_start: 0.7487 (OUTLIER) cc_final: 0.7225 (mp10) REVERT: F 337 ILE cc_start: 0.8135 (OUTLIER) cc_final: 0.7926 (mp) REVERT: F 371 GLU cc_start: 0.6267 (tp30) cc_final: 0.5775 (tp30) REVERT: F 372 ILE cc_start: 0.8654 (OUTLIER) cc_final: 0.7916 (mm) REVERT: F 379 LYS cc_start: 0.7727 (tptm) cc_final: 0.7185 (tptm) REVERT: F 382 ASP cc_start: 0.7713 (t0) cc_final: 0.7438 (m-30) REVERT: F 383 ASP cc_start: 0.7100 (m-30) cc_final: 0.6648 (m-30) REVERT: J 40 ILE cc_start: 0.8296 (mt) cc_final: 0.7978 (pt) REVERT: J 66 ILE cc_start: 0.8661 (mm) cc_final: 0.8282 (mm) REVERT: J 87 ILE cc_start: 0.8632 (tt) cc_final: 0.8391 (pt) REVERT: J 110 VAL cc_start: 0.7591 (m) cc_final: 0.7118 (p) REVERT: J 114 ILE cc_start: 0.8157 (mm) cc_final: 0.7909 (mm) REVERT: J 120 ILE cc_start: 0.8098 (mt) cc_final: 0.7734 (mm) REVERT: J 122 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.7507 (mp) REVERT: J 145 MET cc_start: 0.6750 (tmm) cc_final: 0.6147 (tmm) REVERT: J 161 ILE cc_start: 0.8385 (mm) cc_final: 0.8097 (mt) REVERT: J 181 VAL cc_start: 0.8647 (t) cc_final: 0.8340 (p) REVERT: J 184 MET cc_start: 0.7648 (mtm) cc_final: 0.7442 (mtm) REVERT: J 213 ILE cc_start: 0.8288 (OUTLIER) cc_final: 0.8035 (mt) REVERT: J 216 LEU cc_start: 0.8555 (tp) cc_final: 0.8289 (tt) REVERT: J 217 GLN cc_start: 0.7854 (tp40) cc_final: 0.7489 (tp40) REVERT: J 220 LEU cc_start: 0.8121 (mt) cc_final: 0.7876 (mt) REVERT: J 252 GLU cc_start: 0.7270 (mm-30) cc_final: 0.6685 (mm-30) REVERT: J 268 ARG cc_start: 0.7756 (ttt90) cc_final: 0.7309 (mmm-85) REVERT: J 271 THR cc_start: 0.8366 (m) cc_final: 0.8150 (p) REVERT: J 282 MET cc_start: 0.7747 (ttt) cc_final: 0.7439 (ttm) REVERT: J 297 GLU cc_start: 0.7370 (tt0) cc_final: 0.7141 (tt0) REVERT: J 308 LEU cc_start: 0.7990 (mt) cc_final: 0.7738 (mm) REVERT: J 327 PHE cc_start: 0.6785 (t80) cc_final: 0.5994 (t80) REVERT: J 334 ARG cc_start: 0.7655 (mtm180) cc_final: 0.7424 (mtm180) REVERT: J 342 ILE cc_start: 0.8143 (mm) cc_final: 0.7827 (tp) REVERT: J 343 MET cc_start: 0.7205 (tpp) cc_final: 0.6955 (mpp) REVERT: J 353 TYR cc_start: 0.6980 (m-80) cc_final: 0.6564 (m-80) REVERT: J 395 LEU cc_start: 0.7886 (mt) cc_final: 0.7483 (mt) REVERT: J 402 SER cc_start: 0.8070 (t) cc_final: 0.7836 (m) REVERT: J 403 ASN cc_start: 0.8252 (m-40) cc_final: 0.7839 (m110) REVERT: J 406 ARG cc_start: 0.7284 (ttp80) cc_final: 0.6996 (ttp80) REVERT: J 408 LEU cc_start: 0.7461 (OUTLIER) cc_final: 0.7143 (tt) REVERT: J 416 ILE cc_start: 0.8310 (mt) cc_final: 0.8004 (tp) REVERT: J 420 MET cc_start: 0.7404 (ttt) cc_final: 0.7102 (ttt) REVERT: J 421 TRP cc_start: 0.8096 (t60) cc_final: 0.7637 (t60) REVERT: J 447 TYR cc_start: 0.8424 (m-80) cc_final: 0.8007 (m-80) REVERT: J 455 MET cc_start: 0.7071 (OUTLIER) cc_final: 0.6843 (ptp) REVERT: J 457 GLN cc_start: 0.7747 (mm-40) cc_final: 0.7340 (mm-40) REVERT: J 471 GLN cc_start: 0.7788 (mm-40) cc_final: 0.7240 (mm-40) REVERT: J 489 LEU cc_start: 0.8398 (mt) cc_final: 0.8161 (mt) REVERT: J 491 LEU cc_start: 0.7619 (mt) cc_final: 0.7365 (pp) REVERT: G 3 LEU cc_start: 0.8703 (tt) cc_final: 0.8356 (tp) REVERT: G 5 GLN cc_start: 0.8382 (mt0) cc_final: 0.7759 (mt0) REVERT: G 9 GLN cc_start: 0.7096 (tm-30) cc_final: 0.6684 (tm-30) REVERT: G 17 LEU cc_start: 0.8621 (mp) cc_final: 0.8173 (tt) REVERT: G 24 ARG cc_start: 0.8069 (OUTLIER) cc_final: 0.7670 (tpm170) REVERT: G 29 GLU cc_start: 0.7734 (tp30) cc_final: 0.6557 (tp30) REVERT: G 32 ASN cc_start: 0.8171 (m-40) cc_final: 0.6889 (p0) REVERT: G 76 PHE cc_start: 0.7282 (t80) cc_final: 0.7010 (t80) REVERT: G 87 GLN cc_start: 0.8457 (tp-100) cc_final: 0.8064 (tp40) REVERT: G 94 GLN cc_start: 0.8391 (tp40) cc_final: 0.8093 (mm-40) REVERT: G 103 GLN cc_start: 0.8277 (mt0) cc_final: 0.7893 (mm-40) REVERT: G 104 THR cc_start: 0.8545 (m) cc_final: 0.8345 (p) REVERT: G 117 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8574 (mp) REVERT: G 130 LYS cc_start: 0.8681 (tttt) cc_final: 0.8021 (ttpp) REVERT: G 133 ILE cc_start: 0.8701 (OUTLIER) cc_final: 0.8469 (tp) REVERT: G 168 GLU cc_start: 0.8371 (tt0) cc_final: 0.8019 (tt0) REVERT: G 169 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8413 (mm) REVERT: G 181 GLN cc_start: 0.8366 (mm-40) cc_final: 0.7738 (tm-30) REVERT: G 215 GLU cc_start: 0.7566 (tm-30) cc_final: 0.6562 (tm-30) REVERT: G 217 GLU cc_start: 0.8018 (tm-30) cc_final: 0.7593 (tm-30) REVERT: G 230 GLN cc_start: 0.8504 (OUTLIER) cc_final: 0.7932 (pp30) REVERT: G 231 ASP cc_start: 0.8160 (m-30) cc_final: 0.7644 (m-30) REVERT: G 232 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8809 (tt) REVERT: G 236 GLN cc_start: 0.8422 (mt0) cc_final: 0.8118 (mt0) REVERT: G 279 MET cc_start: 0.4270 (tpt) cc_final: 0.3647 (tpt) REVERT: G 299 ASN cc_start: 0.8333 (m110) cc_final: 0.7933 (m110) REVERT: G 303 LYS cc_start: 0.8690 (mtpp) cc_final: 0.7912 (mtpp) REVERT: G 307 TYR cc_start: 0.7885 (m-80) cc_final: 0.7632 (m-80) REVERT: G 315 GLN cc_start: 0.8618 (tp40) cc_final: 0.8175 (tp-100) REVERT: G 317 GLU cc_start: 0.7948 (tp30) cc_final: 0.7087 (tp30) REVERT: G 321 ARG cc_start: 0.8386 (mtt180) cc_final: 0.7905 (mtt180) REVERT: G 333 ASN cc_start: 0.8610 (m-40) cc_final: 0.8328 (m-40) REVERT: G 344 TYR cc_start: 0.8058 (m-80) cc_final: 0.7745 (m-80) REVERT: G 401 LYS cc_start: 0.8622 (tptm) cc_final: 0.8281 (tppp) REVERT: G 404 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8639 (tp) REVERT: H 14 ASN cc_start: 0.8047 (t0) cc_final: 0.7590 (t0) REVERT: H 19 LYS cc_start: 0.8194 (OUTLIER) cc_final: 0.7599 (tttt) REVERT: H 29 GLU cc_start: 0.7903 (tp30) cc_final: 0.6994 (tp30) REVERT: H 33 GLU cc_start: 0.7012 (pm20) cc_final: 0.6008 (pm20) REVERT: H 89 LYS cc_start: 0.8625 (mmmt) cc_final: 0.8131 (mmmt) REVERT: H 94 GLN cc_start: 0.8049 (tp40) cc_final: 0.7763 (tp40) REVERT: H 129 GLN cc_start: 0.8349 (tt0) cc_final: 0.7987 (tt0) REVERT: H 131 GLU cc_start: 0.8028 (tp30) cc_final: 0.7753 (tp30) REVERT: H 135 ARG cc_start: 0.8098 (OUTLIER) cc_final: 0.7472 (mmm160) REVERT: H 138 ASP cc_start: 0.7959 (OUTLIER) cc_final: 0.7493 (t0) REVERT: H 162 ASP cc_start: 0.8225 (m-30) cc_final: 0.7803 (m-30) REVERT: H 173 ASN cc_start: 0.8433 (m-40) cc_final: 0.8000 (m-40) REVERT: H 180 GLU cc_start: 0.8483 (mm-30) cc_final: 0.7946 (tm-30) REVERT: H 181 GLN cc_start: 0.7950 (tm-30) cc_final: 0.7595 (tm-30) REVERT: H 184 GLN cc_start: 0.8482 (tt0) cc_final: 0.7937 (tm-30) REVERT: H 218 LYS cc_start: 0.8729 (mmtt) cc_final: 0.8466 (mmtt) REVERT: H 231 ASP cc_start: 0.7611 (t0) cc_final: 0.7282 (t70) REVERT: H 234 ARG cc_start: 0.7894 (mmm-85) cc_final: 0.7206 (mmm-85) REVERT: H 236 GLN cc_start: 0.7777 (pp30) cc_final: 0.7339 (pp30) REVERT: H 237 ILE cc_start: 0.8702 (mt) cc_final: 0.7969 (mt) REVERT: H 238 ARG cc_start: 0.8279 (mtt180) cc_final: 0.8028 (mtt90) REVERT: H 239 GLN cc_start: 0.8486 (pp30) cc_final: 0.8205 (pp30) REVERT: H 301 GLN cc_start: 0.8325 (mt0) cc_final: 0.7797 (pm20) REVERT: H 303 LYS cc_start: 0.8358 (mttt) cc_final: 0.7855 (mttt) REVERT: H 314 GLU cc_start: 0.7344 (mm-30) cc_final: 0.6969 (mm-30) REVERT: H 317 GLU cc_start: 0.7642 (tp30) cc_final: 0.7197 (tp30) REVERT: H 340 SER cc_start: 0.8752 (m) cc_final: 0.8215 (p) REVERT: H 356 ASP cc_start: 0.8369 (t0) cc_final: 0.8030 (t0) REVERT: H 362 TYR cc_start: 0.8791 (t80) cc_final: 0.8513 (t80) REVERT: H 374 ASP cc_start: 0.7735 (t0) cc_final: 0.7373 (t0) REVERT: H 392 ASN cc_start: 0.8401 (m-40) cc_final: 0.7876 (t0) REVERT: H 396 ASN cc_start: 0.8165 (m-40) cc_final: 0.7695 (m110) REVERT: H 397 GLN cc_start: 0.8140 (tt0) cc_final: 0.7439 (tm-30) REVERT: I 4 MET cc_start: 0.7868 (mmm) cc_final: 0.7492 (tmm) REVERT: I 8 GLN cc_start: 0.8592 (mm-40) cc_final: 0.8288 (tp-100) REVERT: I 16 GLU cc_start: 0.7989 (mp0) cc_final: 0.7466 (mp0) REVERT: I 24 ARG cc_start: 0.8060 (ttp-170) cc_final: 0.7621 (ttp-110) REVERT: I 29 GLU cc_start: 0.7816 (tp30) cc_final: 0.7108 (tp30) REVERT: I 30 LYS cc_start: 0.8793 (mttt) cc_final: 0.8591 (mttt) REVERT: I 31 ILE cc_start: 0.9124 (mt) cc_final: 0.8837 (mm) REVERT: I 32 ASN cc_start: 0.8600 (m-40) cc_final: 0.8018 (m110) REVERT: I 76 PHE cc_start: 0.7615 (t80) cc_final: 0.6869 (t80) REVERT: I 89 LYS cc_start: 0.8447 (mmtp) cc_final: 0.8202 (mmtp) REVERT: I 99 GLN cc_start: 0.8291 (mt0) cc_final: 0.8015 (mt0) REVERT: I 124 SER cc_start: 0.8623 (t) cc_final: 0.8412 (p) REVERT: I 160 GLN cc_start: 0.8227 (mm-40) cc_final: 0.8007 (mm-40) REVERT: I 185 ILE cc_start: 0.9192 (mt) cc_final: 0.8945 (tt) REVERT: I 188 ASN cc_start: 0.7866 (p0) cc_final: 0.7547 (p0) REVERT: I 213 LEU cc_start: 0.8960 (mt) cc_final: 0.8758 (mt) REVERT: I 215 GLU cc_start: 0.7992 (tp30) cc_final: 0.7499 (tp30) REVERT: I 224 LEU cc_start: 0.8822 (tp) cc_final: 0.7878 (mm) REVERT: I 225 GLN cc_start: 0.7880 (tm-30) cc_final: 0.7214 (tm-30) REVERT: I 227 ARG cc_start: 0.7737 (mtm-85) cc_final: 0.7093 (mtm-85) REVERT: I 230 GLN cc_start: 0.7992 (tm-30) cc_final: 0.7679 (tm-30) REVERT: I 235 GLU cc_start: 0.7767 (tp30) cc_final: 0.7297 (tp30) REVERT: I 236 GLN cc_start: 0.8320 (mt0) cc_final: 0.7962 (mt0) REVERT: I 238 ARG cc_start: 0.8096 (mpt180) cc_final: 0.7690 (mpt180) REVERT: I 297 MET cc_start: 0.6508 (tmm) cc_final: 0.6082 (tmm) REVERT: I 301 GLN cc_start: 0.8403 (tt0) cc_final: 0.8055 (mt0) REVERT: I 302 VAL cc_start: 0.8962 (t) cc_final: 0.8690 (t) REVERT: I 306 GLN cc_start: 0.8376 (mt0) cc_final: 0.8166 (mp10) REVERT: I 314 GLU cc_start: 0.7182 (mt-10) cc_final: 0.6746 (mt-10) REVERT: I 315 GLN cc_start: 0.8097 (mt0) cc_final: 0.7132 (mt0) REVERT: I 325 GLN cc_start: 0.8344 (pp30) cc_final: 0.7890 (pp30) REVERT: I 337 SER cc_start: 0.9054 (t) cc_final: 0.8845 (p) REVERT: I 395 ILE cc_start: 0.9124 (tt) cc_final: 0.8863 (tp) REVERT: I 396 ASN cc_start: 0.8297 (m-40) cc_final: 0.7761 (m-40) REVERT: I 398 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8665 (mt) outliers start: 158 outliers final: 101 residues processed: 1330 average time/residue: 0.4612 time to fit residues: 921.6215 Evaluate side-chains 1370 residues out of total 3232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 1237 time to evaluate : 3.348 ------------------------------------------------------------------------------- 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 131 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 175 ASP 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 251 ASN Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 288 LYS Chi-restraints excluded: chain A residue 347 THR 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 278 ILE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 294 MET Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 335 LEU 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 231 VAL Chi-restraints excluded: chain C residue 265 ASN 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 330 LEU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 340 SER Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain D residue 84 LYS Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 115 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 337 ILE 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 103 LYS Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 160 LEU 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 309 THR Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 342 LEU Chi-restraints excluded: chain E residue 344 SER Chi-restraints excluded: chain E residue 355 LEU 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 136 LEU Chi-restraints excluded: chain F residue 145 ARG Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 153 ASN 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 200 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 303 LEU Chi-restraints excluded: chain F residue 332 GLN Chi-restraints excluded: chain F residue 337 ILE Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain F residue 353 GLN Chi-restraints excluded: chain F residue 372 ILE Chi-restraints excluded: chain F residue 386 LYS Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain J residue 84 TRP Chi-restraints excluded: chain J residue 122 LEU Chi-restraints excluded: chain J residue 213 ILE Chi-restraints excluded: chain J residue 237 LEU Chi-restraints excluded: chain J residue 253 LEU Chi-restraints excluded: chain J residue 290 LEU Chi-restraints excluded: chain J residue 293 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 11 ARG Chi-restraints excluded: chain G residue 24 ARG Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 133 ILE Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain G residue 196 LEU 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 272 THR Chi-restraints excluded: chain G residue 300 SER Chi-restraints excluded: chain G residue 318 SER Chi-restraints excluded: chain G residue 398 LEU Chi-restraints excluded: chain G residue 404 LEU Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 19 LYS Chi-restraints excluded: chain H residue 35 ARG Chi-restraints excluded: chain H residue 135 ARG Chi-restraints excluded: chain H residue 138 ASP Chi-restraints excluded: chain H residue 205 LYS Chi-restraints excluded: chain H residue 221 LEU Chi-restraints excluded: chain H residue 286 LEU Chi-restraints excluded: chain H residue 404 LEU Chi-restraints excluded: chain H residue 413 LEU Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain I residue 58 ASN Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 203 THR Chi-restraints excluded: chain I residue 232 LEU 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 328 ARG Chi-restraints excluded: chain I residue 398 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 242 optimal weight: 1.9990 chunk 276 optimal weight: 4.9990 chunk 307 optimal weight: 0.9990 chunk 351 optimal weight: 4.9990 chunk 14 optimal weight: 0.6980 chunk 222 optimal weight: 2.9990 chunk 341 optimal weight: 2.9990 chunk 301 optimal weight: 1.9990 chunk 302 optimal weight: 1.9990 chunk 257 optimal weight: 3.9990 chunk 266 optimal weight: 0.1980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 140 GLN ** B 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 ASN ** C 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 61 GLN F 251 ASN F 317 GLN F 346 ASN J 34 ASN J 467 GLN J 478 ASN ** G 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 GLN G 156 ASN ** G 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 426 ASN ** H 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 136 GLN I 320 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.112060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.094203 restraints weight = 58866.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.097127 restraints weight = 25857.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.098985 restraints weight = 13981.812| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.6694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 30315 Z= 0.221 Angle : 0.702 18.358 41246 Z= 0.365 Chirality : 0.045 0.334 4889 Planarity : 0.005 0.104 5392 Dihedral : 4.324 20.205 4179 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 5.01 % Allowed : 25.77 % Favored : 69.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.14), residues: 3860 helix: 2.72 (0.11), residues: 2009 sheet: -0.20 (0.23), residues: 493 loop : -1.24 (0.16), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP E 253 HIS 0.011 0.001 HIS I 320 PHE 0.034 0.002 PHE H 309 TYR 0.030 0.002 TYR D 143 ARG 0.010 0.001 ARG I 35 Details of bonding type rmsd hydrogen bonds : bond 0.06646 ( 1888) hydrogen bonds : angle 4.45979 ( 5523) covalent geometry : bond 0.00468 (30315) covalent geometry : angle 0.70180 (41246) *********************** 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 1416 residues out of total 3232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 1254 time to evaluate : 3.163 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 49 PHE cc_start: 0.7215 (m-80) cc_final: 0.6644 (m-80) REVERT: A 50 GLU cc_start: 0.6978 (mm-30) cc_final: 0.6755 (mm-30) REVERT: A 56 TYR cc_start: 0.7746 (m-80) cc_final: 0.7038 (m-80) REVERT: A 130 GLU cc_start: 0.7619 (mm-30) cc_final: 0.7200 (mm-30) REVERT: A 138 LYS cc_start: 0.8235 (tttt) cc_final: 0.7869 (tttm) REVERT: A 142 ASP cc_start: 0.7705 (t0) cc_final: 0.7301 (t0) REVERT: A 143 TYR cc_start: 0.8314 (t80) cc_final: 0.7804 (t80) REVERT: A 158 GLU cc_start: 0.7781 (mm-30) cc_final: 0.6593 (tm-30) REVERT: A 159 GLU cc_start: 0.7418 (pm20) cc_final: 0.7123 (pm20) REVERT: A 175 ASP cc_start: 0.6865 (OUTLIER) cc_final: 0.6384 (m-30) REVERT: A 189 LEU cc_start: 0.8391 (mt) cc_final: 0.8170 (mt) REVERT: A 200 GLN cc_start: 0.7605 (mt0) cc_final: 0.7397 (mm-40) REVERT: A 214 GLU cc_start: 0.7652 (mm-30) cc_final: 0.7213 (mm-30) REVERT: A 228 ARG cc_start: 0.7668 (mtm-85) cc_final: 0.7375 (mtm-85) REVERT: A 259 LYS cc_start: 0.8190 (mtmm) cc_final: 0.7774 (mtmm) REVERT: A 284 LYS cc_start: 0.7481 (mtpp) cc_final: 0.7202 (mtpp) REVERT: A 306 GLN cc_start: 0.7001 (tp-100) cc_final: 0.6793 (tp-100) REVERT: A 317 GLN cc_start: 0.7683 (mm-40) cc_final: 0.7342 (mm-40) REVERT: A 324 GLU cc_start: 0.6275 (tp30) cc_final: 0.5839 (tp30) REVERT: A 347 THR cc_start: 0.7290 (OUTLIER) cc_final: 0.6796 (p) REVERT: A 371 GLU cc_start: 0.7395 (pm20) cc_final: 0.6876 (pm20) REVERT: A 379 LYS cc_start: 0.7966 (tttt) cc_final: 0.7705 (tttt) REVERT: A 381 ILE cc_start: 0.8596 (mt) cc_final: 0.8292 (mt) REVERT: B 50 GLU cc_start: 0.7582 (mm-30) cc_final: 0.7040 (mm-30) REVERT: B 65 MET cc_start: 0.6868 (mtm) cc_final: 0.6606 (mtp) REVERT: B 66 SER cc_start: 0.7770 (t) cc_final: 0.7524 (p) REVERT: B 93 ASP cc_start: 0.7928 (t0) cc_final: 0.7590 (t70) REVERT: B 117 GLN cc_start: 0.7626 (OUTLIER) cc_final: 0.7184 (tt0) REVERT: B 123 LYS cc_start: 0.7584 (mttp) cc_final: 0.6986 (mttp) REVERT: B 130 GLU cc_start: 0.7256 (mm-30) cc_final: 0.6700 (tm-30) REVERT: B 134 ILE cc_start: 0.8440 (mt) cc_final: 0.8170 (mp) REVERT: B 138 LYS cc_start: 0.8635 (ttpp) cc_final: 0.8403 (ttpp) REVERT: B 146 ARG cc_start: 0.7580 (tpp80) cc_final: 0.7177 (mpp80) REVERT: B 158 GLU cc_start: 0.6933 (tt0) cc_final: 0.6379 (tm-30) REVERT: B 161 GLN cc_start: 0.7736 (tp40) cc_final: 0.7317 (mm-40) REVERT: B 162 HIS cc_start: 0.7896 (m-70) cc_final: 0.6815 (m90) REVERT: B 171 GLN cc_start: 0.8046 (tp-100) cc_final: 0.7745 (tp40) REVERT: B 184 ASN cc_start: 0.8034 (t0) cc_final: 0.7817 (t0) REVERT: B 284 LYS cc_start: 0.7884 (mtpt) cc_final: 0.7624 (mtpt) REVERT: B 294 MET cc_start: 0.7227 (OUTLIER) cc_final: 0.6974 (mtp) REVERT: B 328 LYS cc_start: 0.8264 (mmpt) cc_final: 0.7846 (mmpt) REVERT: B 330 LEU cc_start: 0.8172 (tt) cc_final: 0.7949 (tp) REVERT: B 332 GLN cc_start: 0.7548 (mm-40) cc_final: 0.7266 (mm-40) REVERT: B 386 LYS cc_start: 0.8233 (tttt) cc_final: 0.7856 (tttt) REVERT: C 53 ASP cc_start: 0.6791 (t0) cc_final: 0.6588 (t0) REVERT: C 54 ASP cc_start: 0.7492 (t0) cc_final: 0.7198 (t0) REVERT: C 117 GLN cc_start: 0.7323 (mt0) cc_final: 0.6827 (mt0) REVERT: C 121 ASN cc_start: 0.7276 (m-40) cc_final: 0.6970 (m-40) REVERT: C 130 GLU cc_start: 0.7995 (tp30) cc_final: 0.7760 (tp30) REVERT: C 133 LYS cc_start: 0.8273 (mtpt) cc_final: 0.7935 (mtpt) REVERT: C 231 VAL cc_start: 0.8369 (OUTLIER) cc_final: 0.8081 (p) REVERT: C 259 LYS cc_start: 0.7866 (mtmm) cc_final: 0.7665 (mttm) REVERT: C 265 ASN cc_start: 0.8218 (OUTLIER) cc_final: 0.7663 (t0) REVERT: C 274 ILE cc_start: 0.8557 (mt) cc_final: 0.8236 (mp) REVERT: C 284 LYS cc_start: 0.8255 (mmmt) cc_final: 0.7850 (mtmt) REVERT: C 296 THR cc_start: 0.7482 (p) cc_final: 0.7093 (t) REVERT: C 302 LEU cc_start: 0.8597 (tp) cc_final: 0.8221 (tt) REVERT: C 317 GLN cc_start: 0.7911 (mm-40) cc_final: 0.7665 (mm-40) REVERT: C 332 GLN cc_start: 0.7215 (tm-30) cc_final: 0.6971 (tp40) REVERT: C 340 SER cc_start: 0.8330 (OUTLIER) cc_final: 0.8006 (p) REVERT: C 350 ARG cc_start: 0.5781 (mtm-85) cc_final: 0.5549 (mtm-85) REVERT: C 379 LYS cc_start: 0.7830 (ttmt) cc_final: 0.7572 (ttmt) REVERT: D 50 GLU cc_start: 0.6690 (OUTLIER) cc_final: 0.6275 (tp30) REVERT: D 54 ASP cc_start: 0.6796 (t0) cc_final: 0.5862 (t0) REVERT: D 73 THR cc_start: 0.8606 (m) cc_final: 0.8316 (m) REVERT: D 110 SER cc_start: 0.8509 (t) cc_final: 0.8300 (m) REVERT: D 117 GLN cc_start: 0.7921 (tt0) cc_final: 0.7293 (tt0) REVERT: D 120 ILE cc_start: 0.8253 (mm) cc_final: 0.8043 (mt) REVERT: D 121 ASN cc_start: 0.7863 (m-40) cc_final: 0.7422 (m-40) REVERT: D 129 ILE cc_start: 0.8323 (mt) cc_final: 0.8075 (mm) REVERT: D 138 LYS cc_start: 0.8144 (tttt) cc_final: 0.7800 (tttt) REVERT: D 157 ARG cc_start: 0.7488 (mtm110) cc_final: 0.7238 (mtm110) REVERT: D 187 MET cc_start: 0.7365 (mmm) cc_final: 0.7031 (mtp) REVERT: D 314 LYS cc_start: 0.7433 (tptm) cc_final: 0.7084 (tptm) REVERT: D 319 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8489 (tp) REVERT: D 324 GLU cc_start: 0.6815 (tm-30) cc_final: 0.6474 (tm-30) REVERT: D 327 GLN cc_start: 0.7889 (mm-40) cc_final: 0.7673 (mm-40) REVERT: D 331 GLU cc_start: 0.7079 (mp0) cc_final: 0.6598 (mp0) REVERT: D 332 GLN cc_start: 0.7455 (tp40) cc_final: 0.7133 (tp40) REVERT: D 366 VAL cc_start: 0.8611 (t) cc_final: 0.8332 (p) REVERT: D 378 ASN cc_start: 0.7875 (m-40) cc_final: 0.7048 (m-40) REVERT: D 382 ASP cc_start: 0.7304 (m-30) cc_final: 0.6767 (m-30) REVERT: D 385 VAL cc_start: 0.8555 (t) cc_final: 0.8235 (p) REVERT: E 53 ASP cc_start: 0.7067 (t0) cc_final: 0.6573 (t0) REVERT: E 61 GLN cc_start: 0.7657 (mp10) cc_final: 0.7286 (mp10) REVERT: E 71 SER cc_start: 0.7712 (p) cc_final: 0.7392 (t) REVERT: E 85 GLU cc_start: 0.6879 (OUTLIER) cc_final: 0.6515 (tm-30) REVERT: E 125 LEU cc_start: 0.8195 (mt) cc_final: 0.7913 (mp) REVERT: E 142 ASP cc_start: 0.7405 (m-30) cc_final: 0.7084 (m-30) REVERT: E 153 ASN cc_start: 0.7824 (t0) cc_final: 0.7389 (p0) REVERT: E 154 LEU cc_start: 0.7873 (pp) cc_final: 0.7549 (mt) REVERT: E 157 ARG cc_start: 0.7080 (mtp180) cc_final: 0.6726 (mtp180) REVERT: E 160 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8111 (mt) REVERT: E 181 TYR cc_start: 0.8244 (t80) cc_final: 0.8018 (t80) REVERT: E 200 GLN cc_start: 0.7442 (mm-40) cc_final: 0.7006 (mt0) REVERT: E 222 MET cc_start: 0.6446 (tpp) cc_final: 0.6022 (mpp) REVERT: E 251 ASN cc_start: 0.7297 (t0) cc_final: 0.6978 (t0) REVERT: E 283 VAL cc_start: 0.8452 (t) cc_final: 0.8009 (m) REVERT: E 294 MET cc_start: 0.6649 (mmm) cc_final: 0.6256 (mmm) REVERT: E 300 PHE cc_start: 0.7659 (m-10) cc_final: 0.7377 (m-80) REVERT: E 312 TRP cc_start: 0.8026 (t60) cc_final: 0.7774 (t60) REVERT: F 50 GLU cc_start: 0.7837 (mm-30) cc_final: 0.7288 (mm-30) REVERT: F 65 MET cc_start: 0.7520 (mmm) cc_final: 0.7318 (mmm) REVERT: F 80 THR cc_start: 0.8040 (t) cc_final: 0.7683 (p) REVERT: F 122 SER cc_start: 0.8476 (m) cc_final: 0.8128 (p) REVERT: F 124 GLN cc_start: 0.7300 (tp40) cc_final: 0.7008 (tp40) REVERT: F 126 GLN cc_start: 0.7325 (tp40) cc_final: 0.6919 (tp40) REVERT: F 130 GLU cc_start: 0.7685 (tp30) cc_final: 0.7401 (tp30) REVERT: F 138 LYS cc_start: 0.8445 (ttpt) cc_final: 0.8159 (ttpp) REVERT: F 145 ARG cc_start: 0.7304 (OUTLIER) cc_final: 0.7056 (ttm-80) REVERT: F 157 ARG cc_start: 0.7323 (mtm-85) cc_final: 0.7061 (mtm-85) REVERT: F 158 GLU cc_start: 0.7241 (tp30) cc_final: 0.6384 (tp30) REVERT: F 161 GLN cc_start: 0.7421 (tp40) cc_final: 0.6743 (tp40) REVERT: F 164 ARG cc_start: 0.7599 (ttm-80) cc_final: 0.7299 (ttm110) REVERT: F 165 ASP cc_start: 0.7578 (m-30) cc_final: 0.7227 (m-30) REVERT: F 175 ASP cc_start: 0.7589 (m-30) cc_final: 0.7368 (m-30) REVERT: F 192 LYS cc_start: 0.8012 (mttp) cc_final: 0.7676 (mttp) REVERT: F 200 GLN cc_start: 0.7089 (OUTLIER) cc_final: 0.6442 (mp10) REVERT: F 214 GLU cc_start: 0.7624 (tp30) cc_final: 0.7319 (mm-30) REVERT: F 217 ARG cc_start: 0.6646 (ttm110) cc_final: 0.6251 (ptp-110) REVERT: F 277 ASP cc_start: 0.7782 (m-30) cc_final: 0.7393 (m-30) REVERT: F 284 LYS cc_start: 0.7914 (mmtp) cc_final: 0.7641 (mmtp) REVERT: F 288 LYS cc_start: 0.8346 (OUTLIER) cc_final: 0.7851 (mtmt) REVERT: F 317 GLN cc_start: 0.7397 (mm110) cc_final: 0.7057 (mp10) REVERT: F 332 GLN cc_start: 0.7526 (OUTLIER) cc_final: 0.7053 (mp10) REVERT: F 371 GLU cc_start: 0.6281 (tp30) cc_final: 0.5831 (tp30) REVERT: F 372 ILE cc_start: 0.8684 (OUTLIER) cc_final: 0.7923 (mm) REVERT: F 379 LYS cc_start: 0.7743 (tptm) cc_final: 0.7208 (tptm) REVERT: F 382 ASP cc_start: 0.7737 (t0) cc_final: 0.7445 (m-30) REVERT: F 383 ASP cc_start: 0.7107 (m-30) cc_final: 0.6656 (m-30) REVERT: J 40 ILE cc_start: 0.8329 (mt) cc_final: 0.8054 (pt) REVERT: J 66 ILE cc_start: 0.8664 (mm) cc_final: 0.8292 (mm) REVERT: J 87 ILE cc_start: 0.8645 (tt) cc_final: 0.8414 (pt) REVERT: J 114 ILE cc_start: 0.8163 (mm) cc_final: 0.7921 (mm) REVERT: J 120 ILE cc_start: 0.8093 (mt) cc_final: 0.7723 (mm) REVERT: J 122 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.7571 (mp) REVERT: J 145 MET cc_start: 0.6773 (tmm) cc_final: 0.6243 (tmm) REVERT: J 161 ILE cc_start: 0.8396 (mm) cc_final: 0.8063 (mp) REVERT: J 181 VAL cc_start: 0.8653 (t) cc_final: 0.8335 (p) REVERT: J 213 ILE cc_start: 0.8277 (OUTLIER) cc_final: 0.7998 (mt) REVERT: J 217 GLN cc_start: 0.7869 (tp40) cc_final: 0.7525 (tp40) REVERT: J 220 LEU cc_start: 0.8169 (mt) cc_final: 0.7943 (mt) REVERT: J 252 GLU cc_start: 0.7277 (mm-30) cc_final: 0.6742 (mm-30) REVERT: J 268 ARG cc_start: 0.7749 (ttt90) cc_final: 0.7144 (mmm-85) REVERT: J 271 THR cc_start: 0.8375 (m) cc_final: 0.8169 (p) REVERT: J 282 MET cc_start: 0.7815 (ttt) cc_final: 0.7512 (ttm) REVERT: J 297 GLU cc_start: 0.7417 (tt0) cc_final: 0.7170 (tt0) REVERT: J 308 LEU cc_start: 0.7966 (mt) cc_final: 0.7727 (mm) REVERT: J 327 PHE cc_start: 0.6781 (t80) cc_final: 0.5978 (t80) REVERT: J 334 ARG cc_start: 0.7688 (mtm180) cc_final: 0.7395 (mtm180) REVERT: J 342 ILE cc_start: 0.8174 (mm) cc_final: 0.7878 (tt) REVERT: J 353 TYR cc_start: 0.7029 (m-80) cc_final: 0.6587 (m-80) REVERT: J 395 LEU cc_start: 0.7965 (mt) cc_final: 0.7560 (mt) REVERT: J 402 SER cc_start: 0.8075 (t) cc_final: 0.7839 (m) REVERT: J 403 ASN cc_start: 0.8250 (m-40) cc_final: 0.7835 (m110) REVERT: J 404 PHE cc_start: 0.8285 (t80) cc_final: 0.8045 (t80) REVERT: J 406 ARG cc_start: 0.7300 (ttp80) cc_final: 0.6996 (ttp80) REVERT: J 408 LEU cc_start: 0.7537 (OUTLIER) cc_final: 0.7229 (tt) REVERT: J 416 ILE cc_start: 0.8317 (mt) cc_final: 0.8002 (tp) REVERT: J 421 TRP cc_start: 0.8144 (t60) cc_final: 0.7872 (t60) REVERT: J 436 VAL cc_start: 0.8070 (t) cc_final: 0.7579 (m) REVERT: J 471 GLN cc_start: 0.7798 (mm-40) cc_final: 0.7232 (mm-40) REVERT: J 489 LEU cc_start: 0.8418 (mt) cc_final: 0.8198 (mt) REVERT: J 491 LEU cc_start: 0.7722 (mt) cc_final: 0.7432 (pp) REVERT: G 5 GLN cc_start: 0.8383 (mt0) cc_final: 0.7710 (mt0) REVERT: G 9 GLN cc_start: 0.7155 (tm-30) cc_final: 0.6878 (tm-30) REVERT: G 17 LEU cc_start: 0.8663 (mp) cc_final: 0.8283 (tt) REVERT: G 29 GLU cc_start: 0.7815 (tp30) cc_final: 0.6803 (tp30) REVERT: G 32 ASN cc_start: 0.8204 (m-40) cc_final: 0.6976 (p0) REVERT: G 76 PHE cc_start: 0.7269 (t80) cc_final: 0.6940 (t80) REVERT: G 78 MET cc_start: 0.6594 (ptp) cc_final: 0.6176 (ppp) REVERT: G 80 LYS cc_start: 0.8478 (mttp) cc_final: 0.8271 (mmtp) REVERT: G 87 GLN cc_start: 0.8473 (tp-100) cc_final: 0.8116 (tp40) REVERT: G 94 GLN cc_start: 0.8338 (tp-100) cc_final: 0.8007 (mm-40) REVERT: G 98 TYR cc_start: 0.8146 (t80) cc_final: 0.7581 (t80) REVERT: G 101 ASP cc_start: 0.7639 (t0) cc_final: 0.6987 (t0) REVERT: G 103 GLN cc_start: 0.8266 (mt0) cc_final: 0.7869 (mm-40) REVERT: G 117 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8727 (mp) REVERT: G 130 LYS cc_start: 0.8673 (tttt) cc_final: 0.8014 (ttpp) REVERT: G 133 ILE cc_start: 0.8691 (OUTLIER) cc_final: 0.8461 (tp) REVERT: G 168 GLU cc_start: 0.8350 (tt0) cc_final: 0.7969 (tt0) REVERT: G 169 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8479 (mm) REVERT: G 181 GLN cc_start: 0.8415 (mm-40) cc_final: 0.7770 (tm-30) REVERT: G 215 GLU cc_start: 0.7624 (tm-30) cc_final: 0.6606 (tm-30) REVERT: G 217 GLU cc_start: 0.8039 (tm-30) cc_final: 0.7623 (tm-30) REVERT: G 230 GLN cc_start: 0.8546 (OUTLIER) cc_final: 0.7952 (pp30) REVERT: G 231 ASP cc_start: 0.8217 (m-30) cc_final: 0.7698 (m-30) REVERT: G 232 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8822 (tt) REVERT: G 236 GLN cc_start: 0.8480 (mt0) cc_final: 0.8181 (mt0) REVERT: G 279 MET cc_start: 0.4254 (tpt) cc_final: 0.3639 (tpt) REVERT: G 299 ASN cc_start: 0.8437 (m110) cc_final: 0.8117 (m110) REVERT: G 303 LYS cc_start: 0.8715 (mtpp) cc_final: 0.7957 (mtpp) REVERT: G 307 TYR cc_start: 0.7946 (m-80) cc_final: 0.7677 (m-80) REVERT: G 315 GLN cc_start: 0.8630 (tp40) cc_final: 0.8200 (tp-100) REVERT: G 317 GLU cc_start: 0.7974 (tp30) cc_final: 0.7114 (tp30) REVERT: G 321 ARG cc_start: 0.8386 (mtt180) cc_final: 0.7946 (mtt180) REVERT: G 333 ASN cc_start: 0.8621 (m-40) cc_final: 0.8333 (m-40) REVERT: G 344 TYR cc_start: 0.8089 (m-80) cc_final: 0.7755 (m-80) REVERT: G 385 GLU cc_start: 0.7700 (mm-30) cc_final: 0.7218 (mm-30) REVERT: G 401 LYS cc_start: 0.8544 (tptm) cc_final: 0.8201 (tppp) REVERT: G 404 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8658 (tp) REVERT: G 411 ASP cc_start: 0.6267 (t0) cc_final: 0.5892 (t0) REVERT: H 14 ASN cc_start: 0.8099 (t0) cc_final: 0.7689 (t0) REVERT: H 19 LYS cc_start: 0.8255 (OUTLIER) cc_final: 0.7737 (tttt) REVERT: H 29 GLU cc_start: 0.7934 (tp30) cc_final: 0.6891 (tp30) REVERT: H 33 GLU cc_start: 0.7115 (pm20) cc_final: 0.5962 (pm20) REVERT: H 89 LYS cc_start: 0.8648 (mmmt) cc_final: 0.8158 (mmmt) REVERT: H 94 GLN cc_start: 0.8079 (tp40) cc_final: 0.7796 (tp40) REVERT: H 129 GLN cc_start: 0.8426 (tt0) cc_final: 0.8104 (tt0) REVERT: H 131 GLU cc_start: 0.8079 (tp30) cc_final: 0.7786 (tp30) REVERT: H 135 ARG cc_start: 0.8110 (OUTLIER) cc_final: 0.7465 (mmm160) REVERT: H 136 GLN cc_start: 0.8320 (tp40) cc_final: 0.7868 (tp40) REVERT: H 138 ASP cc_start: 0.7985 (OUTLIER) cc_final: 0.7516 (t0) REVERT: H 162 ASP cc_start: 0.8233 (m-30) cc_final: 0.7834 (m-30) REVERT: H 173 ASN cc_start: 0.8459 (m-40) cc_final: 0.7998 (m-40) REVERT: H 180 GLU cc_start: 0.8472 (mm-30) cc_final: 0.7911 (tm-30) REVERT: H 181 GLN cc_start: 0.7944 (tm-30) cc_final: 0.7623 (tm-30) REVERT: H 184 GLN cc_start: 0.8506 (tt0) cc_final: 0.8011 (tm-30) REVERT: H 214 LYS cc_start: 0.8776 (mtmm) cc_final: 0.8261 (ptpp) REVERT: H 218 LYS cc_start: 0.8773 (mmtt) cc_final: 0.8489 (mmtt) REVERT: H 231 ASP cc_start: 0.7655 (t0) cc_final: 0.7317 (t70) REVERT: H 234 ARG cc_start: 0.7925 (mmm-85) cc_final: 0.7267 (mmm-85) REVERT: H 236 GLN cc_start: 0.7757 (pp30) cc_final: 0.7306 (pp30) REVERT: H 237 ILE cc_start: 0.8711 (mt) cc_final: 0.7997 (mt) REVERT: H 238 ARG cc_start: 0.8365 (mtt180) cc_final: 0.8130 (mtt90) REVERT: H 239 GLN cc_start: 0.8499 (pp30) cc_final: 0.8185 (pp30) REVERT: H 301 GLN cc_start: 0.8183 (mt0) cc_final: 0.7820 (mp10) REVERT: H 303 LYS cc_start: 0.8376 (mttt) cc_final: 0.7831 (mttt) REVERT: H 314 GLU cc_start: 0.7395 (mm-30) cc_final: 0.7012 (mm-30) REVERT: H 317 GLU cc_start: 0.7657 (tp30) cc_final: 0.7211 (tp30) REVERT: H 340 SER cc_start: 0.8760 (m) cc_final: 0.8227 (p) REVERT: H 341 ILE cc_start: 0.8909 (OUTLIER) cc_final: 0.8640 (tt) REVERT: H 356 ASP cc_start: 0.8389 (t0) cc_final: 0.8056 (t0) REVERT: H 362 TYR cc_start: 0.8786 (t80) cc_final: 0.8510 (t80) REVERT: H 367 ARG cc_start: 0.7907 (mtm-85) cc_final: 0.7693 (mtm-85) REVERT: H 374 ASP cc_start: 0.7788 (t0) cc_final: 0.7384 (t0) REVERT: H 390 ARG cc_start: 0.8670 (mtt-85) cc_final: 0.8436 (ttm170) REVERT: H 392 ASN cc_start: 0.8412 (m-40) cc_final: 0.7918 (t0) REVERT: H 396 ASN cc_start: 0.8190 (m-40) cc_final: 0.7760 (m110) REVERT: H 397 GLN cc_start: 0.8153 (tt0) cc_final: 0.7476 (tm-30) REVERT: I 4 MET cc_start: 0.7890 (mmm) cc_final: 0.7556 (tmm) REVERT: I 8 GLN cc_start: 0.8582 (mm-40) cc_final: 0.7902 (tp-100) REVERT: I 16 GLU cc_start: 0.8012 (mp0) cc_final: 0.7487 (mp0) REVERT: I 28 PHE cc_start: 0.8125 (m-80) cc_final: 0.7910 (m-80) REVERT: I 29 GLU cc_start: 0.7844 (tp30) cc_final: 0.7062 (tp30) REVERT: I 30 LYS cc_start: 0.8862 (mttt) cc_final: 0.8650 (mttt) REVERT: I 31 ILE cc_start: 0.9114 (mt) cc_final: 0.8900 (mm) REVERT: I 32 ASN cc_start: 0.8629 (m-40) cc_final: 0.8063 (m110) REVERT: I 76 PHE cc_start: 0.7615 (t80) cc_final: 0.6850 (t80) REVERT: I 89 LYS cc_start: 0.8477 (mmtp) cc_final: 0.8239 (mmtp) REVERT: I 99 GLN cc_start: 0.8330 (mt0) cc_final: 0.8062 (mt0) REVERT: I 124 SER cc_start: 0.8625 (t) cc_final: 0.8419 (p) REVERT: I 160 GLN cc_start: 0.8257 (mm-40) cc_final: 0.8041 (mm-40) REVERT: I 185 ILE cc_start: 0.9196 (mt) cc_final: 0.8958 (tt) REVERT: I 188 ASN cc_start: 0.7866 (p0) cc_final: 0.7545 (p0) REVERT: I 215 GLU cc_start: 0.8052 (tp30) cc_final: 0.7557 (tp30) REVERT: I 224 LEU cc_start: 0.8867 (tp) cc_final: 0.7780 (mm) REVERT: I 225 GLN cc_start: 0.7917 (tm-30) cc_final: 0.7268 (tm-30) REVERT: I 227 ARG cc_start: 0.7781 (mtm-85) cc_final: 0.7122 (mtm-85) REVERT: I 230 GLN cc_start: 0.8023 (tm-30) cc_final: 0.7712 (tm-30) REVERT: I 235 GLU cc_start: 0.7818 (tp30) cc_final: 0.7391 (tp30) REVERT: I 236 GLN cc_start: 0.8360 (mt0) cc_final: 0.7990 (mt0) REVERT: I 238 ARG cc_start: 0.8153 (mpt180) cc_final: 0.7931 (mpt180) REVERT: I 297 MET cc_start: 0.6601 (tmm) cc_final: 0.6211 (tmm) REVERT: I 301 GLN cc_start: 0.8429 (tt0) cc_final: 0.8102 (mt0) REVERT: I 306 GLN cc_start: 0.8413 (mt0) cc_final: 0.8170 (pm20) REVERT: I 314 GLU cc_start: 0.7263 (mt-10) cc_final: 0.6846 (mt-10) REVERT: I 315 GLN cc_start: 0.8140 (mt0) cc_final: 0.7085 (mp10) REVERT: I 325 GLN cc_start: 0.8370 (pp30) cc_final: 0.7897 (pp30) REVERT: I 395 ILE cc_start: 0.9125 (tt) cc_final: 0.8862 (tp) REVERT: I 396 ASN cc_start: 0.8308 (m-40) cc_final: 0.7770 (m-40) REVERT: I 398 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8672 (mt) outliers start: 162 outliers final: 112 residues processed: 1327 average time/residue: 0.4560 time to fit residues: 911.3939 Evaluate side-chains 1384 residues out of total 3232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 1242 time to evaluate : 3.051 ------------------------------------------------------------------------------- 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 147 VAL 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 250 THR Chi-restraints excluded: chain A residue 251 ASN Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain B residue 110 SER 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 278 ILE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 294 MET Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 335 LEU 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 231 VAL Chi-restraints excluded: chain C residue 265 ASN 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 344 SER Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain D residue 84 LYS Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 115 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 319 LEU 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 65 MET Chi-restraints excluded: chain E residue 85 GLU Chi-restraints excluded: chain E residue 103 LYS Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 167 VAL 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 325 LEU Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 342 LEU Chi-restraints excluded: chain E residue 344 SER Chi-restraints excluded: chain E residue 355 LEU Chi-restraints excluded: chain E residue 373 SER Chi-restraints excluded: chain E residue 380 LEU 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 145 ARG Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 153 ASN Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 194 GLU Chi-restraints excluded: chain F residue 200 GLN 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 332 GLN Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain F residue 353 GLN Chi-restraints excluded: chain F residue 372 ILE Chi-restraints excluded: chain J residue 48 LEU Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain J residue 84 TRP Chi-restraints excluded: chain J residue 104 MET Chi-restraints excluded: chain J residue 122 LEU Chi-restraints excluded: chain J residue 213 ILE Chi-restraints excluded: chain J residue 237 LEU Chi-restraints excluded: chain J residue 253 LEU Chi-restraints excluded: chain J residue 290 LEU Chi-restraints excluded: chain J residue 293 GLN Chi-restraints excluded: chain J residue 408 LEU Chi-restraints excluded: chain J residue 490 VAL Chi-restraints excluded: chain J residue 494 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 117 LEU Chi-restraints excluded: chain G residue 133 ILE Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain G residue 196 LEU 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 272 THR Chi-restraints excluded: chain G residue 300 SER Chi-restraints excluded: chain G residue 318 SER Chi-restraints excluded: chain G residue 334 ILE Chi-restraints excluded: chain G residue 398 LEU Chi-restraints excluded: chain G residue 404 LEU Chi-restraints excluded: chain G residue 426 ASN Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 19 LYS Chi-restraints excluded: chain H residue 35 ARG Chi-restraints excluded: chain H residue 135 ARG Chi-restraints excluded: chain H residue 138 ASP Chi-restraints excluded: chain H residue 205 LYS Chi-restraints excluded: chain H residue 221 LEU Chi-restraints excluded: chain H residue 286 LEU 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 12 LEU Chi-restraints excluded: chain I residue 58 ASN Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 203 THR Chi-restraints excluded: chain I residue 232 LEU 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 328 ARG 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 222 optimal weight: 3.9990 chunk 294 optimal weight: 2.9990 chunk 162 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 327 optimal weight: 1.9990 chunk 213 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 370 optimal weight: 0.7980 chunk 348 optimal weight: 2.9990 chunk 283 optimal weight: 20.0000 chunk 310 optimal weight: 4.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN ** B 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 ASN ** C 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 251 ASN F 346 ASN J 34 ASN ** J 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 368 GLN J 449 GLN J 457 GLN J 478 ASN ** G 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 32 ASN G 94 GLN G 108 ASN G 156 ASN ** G 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 426 ASN ** H 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 188 ASN ** I 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 320 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.110929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.093224 restraints weight = 59156.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.096164 restraints weight = 25914.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.098013 restraints weight = 13952.384| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.6844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 30315 Z= 0.273 Angle : 0.746 14.842 41246 Z= 0.392 Chirality : 0.047 0.264 4889 Planarity : 0.005 0.067 5392 Dihedral : 4.506 21.908 4179 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 4.98 % Allowed : 26.11 % Favored : 68.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.14), residues: 3860 helix: 2.54 (0.11), residues: 1996 sheet: -0.24 (0.23), residues: 491 loop : -1.35 (0.16), residues: 1373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.003 TRP G 81 HIS 0.011 0.001 HIS I 320 PHE 0.034 0.002 PHE H 309 TYR 0.031 0.002 TYR D 143 ARG 0.010 0.001 ARG I 35 Details of bonding type rmsd hydrogen bonds : bond 0.06945 ( 1888) hydrogen bonds : angle 4.61350 ( 5523) covalent geometry : bond 0.00575 (30315) covalent geometry : angle 0.74649 (41246) ********************** 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 1407 residues out of total 3232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 1246 time to evaluate : 3.466 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: A 50 GLU cc_start: 0.7046 (mm-30) cc_final: 0.6804 (mm-30) REVERT: A 56 TYR cc_start: 0.7723 (m-80) cc_final: 0.6833 (m-80) REVERT: A 57 VAL cc_start: 0.8601 (t) cc_final: 0.8328 (p) REVERT: A 119 MET cc_start: 0.7380 (OUTLIER) cc_final: 0.7023 (mpp) REVERT: A 125 LEU cc_start: 0.8003 (mt) cc_final: 0.7750 (mp) REVERT: A 130 GLU cc_start: 0.7627 (mm-30) cc_final: 0.7209 (mm-30) REVERT: A 138 LYS cc_start: 0.8259 (tttt) cc_final: 0.7904 (tttm) REVERT: A 143 TYR cc_start: 0.8309 (t80) cc_final: 0.7832 (t80) REVERT: A 146 ARG cc_start: 0.7706 (mtm-85) cc_final: 0.7432 (mtm-85) REVERT: A 158 GLU cc_start: 0.7703 (mm-30) cc_final: 0.5942 (tm-30) REVERT: A 159 GLU cc_start: 0.7492 (pm20) cc_final: 0.7239 (pm20) REVERT: A 162 HIS cc_start: 0.8016 (m-70) cc_final: 0.6863 (m-70) REVERT: A 171 GLN cc_start: 0.8070 (tp40) cc_final: 0.7117 (tp40) REVERT: A 175 ASP cc_start: 0.6849 (OUTLIER) cc_final: 0.6228 (m-30) REVERT: A 189 LEU cc_start: 0.8421 (mt) cc_final: 0.8214 (mt) REVERT: A 201 GLN cc_start: 0.6898 (mm110) cc_final: 0.6538 (mm110) REVERT: A 214 GLU cc_start: 0.7615 (mm-30) cc_final: 0.7177 (mm-30) REVERT: A 228 ARG cc_start: 0.7750 (mtm-85) cc_final: 0.7329 (mtm-85) REVERT: A 259 LYS cc_start: 0.8212 (mtmm) cc_final: 0.7839 (mtmm) REVERT: A 284 LYS cc_start: 0.7452 (mtpp) cc_final: 0.7196 (mtpp) REVERT: A 317 GLN cc_start: 0.7668 (mm-40) cc_final: 0.7329 (mm-40) REVERT: A 324 GLU cc_start: 0.6273 (tp30) cc_final: 0.5944 (tp30) REVERT: A 347 THR cc_start: 0.7425 (OUTLIER) cc_final: 0.6903 (p) REVERT: A 371 GLU cc_start: 0.7390 (pm20) cc_final: 0.6776 (pm20) REVERT: A 379 LYS cc_start: 0.7974 (tttt) cc_final: 0.7718 (tttt) REVERT: A 381 ILE cc_start: 0.8576 (mt) cc_final: 0.8268 (mt) REVERT: B 50 GLU cc_start: 0.7591 (mm-30) cc_final: 0.7042 (mm-30) REVERT: B 66 SER cc_start: 0.7795 (t) cc_final: 0.7522 (p) REVERT: B 93 ASP cc_start: 0.7930 (t0) cc_final: 0.7594 (t70) REVERT: B 117 GLN cc_start: 0.7605 (OUTLIER) cc_final: 0.7115 (tt0) REVERT: B 120 ILE cc_start: 0.7989 (mm) cc_final: 0.7543 (mm) REVERT: B 123 LYS cc_start: 0.7623 (mttp) cc_final: 0.6956 (mttp) REVERT: B 130 GLU cc_start: 0.7241 (mm-30) cc_final: 0.6688 (tm-30) REVERT: B 134 ILE cc_start: 0.8427 (mt) cc_final: 0.8167 (mp) REVERT: B 138 LYS cc_start: 0.8639 (ttpp) cc_final: 0.8416 (ttpp) REVERT: B 146 ARG cc_start: 0.7592 (tpp80) cc_final: 0.7193 (mpp80) REVERT: B 158 GLU cc_start: 0.6937 (tt0) cc_final: 0.6482 (tm-30) REVERT: B 161 GLN cc_start: 0.7888 (tp40) cc_final: 0.7384 (mm-40) REVERT: B 162 HIS cc_start: 0.7884 (m-70) cc_final: 0.6884 (m90) REVERT: B 171 GLN cc_start: 0.8082 (tp-100) cc_final: 0.7765 (tp40) REVERT: B 284 LYS cc_start: 0.7939 (mtpt) cc_final: 0.7696 (mtpt) REVERT: B 294 MET cc_start: 0.7069 (OUTLIER) cc_final: 0.6843 (mtp) REVERT: B 318 ARG cc_start: 0.8186 (ptp-110) cc_final: 0.7894 (mtp85) REVERT: B 328 LYS cc_start: 0.8298 (mmpt) cc_final: 0.7832 (mmpt) REVERT: B 329 GLN cc_start: 0.7151 (mt0) cc_final: 0.6824 (mp10) REVERT: B 330 LEU cc_start: 0.8197 (tt) cc_final: 0.7968 (tp) REVERT: B 332 GLN cc_start: 0.7493 (mm-40) cc_final: 0.7207 (mm-40) REVERT: B 386 LYS cc_start: 0.8239 (tttt) cc_final: 0.7883 (tttt) REVERT: C 54 ASP cc_start: 0.7483 (t0) cc_final: 0.7239 (t0) REVERT: C 121 ASN cc_start: 0.7215 (m-40) cc_final: 0.6848 (m-40) REVERT: C 130 GLU cc_start: 0.8009 (tp30) cc_final: 0.7807 (tp30) REVERT: C 133 LYS cc_start: 0.8280 (mtpt) cc_final: 0.7954 (mtpt) REVERT: C 231 VAL cc_start: 0.8381 (OUTLIER) cc_final: 0.8087 (p) REVERT: C 265 ASN cc_start: 0.8183 (OUTLIER) cc_final: 0.7717 (t0) REVERT: C 272 VAL cc_start: 0.8103 (t) cc_final: 0.7827 (p) REVERT: C 274 ILE cc_start: 0.8567 (mt) cc_final: 0.8270 (mp) REVERT: C 284 LYS cc_start: 0.8275 (mmmt) cc_final: 0.7949 (mtmt) REVERT: C 302 LEU cc_start: 0.8596 (tp) cc_final: 0.8202 (tt) REVERT: C 317 GLN cc_start: 0.7904 (mm-40) cc_final: 0.7667 (mm110) REVERT: C 332 GLN cc_start: 0.7261 (tm-30) cc_final: 0.7045 (tp40) REVERT: C 340 SER cc_start: 0.8291 (OUTLIER) cc_final: 0.7978 (p) REVERT: C 379 LYS cc_start: 0.7816 (ttmt) cc_final: 0.7565 (ttmt) REVERT: D 50 GLU cc_start: 0.6741 (OUTLIER) cc_final: 0.6365 (tp30) REVERT: D 54 ASP cc_start: 0.6785 (t0) cc_final: 0.5789 (t0) REVERT: D 73 THR cc_start: 0.8585 (OUTLIER) cc_final: 0.8298 (m) REVERT: D 110 SER cc_start: 0.8523 (t) cc_final: 0.8312 (m) REVERT: D 117 GLN cc_start: 0.7916 (tt0) cc_final: 0.7295 (tt0) REVERT: D 120 ILE cc_start: 0.8276 (mm) cc_final: 0.8065 (mt) REVERT: D 121 ASN cc_start: 0.7885 (m-40) cc_final: 0.7442 (m-40) REVERT: D 129 ILE cc_start: 0.8321 (mt) cc_final: 0.8088 (mm) REVERT: D 138 LYS cc_start: 0.8140 (tttt) cc_final: 0.7731 (tttt) REVERT: D 145 ARG cc_start: 0.7904 (mtt90) cc_final: 0.7684 (mtm180) REVERT: D 157 ARG cc_start: 0.7431 (mtm110) cc_final: 0.7184 (mtm110) REVERT: D 187 MET cc_start: 0.7390 (mmm) cc_final: 0.7085 (mtp) REVERT: D 251 ASN cc_start: 0.7592 (p0) cc_final: 0.7317 (p0) REVERT: D 314 LYS cc_start: 0.7456 (tptm) cc_final: 0.7149 (tptm) REVERT: D 319 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8487 (tp) REVERT: D 324 GLU cc_start: 0.6832 (tm-30) cc_final: 0.6510 (tm-30) REVERT: D 331 GLU cc_start: 0.7107 (mp0) cc_final: 0.6705 (mp0) REVERT: D 332 GLN cc_start: 0.7495 (tp40) cc_final: 0.7165 (tp40) REVERT: D 366 VAL cc_start: 0.8644 (t) cc_final: 0.8372 (p) REVERT: D 378 ASN cc_start: 0.7895 (m-40) cc_final: 0.7103 (m-40) REVERT: D 382 ASP cc_start: 0.7335 (m-30) cc_final: 0.6786 (m-30) REVERT: D 385 VAL cc_start: 0.8561 (t) cc_final: 0.8234 (p) REVERT: E 53 ASP cc_start: 0.7058 (t0) cc_final: 0.6502 (t0) REVERT: E 61 GLN cc_start: 0.7663 (mp10) cc_final: 0.7303 (mp10) REVERT: E 71 SER cc_start: 0.7720 (p) cc_final: 0.7404 (t) REVERT: E 85 GLU cc_start: 0.6934 (OUTLIER) cc_final: 0.6518 (tm-30) REVERT: E 125 LEU cc_start: 0.8199 (mt) cc_final: 0.7934 (mp) REVERT: E 142 ASP cc_start: 0.7426 (m-30) cc_final: 0.6999 (m-30) REVERT: E 153 ASN cc_start: 0.7971 (t0) cc_final: 0.7563 (t0) REVERT: E 154 LEU cc_start: 0.7998 (pp) cc_final: 0.7789 (mp) REVERT: E 160 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8228 (mm) REVERT: E 181 TYR cc_start: 0.8247 (t80) cc_final: 0.8003 (t80) REVERT: E 200 GLN cc_start: 0.7463 (mm-40) cc_final: 0.7149 (mt0) REVERT: E 207 ARG cc_start: 0.8484 (ttm110) cc_final: 0.8142 (ttm110) REVERT: E 222 MET cc_start: 0.6489 (tpp) cc_final: 0.6058 (mpp) REVERT: E 228 ARG cc_start: 0.7267 (mtm-85) cc_final: 0.6959 (mtt180) REVERT: E 229 ARG cc_start: 0.7949 (ptm-80) cc_final: 0.7693 (ttp80) REVERT: E 251 ASN cc_start: 0.7311 (t0) cc_final: 0.7046 (t0) REVERT: E 294 MET cc_start: 0.6602 (mmm) cc_final: 0.6346 (tpp) REVERT: E 300 PHE cc_start: 0.7646 (m-10) cc_final: 0.7366 (m-10) REVERT: E 312 TRP cc_start: 0.8047 (t60) cc_final: 0.7771 (t60) REVERT: F 50 GLU cc_start: 0.7823 (mm-30) cc_final: 0.7268 (mm-30) REVERT: F 80 THR cc_start: 0.8050 (t) cc_final: 0.7688 (p) REVERT: F 105 LYS cc_start: 0.8020 (mttt) cc_final: 0.7778 (mttt) REVERT: F 122 SER cc_start: 0.8466 (m) cc_final: 0.8054 (p) REVERT: F 126 GLN cc_start: 0.7266 (tp40) cc_final: 0.6910 (tp40) REVERT: F 133 LYS cc_start: 0.8019 (OUTLIER) cc_final: 0.7454 (tttt) REVERT: F 138 LYS cc_start: 0.8511 (ttpt) cc_final: 0.8241 (ttpp) REVERT: F 158 GLU cc_start: 0.7241 (tp30) cc_final: 0.6393 (tp30) REVERT: F 161 GLN cc_start: 0.7501 (tp40) cc_final: 0.6736 (tp40) REVERT: F 164 ARG cc_start: 0.7635 (ttm-80) cc_final: 0.7197 (ttm110) REVERT: F 165 ASP cc_start: 0.7613 (m-30) cc_final: 0.7185 (m-30) REVERT: F 185 GLN cc_start: 0.7668 (tp40) cc_final: 0.7285 (tp40) REVERT: F 192 LYS cc_start: 0.8025 (mttp) cc_final: 0.7706 (mttp) REVERT: F 200 GLN cc_start: 0.7087 (OUTLIER) cc_final: 0.6446 (mp10) REVERT: F 205 GLU cc_start: 0.7515 (mm-30) cc_final: 0.7289 (mm-30) REVERT: F 214 GLU cc_start: 0.7605 (tp30) cc_final: 0.7308 (mm-30) REVERT: F 217 ARG cc_start: 0.6672 (ttm110) cc_final: 0.6265 (ptp-110) REVERT: F 277 ASP cc_start: 0.7835 (m-30) cc_final: 0.7419 (m-30) REVERT: F 284 LYS cc_start: 0.7976 (mmtp) cc_final: 0.7697 (mmtp) REVERT: F 288 LYS cc_start: 0.8349 (OUTLIER) cc_final: 0.7843 (mtmt) REVERT: F 317 GLN cc_start: 0.7364 (mm110) cc_final: 0.6965 (mp10) REVERT: F 332 GLN cc_start: 0.7528 (OUTLIER) cc_final: 0.7286 (mp10) REVERT: F 371 GLU cc_start: 0.6259 (tp30) cc_final: 0.5872 (tp30) REVERT: F 372 ILE cc_start: 0.8706 (OUTLIER) cc_final: 0.7943 (mm) REVERT: F 379 LYS cc_start: 0.7777 (tptm) cc_final: 0.7218 (tptm) REVERT: F 382 ASP cc_start: 0.7733 (t0) cc_final: 0.7467 (m-30) REVERT: F 383 ASP cc_start: 0.7143 (m-30) cc_final: 0.6773 (m-30) REVERT: J 40 ILE cc_start: 0.8360 (mt) cc_final: 0.7984 (pt) REVERT: J 66 ILE cc_start: 0.8656 (mm) cc_final: 0.8277 (mm) REVERT: J 87 ILE cc_start: 0.8687 (tt) cc_final: 0.8457 (pt) REVERT: J 114 ILE cc_start: 0.8155 (mm) cc_final: 0.7929 (mm) REVERT: J 122 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.7630 (mp) REVERT: J 145 MET cc_start: 0.6804 (tmm) cc_final: 0.6112 (tmm) REVERT: J 148 ILE cc_start: 0.8216 (mt) cc_final: 0.7937 (tp) REVERT: J 161 ILE cc_start: 0.8408 (mm) cc_final: 0.8083 (mp) REVERT: J 184 MET cc_start: 0.7728 (mtm) cc_final: 0.7434 (mtm) REVERT: J 213 ILE cc_start: 0.8296 (OUTLIER) cc_final: 0.8021 (mt) REVERT: J 217 GLN cc_start: 0.7885 (tp40) cc_final: 0.7548 (tp40) REVERT: J 220 LEU cc_start: 0.8200 (mt) cc_final: 0.7991 (mt) REVERT: J 252 GLU cc_start: 0.7263 (mm-30) cc_final: 0.6740 (mm-30) REVERT: J 268 ARG cc_start: 0.7735 (ttt90) cc_final: 0.7203 (mmm-85) REVERT: J 282 MET cc_start: 0.7828 (ttt) cc_final: 0.7518 (ttm) REVERT: J 283 LEU cc_start: 0.7600 (mt) cc_final: 0.7316 (mt) REVERT: J 297 GLU cc_start: 0.7391 (tt0) cc_final: 0.7155 (tt0) REVERT: J 308 LEU cc_start: 0.7983 (mt) cc_final: 0.7742 (mm) REVERT: J 327 PHE cc_start: 0.6770 (t80) cc_final: 0.5969 (t80) REVERT: J 342 ILE cc_start: 0.8225 (mm) cc_final: 0.7905 (tt) REVERT: J 343 MET cc_start: 0.7301 (tpp) cc_final: 0.7081 (mpp) REVERT: J 395 LEU cc_start: 0.8048 (mt) cc_final: 0.7634 (mt) REVERT: J 402 SER cc_start: 0.8043 (t) cc_final: 0.7786 (m) REVERT: J 403 ASN cc_start: 0.8269 (m-40) cc_final: 0.7867 (m-40) REVERT: J 404 PHE cc_start: 0.8293 (t80) cc_final: 0.8075 (t80) REVERT: J 406 ARG cc_start: 0.7305 (ttp80) cc_final: 0.7029 (ttp80) REVERT: J 408 LEU cc_start: 0.7604 (OUTLIER) cc_final: 0.7330 (tt) REVERT: J 416 ILE cc_start: 0.8343 (mt) cc_final: 0.8026 (tp) REVERT: J 436 VAL cc_start: 0.8111 (t) cc_final: 0.7646 (m) REVERT: J 471 GLN cc_start: 0.7832 (mm-40) cc_final: 0.7275 (mm-40) REVERT: J 488 PHE cc_start: 0.8246 (m-80) cc_final: 0.7585 (m-80) REVERT: J 489 LEU cc_start: 0.8435 (mt) cc_final: 0.8229 (mt) REVERT: J 491 LEU cc_start: 0.7810 (mt) cc_final: 0.7519 (pp) REVERT: G 3 LEU cc_start: 0.8802 (tt) cc_final: 0.8426 (tp) REVERT: G 5 GLN cc_start: 0.8460 (mt0) cc_final: 0.7793 (mt0) REVERT: G 9 GLN cc_start: 0.7078 (tm-30) cc_final: 0.6847 (tm-30) REVERT: G 17 LEU cc_start: 0.8630 (mp) cc_final: 0.8246 (tt) REVERT: G 29 GLU cc_start: 0.7808 (tp30) cc_final: 0.7318 (tp30) REVERT: G 32 ASN cc_start: 0.8145 (m110) cc_final: 0.7488 (m110) REVERT: G 76 PHE cc_start: 0.7261 (t80) cc_final: 0.6974 (t80) REVERT: G 78 MET cc_start: 0.6724 (ptp) cc_final: 0.6318 (ppp) REVERT: G 80 LYS cc_start: 0.8583 (mttp) cc_final: 0.8268 (mttp) REVERT: G 87 GLN cc_start: 0.8444 (tp-100) cc_final: 0.8084 (tp40) REVERT: G 94 GLN cc_start: 0.8394 (tp40) cc_final: 0.8158 (mm-40) REVERT: G 98 TYR cc_start: 0.8229 (t80) cc_final: 0.7729 (t80) REVERT: G 99 GLN cc_start: 0.7395 (mm110) cc_final: 0.7136 (mm110) REVERT: G 101 ASP cc_start: 0.7539 (t0) cc_final: 0.7116 (t0) REVERT: G 103 GLN cc_start: 0.8238 (mt0) cc_final: 0.8014 (mm-40) REVERT: G 117 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8711 (mp) REVERT: G 130 LYS cc_start: 0.8669 (tttt) cc_final: 0.8010 (ttpp) REVERT: G 133 ILE cc_start: 0.8695 (OUTLIER) cc_final: 0.8469 (tp) REVERT: G 168 GLU cc_start: 0.8365 (tt0) cc_final: 0.7973 (tt0) REVERT: G 169 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8462 (mm) REVERT: G 181 GLN cc_start: 0.8440 (mm-40) cc_final: 0.7776 (tm-30) REVERT: G 215 GLU cc_start: 0.7628 (tm-30) cc_final: 0.6708 (tm-30) REVERT: G 217 GLU cc_start: 0.8036 (tm-30) cc_final: 0.7636 (tm-30) REVERT: G 230 GLN cc_start: 0.8556 (OUTLIER) cc_final: 0.7982 (pp30) REVERT: G 231 ASP cc_start: 0.8318 (m-30) cc_final: 0.7791 (m-30) REVERT: G 232 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8822 (tt) REVERT: G 236 GLN cc_start: 0.8457 (mt0) cc_final: 0.8135 (mt0) REVERT: G 279 MET cc_start: 0.3884 (tpt) cc_final: 0.3510 (tpt) REVERT: G 299 ASN cc_start: 0.8486 (m110) cc_final: 0.8202 (m110) REVERT: G 303 LYS cc_start: 0.8737 (mtpp) cc_final: 0.7807 (mtpp) REVERT: G 307 TYR cc_start: 0.7978 (m-80) cc_final: 0.7689 (m-80) REVERT: G 315 GLN cc_start: 0.8637 (tp40) cc_final: 0.8188 (tp-100) REVERT: G 317 GLU cc_start: 0.7958 (tp30) cc_final: 0.7173 (tp30) REVERT: G 321 ARG cc_start: 0.8394 (mtt180) cc_final: 0.8019 (mtt180) REVERT: G 333 ASN cc_start: 0.8619 (m-40) cc_final: 0.8331 (m-40) REVERT: G 344 TYR cc_start: 0.8103 (m-80) cc_final: 0.7835 (m-80) REVERT: G 401 LYS cc_start: 0.8528 (tptm) cc_final: 0.8190 (tppp) REVERT: H 14 ASN cc_start: 0.8165 (t0) cc_final: 0.7804 (t0) REVERT: H 19 LYS cc_start: 0.8272 (OUTLIER) cc_final: 0.7749 (tttt) REVERT: H 25 ASP cc_start: 0.7916 (m-30) cc_final: 0.7463 (t0) REVERT: H 29 GLU cc_start: 0.7954 (tp30) cc_final: 0.7108 (tp30) REVERT: H 33 GLU cc_start: 0.7204 (pm20) cc_final: 0.5871 (pm20) REVERT: H 89 LYS cc_start: 0.8672 (mmmt) cc_final: 0.8318 (mmmt) REVERT: H 94 GLN cc_start: 0.8067 (tp40) cc_final: 0.7780 (tp40) REVERT: H 129 GLN cc_start: 0.8448 (tt0) cc_final: 0.8152 (tt0) REVERT: H 131 GLU cc_start: 0.8084 (tp30) cc_final: 0.7794 (tp30) REVERT: H 135 ARG cc_start: 0.8142 (OUTLIER) cc_final: 0.7472 (mmm160) REVERT: H 138 ASP cc_start: 0.8009 (OUTLIER) cc_final: 0.7503 (t0) REVERT: H 162 ASP cc_start: 0.8260 (m-30) cc_final: 0.7962 (m-30) REVERT: H 173 ASN cc_start: 0.8472 (m-40) cc_final: 0.8129 (m-40) REVERT: H 180 GLU cc_start: 0.8545 (mm-30) cc_final: 0.7977 (tp30) REVERT: H 184 GLN cc_start: 0.8572 (tt0) cc_final: 0.8065 (tm-30) REVERT: H 210 ASN cc_start: 0.8378 (m-40) cc_final: 0.8164 (p0) REVERT: H 218 LYS cc_start: 0.8776 (mmtt) cc_final: 0.8489 (mmtt) REVERT: H 231 ASP cc_start: 0.7712 (t0) cc_final: 0.7284 (t0) REVERT: H 234 ARG cc_start: 0.7952 (mmm-85) cc_final: 0.7322 (mmm-85) REVERT: H 236 GLN cc_start: 0.7777 (pp30) cc_final: 0.7297 (pp30) REVERT: H 237 ILE cc_start: 0.8729 (mt) cc_final: 0.7988 (mt) REVERT: H 239 GLN cc_start: 0.8476 (pp30) cc_final: 0.8157 (pp30) REVERT: H 303 LYS cc_start: 0.8410 (mttt) cc_final: 0.7928 (mttt) REVERT: H 309 PHE cc_start: 0.8786 (t80) cc_final: 0.8500 (t80) REVERT: H 314 GLU cc_start: 0.7490 (mm-30) cc_final: 0.7142 (mm-30) REVERT: H 317 GLU cc_start: 0.7669 (tp30) cc_final: 0.7248 (tp30) REVERT: H 340 SER cc_start: 0.8774 (m) cc_final: 0.8259 (p) REVERT: H 341 ILE cc_start: 0.8919 (OUTLIER) cc_final: 0.8654 (tt) REVERT: H 356 ASP cc_start: 0.8408 (t0) cc_final: 0.8096 (t0) REVERT: H 362 TYR cc_start: 0.8786 (t80) cc_final: 0.8493 (t80) REVERT: H 374 ASP cc_start: 0.7826 (t0) cc_final: 0.7421 (t0) REVERT: H 390 ARG cc_start: 0.8673 (mtt-85) cc_final: 0.8443 (ttm170) REVERT: H 392 ASN cc_start: 0.8422 (m-40) cc_final: 0.7902 (t0) REVERT: H 396 ASN cc_start: 0.8206 (m-40) cc_final: 0.7756 (m-40) REVERT: H 397 GLN cc_start: 0.8153 (tt0) cc_final: 0.7460 (tm-30) REVERT: I 4 MET cc_start: 0.7919 (mmm) cc_final: 0.7623 (tmm) REVERT: I 8 GLN cc_start: 0.8608 (mm-40) cc_final: 0.7955 (tp-100) REVERT: I 16 GLU cc_start: 0.8029 (mp0) cc_final: 0.7500 (mp0) REVERT: I 31 ILE cc_start: 0.9109 (mt) cc_final: 0.8900 (mm) REVERT: I 76 PHE cc_start: 0.7588 (t80) cc_final: 0.6859 (t80) REVERT: I 89 LYS cc_start: 0.8514 (mmtp) cc_final: 0.8270 (mmtp) REVERT: I 99 GLN cc_start: 0.8384 (mt0) cc_final: 0.8096 (mt0) REVERT: I 124 SER cc_start: 0.8635 (t) cc_final: 0.8428 (p) REVERT: I 143 ARG cc_start: 0.7945 (ttm110) cc_final: 0.7470 (ttm110) REVERT: I 160 GLN cc_start: 0.8285 (mm-40) cc_final: 0.8039 (mm-40) REVERT: I 185 ILE cc_start: 0.9204 (mt) cc_final: 0.8972 (tt) REVERT: I 213 LEU cc_start: 0.8942 (mt) cc_final: 0.8701 (mt) REVERT: I 215 GLU cc_start: 0.8104 (tp30) cc_final: 0.7619 (tp30) REVERT: I 217 GLU cc_start: 0.7578 (mm-30) cc_final: 0.7267 (mm-30) REVERT: I 224 LEU cc_start: 0.8885 (tp) cc_final: 0.7854 (mm) REVERT: I 225 GLN cc_start: 0.7965 (tm-30) cc_final: 0.7321 (tm-30) REVERT: I 227 ARG cc_start: 0.7791 (mtm-85) cc_final: 0.7111 (mtm-85) REVERT: I 230 GLN cc_start: 0.8050 (tm-30) cc_final: 0.7745 (tm-30) REVERT: I 235 GLU cc_start: 0.7829 (tp30) cc_final: 0.7464 (tp30) REVERT: I 236 GLN cc_start: 0.8375 (mt0) cc_final: 0.7985 (mt0) REVERT: I 237 ILE cc_start: 0.8737 (mt) cc_final: 0.8476 (mm) REVERT: I 238 ARG cc_start: 0.8146 (mpt180) cc_final: 0.7753 (mpt180) REVERT: I 297 MET cc_start: 0.6781 (tmm) cc_final: 0.6458 (tmm) REVERT: I 301 GLN cc_start: 0.8452 (tt0) cc_final: 0.8131 (mt0) REVERT: I 306 GLN cc_start: 0.8457 (mt0) cc_final: 0.8254 (pm20) REVERT: I 314 GLU cc_start: 0.7314 (mt-10) cc_final: 0.6884 (mt-10) REVERT: I 315 GLN cc_start: 0.8160 (mt0) cc_final: 0.7098 (mp10) REVERT: I 325 GLN cc_start: 0.8400 (pp30) cc_final: 0.8060 (pp30) REVERT: I 395 ILE cc_start: 0.9138 (tt) cc_final: 0.8906 (tp) REVERT: I 398 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8682 (mt) outliers start: 161 outliers final: 115 residues processed: 1316 average time/residue: 0.5004 time to fit residues: 1006.3726 Evaluate side-chains 1386 residues out of total 3232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 1240 time to evaluate : 3.064 ------------------------------------------------------------------------------- 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 119 MET Chi-restraints excluded: chain A residue 147 VAL 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 250 THR Chi-restraints excluded: chain A residue 251 ASN Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 288 LYS Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 112 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 278 ILE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 294 MET Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 335 LEU 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 231 VAL Chi-restraints excluded: chain C residue 265 ASN 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 330 LEU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 340 SER Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain C residue 364 VAL 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 115 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 319 LEU 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 65 MET Chi-restraints excluded: chain E residue 85 GLU Chi-restraints excluded: chain E residue 103 LYS Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 167 VAL 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 325 LEU Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 342 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 373 SER Chi-restraints excluded: chain E residue 380 LEU 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 129 ILE Chi-restraints excluded: chain F residue 133 LYS Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 153 ASN Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 194 GLU Chi-restraints excluded: chain F residue 200 GLN 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 332 GLN Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain F residue 372 ILE Chi-restraints excluded: chain J residue 48 LEU Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain J residue 84 TRP Chi-restraints excluded: chain J residue 104 MET Chi-restraints excluded: chain J residue 122 LEU Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 213 ILE Chi-restraints excluded: chain J residue 237 LEU Chi-restraints excluded: chain J residue 253 LEU Chi-restraints excluded: chain J residue 290 LEU Chi-restraints excluded: chain J residue 293 GLN Chi-restraints excluded: chain J residue 333 MET Chi-restraints excluded: chain J residue 408 LEU Chi-restraints excluded: chain J residue 419 THR Chi-restraints excluded: chain J residue 457 GLN Chi-restraints excluded: chain J residue 490 VAL Chi-restraints excluded: chain J residue 494 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 117 LEU Chi-restraints excluded: chain G residue 133 ILE Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain G residue 196 LEU 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 272 THR Chi-restraints excluded: chain G residue 300 SER Chi-restraints excluded: chain G residue 318 SER Chi-restraints excluded: chain G residue 334 ILE Chi-restraints excluded: chain G residue 426 ASN Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 19 LYS Chi-restraints excluded: chain H residue 35 ARG Chi-restraints excluded: chain H residue 135 ARG Chi-restraints excluded: chain H residue 138 ASP Chi-restraints excluded: chain H residue 205 LYS Chi-restraints excluded: chain H residue 221 LEU Chi-restraints excluded: chain H residue 286 LEU 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 12 LEU Chi-restraints excluded: chain I residue 58 ASN Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 188 ASN Chi-restraints excluded: chain I residue 203 THR Chi-restraints excluded: chain I residue 232 LEU Chi-restraints excluded: chain I residue 250 LEU Chi-restraints excluded: chain I residue 272 THR 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 72 optimal weight: 0.4980 chunk 293 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 186 optimal weight: 0.5980 chunk 55 optimal weight: 0.9990 chunk 160 optimal weight: 0.9980 chunk 263 optimal weight: 2.9990 chunk 337 optimal weight: 3.9990 chunk 206 optimal weight: 0.5980 chunk 323 optimal weight: 10.0000 chunk 205 optimal weight: 4.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 251 ASN F 346 ASN ** J 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 403 ASN J 444 GLN J 449 GLN J 467 GLN J 478 ASN ** G 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 156 ASN ** G 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 426 ASN ** H 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 299 ASN I 2 ASN ** I 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 320 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.112890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.095235 restraints weight = 58849.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.098206 restraints weight = 25748.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.100050 restraints weight = 13821.996| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.6898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 30315 Z= 0.176 Angle : 0.713 14.596 41246 Z= 0.365 Chirality : 0.044 0.219 4889 Planarity : 0.005 0.066 5392 Dihedral : 4.314 21.105 4179 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 4.30 % Allowed : 26.79 % Favored : 68.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.14), residues: 3860 helix: 2.72 (0.11), residues: 1998 sheet: -0.24 (0.23), residues: 495 loop : -1.28 (0.16), residues: 1367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP G 81 HIS 0.012 0.001 HIS I 320 PHE 0.031 0.002 PHE J 339 TYR 0.032 0.002 TYR D 143 ARG 0.010 0.001 ARG G 24 Details of bonding type rmsd hydrogen bonds : bond 0.06450 ( 1888) hydrogen bonds : angle 4.40297 ( 5523) covalent geometry : bond 0.00376 (30315) covalent geometry : angle 0.71272 (41246) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15452.26 seconds wall clock time: 268 minutes 6.37 seconds (16086.37 seconds total)