Starting phenix.real_space_refine on Tue Aug 26 05:44:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cae_45388/08_2025/9cae_45388.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cae_45388/08_2025/9cae_45388.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cae_45388/08_2025/9cae_45388.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cae_45388/08_2025/9cae_45388.map" model { file = "/net/cci-nas-00/data/ceres_data/9cae_45388/08_2025/9cae_45388.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cae_45388/08_2025/9cae_45388.cif" } resolution = 3.07 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 24 5.49 5 Mg 8 5.21 5 S 178 5.16 5 C 21383 2.51 5 N 5925 2.21 5 O 6487 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34005 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 4975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 607, 4975 Classifications: {'peptide': 607} Link IDs: {'PTRANS': 35, 'TRANS': 571} Chain breaks: 5 Chain: "B" Number of atoms: 721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 721 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 12, 'TRANS': 77} Chain breaks: 1 Chain: "C" Number of atoms: 769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 769 Classifications: {'peptide': 93} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 85} Chain breaks: 1 Chain: "E" Number of atoms: 3249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3249 Classifications: {'peptide': 422} Link IDs: {'PTRANS': 16, 'TRANS': 405} Chain breaks: 1 Chain: "F" Number of atoms: 3381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3381 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 11, 'TRANS': 423} Chain breaks: 1 Chain: "G" Number of atoms: 3308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3308 Classifications: {'peptide': 429} Link IDs: {'PTRANS': 17, 'TRANS': 411} Chain breaks: 2 Chain: "H" Number of atoms: 3327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3327 Classifications: {'peptide': 428} Link IDs: {'PTRANS': 10, 'TRANS': 417} Chain breaks: 1 Chain: "I" Number of atoms: 3269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 3269 Classifications: {'peptide': 425} Link IDs: {'PTRANS': 16, 'TRANS': 408} Chain breaks: 1 Chain: "J" Number of atoms: 3198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3198 Classifications: {'peptide': 412} Link IDs: {'PTRANS': 10, 'TRANS': 401} Chain breaks: 2 Chain: "L" Number of atoms: 2786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2786 Classifications: {'peptide': 357} Link IDs: {'PTRANS': 19, 'TRANS': 337} Chain breaks: 1 Chain: "M" Number of atoms: 3138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3138 Classifications: {'peptide': 401} Link IDs: {'PTRANS': 22, 'TRANS': 378} Chain breaks: 2 Chain: "N" Number of atoms: 1628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1628 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 10, 'TRANS': 179} Chain breaks: 1 Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.95, per 1000 atoms: 0.20 Number of scatterers: 34005 At special positions: 0 Unit cell: (185.856, 187.308, 161.898, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 178 16.00 P 24 15.00 Mg 8 11.99 O 6487 8.00 N 5925 7.00 C 21383 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.92 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 715.3 nanoseconds 8454 Ramachandran restraints generated. 4227 Oldfield, 0 Emsley, 4227 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8002 Finding SS restraints... Secondary structure from input PDB file: 196 helices and 45 sheets defined 48.9% alpha, 12.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.20 Creating SS restraints... Processing helix chain 'A' and resid 779 through 791 Processing helix chain 'A' and resid 794 through 798 removed outlier: 3.514A pdb=" N ARG A 798 " --> pdb=" O SER A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 810 through 856 Processing helix chain 'A' and resid 1329 through 1342 Processing helix chain 'A' and resid 1342 through 1352 removed outlier: 3.878A pdb=" N ALA A1348 " --> pdb=" O GLY A1344 " (cutoff:3.500A) Processing helix chain 'A' and resid 1353 through 1370 removed outlier: 3.823A pdb=" N ARG A1366 " --> pdb=" O VAL A1362 " (cutoff:3.500A) Processing helix chain 'A' and resid 1371 through 1374 Processing helix chain 'A' and resid 1393 through 1399 removed outlier: 4.200A pdb=" N LEU A1397 " --> pdb=" O ALA A1393 " (cutoff:3.500A) Processing helix chain 'A' and resid 1403 through 1407 Processing helix chain 'A' and resid 1409 through 1414 Processing helix chain 'A' and resid 1415 through 1419 Processing helix chain 'A' and resid 1423 through 1433 Processing helix chain 'A' and resid 1436 through 1444 removed outlier: 3.502A pdb=" N MET A1440 " --> pdb=" O PRO A1436 " (cutoff:3.500A) Processing helix chain 'A' and resid 1459 through 1464 Processing helix chain 'A' and resid 1746 through 1762 Processing helix chain 'A' and resid 1768 through 1776 Processing helix chain 'A' and resid 1824 through 1830 removed outlier: 3.621A pdb=" N ARG A1830 " --> pdb=" O ASP A1826 " (cutoff:3.500A) Processing helix chain 'A' and resid 1851 through 1870 Processing helix chain 'A' and resid 1872 through 1879 Processing helix chain 'A' and resid 1890 through 1896 removed outlier: 3.907A pdb=" N GLN A1894 " --> pdb=" O LEU A1890 " (cutoff:3.500A) Processing helix chain 'A' and resid 1897 through 1912 Processing helix chain 'A' and resid 1923 through 1937 Processing helix chain 'A' and resid 1949 through 1963 removed outlier: 3.806A pdb=" N GLN A1954 " --> pdb=" O SER A1950 " (cutoff:3.500A) Processing helix chain 'A' and resid 1996 through 2014 Processing helix chain 'A' and resid 2027 through 2032 Processing helix chain 'A' and resid 2033 through 2045 removed outlier: 4.076A pdb=" N LYS A2037 " --> pdb=" O LYS A2033 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA A2045 " --> pdb=" O ARG A2041 " (cutoff:3.500A) Processing helix chain 'A' and resid 2056 through 2065 removed outlier: 3.579A pdb=" N PHE A2064 " --> pdb=" O ILE A2060 " (cutoff:3.500A) Processing helix chain 'A' and resid 2189 through 2217 removed outlier: 3.659A pdb=" N GLU A2217 " --> pdb=" O LEU A2213 " (cutoff:3.500A) Processing helix chain 'A' and resid 2224 through 2230 Processing helix chain 'A' and resid 2265 through 2269 Processing helix chain 'B' and resid 270 through 278 Processing helix chain 'B' and resid 312 through 331 Processing helix chain 'C' and resid 399 through 403 removed outlier: 3.575A pdb=" N PHE C 402 " --> pdb=" O ASP C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 427 through 431 Processing helix chain 'C' and resid 435 through 437 No H-bonds generated for 'chain 'C' and resid 435 through 437' Processing helix chain 'C' and resid 474 through 481 Processing helix chain 'E' and resid 42 through 59 removed outlier: 3.822A pdb=" N LYS E 59 " --> pdb=" O LEU E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 75 through 88 Processing helix chain 'E' and resid 97 through 102 removed outlier: 3.773A pdb=" N TYR E 102 " --> pdb=" O SER E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 119 Processing helix chain 'E' and resid 173 through 184 Processing helix chain 'E' and resid 208 through 212 removed outlier: 4.217A pdb=" N THR E 211 " --> pdb=" O THR E 208 " (cutoff:3.500A) Processing helix chain 'E' and resid 240 through 249 Processing helix chain 'E' and resid 255 through 263 Processing helix chain 'E' and resid 272 through 290 Processing helix chain 'E' and resid 303 through 307 removed outlier: 3.518A pdb=" N MET E 306 " --> pdb=" O GLU E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 320 removed outlier: 3.759A pdb=" N ARG E 317 " --> pdb=" O THR E 313 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 356 Processing helix chain 'E' and resid 367 through 382 Processing helix chain 'E' and resid 387 through 400 Processing helix chain 'E' and resid 402 through 409 Processing helix chain 'E' and resid 409 through 420 Processing helix chain 'E' and resid 426 through 437 Processing helix chain 'E' and resid 439 through 448 Processing helix chain 'F' and resid 49 through 66 Processing helix chain 'F' and resid 82 through 95 Processing helix chain 'F' and resid 106 through 109 removed outlier: 3.629A pdb=" N PHE F 109 " --> pdb=" O SER F 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 106 through 109' Processing helix chain 'F' and resid 114 through 126 removed outlier: 3.562A pdb=" N SER F 126 " --> pdb=" O ALA F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 175 through 186 Processing helix chain 'F' and resid 244 through 253 removed outlier: 4.103A pdb=" N ARG F 253 " --> pdb=" O VAL F 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 256 through 263 removed outlier: 3.551A pdb=" N LEU F 260 " --> pdb=" O GLY F 256 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N PHE F 261 " --> pdb=" O PHE F 257 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 286 Processing helix chain 'F' and resid 300 through 304 Processing helix chain 'F' and resid 305 through 316 removed outlier: 3.659A pdb=" N ARG F 314 " --> pdb=" O SER F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 347 through 352 Processing helix chain 'F' and resid 363 through 379 Processing helix chain 'F' and resid 383 through 397 Processing helix chain 'F' and resid 398 through 416 removed outlier: 3.714A pdb=" N THR F 407 " --> pdb=" O ILE F 403 " (cutoff:3.500A) Processing helix chain 'F' and resid 422 through 433 Processing helix chain 'F' and resid 435 through 446 Processing helix chain 'F' and resid 447 through 450 Processing helix chain 'G' and resid 42 through 59 removed outlier: 3.758A pdb=" N LYS G 59 " --> pdb=" O LEU G 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 75 through 88 Processing helix chain 'G' and resid 99 through 102 removed outlier: 3.631A pdb=" N TYR G 102 " --> pdb=" O SER G 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 99 through 102' Processing helix chain 'G' and resid 107 through 119 removed outlier: 3.522A pdb=" N ALA G 119 " --> pdb=" O ASN G 115 " (cutoff:3.500A) Processing helix chain 'G' and resid 173 through 175 No H-bonds generated for 'chain 'G' and resid 173 through 175' Processing helix chain 'G' and resid 176 through 183 Processing helix chain 'G' and resid 208 through 210 No H-bonds generated for 'chain 'G' and resid 208 through 210' Processing helix chain 'G' and resid 240 through 249 Processing helix chain 'G' and resid 257 through 264 Processing helix chain 'G' and resid 272 through 289 Processing helix chain 'G' and resid 303 through 307 Processing helix chain 'G' and resid 308 through 320 removed outlier: 3.639A pdb=" N ARG G 317 " --> pdb=" O THR G 313 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU G 320 " --> pdb=" O HIS G 316 " (cutoff:3.500A) Processing helix chain 'G' and resid 351 through 356 Processing helix chain 'G' and resid 367 through 382 Processing helix chain 'G' and resid 387 through 400 Processing helix chain 'G' and resid 402 through 409 Processing helix chain 'G' and resid 409 through 420 Processing helix chain 'G' and resid 426 through 437 Processing helix chain 'G' and resid 439 through 449 Processing helix chain 'H' and resid 49 through 66 Processing helix chain 'H' and resid 82 through 94 Processing helix chain 'H' and resid 106 through 109 removed outlier: 3.630A pdb=" N PHE H 109 " --> pdb=" O SER H 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 106 through 109' Processing helix chain 'H' and resid 114 through 126 removed outlier: 3.559A pdb=" N SER H 126 " --> pdb=" O ALA H 122 " (cutoff:3.500A) Processing helix chain 'H' and resid 175 through 185 Processing helix chain 'H' and resid 210 through 214 removed outlier: 3.751A pdb=" N ASP H 214 " --> pdb=" O ARG H 211 " (cutoff:3.500A) Processing helix chain 'H' and resid 244 through 251 Processing helix chain 'H' and resid 255 through 257 No H-bonds generated for 'chain 'H' and resid 255 through 257' Processing helix chain 'H' and resid 258 through 263 Processing helix chain 'H' and resid 269 through 286 Processing helix chain 'H' and resid 300 through 304 Processing helix chain 'H' and resid 305 through 316 removed outlier: 3.710A pdb=" N ARG H 314 " --> pdb=" O SER H 310 " (cutoff:3.500A) Processing helix chain 'H' and resid 347 through 352 Processing helix chain 'H' and resid 363 through 379 Processing helix chain 'H' and resid 383 through 397 Processing helix chain 'H' and resid 398 through 416 removed outlier: 3.834A pdb=" N THR H 407 " --> pdb=" O ILE H 403 " (cutoff:3.500A) Processing helix chain 'H' and resid 422 through 433 Processing helix chain 'H' and resid 435 through 446 Processing helix chain 'I' and resid 42 through 59 removed outlier: 3.723A pdb=" N LYS I 59 " --> pdb=" O LEU I 55 " (cutoff:3.500A) Processing helix chain 'I' and resid 75 through 88 Processing helix chain 'I' and resid 99 through 102 removed outlier: 3.595A pdb=" N TYR I 102 " --> pdb=" O SER I 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 99 through 102' Processing helix chain 'I' and resid 107 through 119 Processing helix chain 'I' and resid 174 through 183 removed outlier: 4.114A pdb=" N GLU I 178 " --> pdb=" O PRO I 174 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N SER I 179 " --> pdb=" O SER I 175 " (cutoff:3.500A) Processing helix chain 'I' and resid 208 through 210 No H-bonds generated for 'chain 'I' and resid 208 through 210' Processing helix chain 'I' and resid 240 through 247 Processing helix chain 'I' and resid 255 through 264 Processing helix chain 'I' and resid 272 through 290 Processing helix chain 'I' and resid 304 through 307 Processing helix chain 'I' and resid 308 through 321 removed outlier: 4.199A pdb=" N ARG I 317 " --> pdb=" O THR I 313 " (cutoff:3.500A) Processing helix chain 'I' and resid 347 through 350 Processing helix chain 'I' and resid 351 through 356 Processing helix chain 'I' and resid 367 through 383 Processing helix chain 'I' and resid 387 through 401 Processing helix chain 'I' and resid 402 through 409 Processing helix chain 'I' and resid 409 through 420 Processing helix chain 'I' and resid 426 through 437 Processing helix chain 'I' and resid 439 through 449 Processing helix chain 'J' and resid 49 through 66 Processing helix chain 'J' and resid 82 through 94 Processing helix chain 'J' and resid 106 through 109 removed outlier: 3.501A pdb=" N PHE J 109 " --> pdb=" O SER J 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 106 through 109' Processing helix chain 'J' and resid 114 through 126 Processing helix chain 'J' and resid 175 through 185 Processing helix chain 'J' and resid 244 through 253 removed outlier: 4.147A pdb=" N ARG J 253 " --> pdb=" O VAL J 249 " (cutoff:3.500A) Processing helix chain 'J' and resid 255 through 257 No H-bonds generated for 'chain 'J' and resid 255 through 257' Processing helix chain 'J' and resid 258 through 263 Processing helix chain 'J' and resid 269 through 287 removed outlier: 3.510A pdb=" N ARG J 273 " --> pdb=" O LYS J 269 " (cutoff:3.500A) Processing helix chain 'J' and resid 300 through 304 Processing helix chain 'J' and resid 305 through 316 removed outlier: 3.684A pdb=" N ARG J 314 " --> pdb=" O SER J 310 " (cutoff:3.500A) Processing helix chain 'J' and resid 347 through 352 Processing helix chain 'J' and resid 363 through 378 Processing helix chain 'J' and resid 383 through 397 Processing helix chain 'J' and resid 398 through 416 removed outlier: 3.740A pdb=" N THR J 407 " --> pdb=" O ILE J 403 " (cutoff:3.500A) Processing helix chain 'J' and resid 422 through 433 Processing helix chain 'J' and resid 435 through 446 Processing helix chain 'J' and resid 447 through 450 Processing helix chain 'L' and resid 55 through 60 Processing helix chain 'L' and resid 78 through 93 Processing helix chain 'L' and resid 112 through 126 Processing helix chain 'L' and resid 137 through 146 Processing helix chain 'L' and resid 172 through 175 removed outlier: 3.504A pdb=" N ILE L 175 " --> pdb=" O PRO L 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 172 through 175' Processing helix chain 'L' and resid 181 through 196 Processing helix chain 'L' and resid 205 through 217 removed outlier: 3.515A pdb=" N CYS L 217 " --> pdb=" O LYS L 213 " (cutoff:3.500A) Processing helix chain 'L' and resid 222 through 233 Processing helix chain 'L' and resid 234 through 237 Processing helix chain 'L' and resid 252 through 263 removed outlier: 3.670A pdb=" N CYS L 257 " --> pdb=" O GLU L 253 " (cutoff:3.500A) Proline residue: L 258 - end of helix removed outlier: 4.373A pdb=" N LEU L 261 " --> pdb=" O CYS L 257 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N PHE L 262 " --> pdb=" O PRO L 258 " (cutoff:3.500A) Processing helix chain 'L' and resid 264 through 267 Processing helix chain 'L' and resid 273 through 284 Processing helix chain 'L' and resid 289 through 296 Processing helix chain 'L' and resid 301 through 305 Processing helix chain 'L' and resid 308 through 321 Processing helix chain 'L' and resid 337 through 348 Processing helix chain 'L' and resid 350 through 356 removed outlier: 3.661A pdb=" N GLN L 354 " --> pdb=" O THR L 351 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N TRP L 356 " --> pdb=" O GLN L 353 " (cutoff:3.500A) Processing helix chain 'L' and resid 359 through 366 Processing helix chain 'L' and resid 368 through 374 removed outlier: 3.624A pdb=" N ARG L 372 " --> pdb=" O SER L 368 " (cutoff:3.500A) Processing helix chain 'M' and resid 71 through 76 Processing helix chain 'M' and resid 95 through 110 Processing helix chain 'M' and resid 114 through 118 removed outlier: 3.775A pdb=" N HIS M 118 " --> pdb=" O ALA M 115 " (cutoff:3.500A) Processing helix chain 'M' and resid 129 through 143 Processing helix chain 'M' and resid 154 through 162 removed outlier: 3.539A pdb=" N ASN M 162 " --> pdb=" O THR M 158 " (cutoff:3.500A) Processing helix chain 'M' and resid 189 through 192 Processing helix chain 'M' and resid 198 through 213 Processing helix chain 'M' and resid 219 through 221 No H-bonds generated for 'chain 'M' and resid 219 through 221' Processing helix chain 'M' and resid 247 through 266 Processing helix chain 'M' and resid 275 through 282 Processing helix chain 'M' and resid 299 through 304 Processing helix chain 'M' and resid 305 through 309 Processing helix chain 'M' and resid 310 through 314 Processing helix chain 'M' and resid 324 through 335 removed outlier: 3.501A pdb=" N MET M 335 " --> pdb=" O THR M 331 " (cutoff:3.500A) Processing helix chain 'M' and resid 340 through 347 Processing helix chain 'M' and resid 352 through 357 removed outlier: 3.741A pdb=" N ILE M 357 " --> pdb=" O ASN M 354 " (cutoff:3.500A) Processing helix chain 'M' and resid 359 through 372 Processing helix chain 'M' and resid 385 through 391 Processing helix chain 'M' and resid 391 through 403 Processing helix chain 'M' and resid 404 through 409 removed outlier: 3.821A pdb=" N GLN M 408 " --> pdb=" O THR M 405 " (cutoff:3.500A) Processing helix chain 'M' and resid 413 through 420 removed outlier: 3.715A pdb=" N GLU M 418 " --> pdb=" O GLN M 414 " (cutoff:3.500A) Processing helix chain 'M' and resid 421 through 428 removed outlier: 4.524A pdb=" N GLU M 425 " --> pdb=" O LYS M 421 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ARG M 426 " --> pdb=" O GLN M 422 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N CYS M 428 " --> pdb=" O VAL M 424 " (cutoff:3.500A) Processing helix chain 'N' and resid 80 through 82 No H-bonds generated for 'chain 'N' and resid 80 through 82' Processing helix chain 'N' and resid 83 through 89 Processing helix chain 'N' and resid 118 through 120 No H-bonds generated for 'chain 'N' and resid 118 through 120' Processing helix chain 'N' and resid 124 through 130 Processing helix chain 'N' and resid 139 through 146 Processing helix chain 'N' and resid 153 through 168 Processing helix chain 'N' and resid 170 through 178 Processing helix chain 'N' and resid 187 through 206 Processing helix chain 'N' and resid 219 through 236 removed outlier: 3.715A pdb=" N ARG N 236 " --> pdb=" O ARG N 232 " (cutoff:3.500A) Processing helix chain 'N' and resid 237 through 251 removed outlier: 3.816A pdb=" N GLU N 244 " --> pdb=" O GLN N 240 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 801 through 802 Processing sheet with id=AA2, first strand: chain 'A' and resid 1319 through 1326 removed outlier: 3.996A pdb=" N TYR A1320 " --> pdb=" O ILE A2016 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE A2018 " --> pdb=" O TYR A1320 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N HIS A1322 " --> pdb=" O ILE A2018 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N LEU A1918 " --> pdb=" O VAL A1989 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL A1917 " --> pdb=" O ALA A1969 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N LEU A1971 " --> pdb=" O VAL A1917 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ILE A1919 " --> pdb=" O LEU A1971 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL A1942 " --> pdb=" O ILE A1970 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N SER A1972 " --> pdb=" O VAL A1942 " (cutoff:3.500A) removed outlier: 8.457A pdb=" N ILE A1944 " --> pdb=" O SER A1972 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1380 through 1381 Processing sheet with id=AA4, first strand: chain 'A' and resid 1383 through 1385 Processing sheet with id=AA5, first strand: chain 'A' and resid 1390 through 1391 removed outlier: 6.122A pdb=" N TYR A1390 " --> pdb=" O ARG A1846 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 1467 through 1468 removed outlier: 6.237A pdb=" N VAL A1467 " --> pdb=" O LYS N 91 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 2222 through 2223 Processing sheet with id=AA8, first strand: chain 'A' and resid 2232 through 2236 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 2242 through 2244 current: chain 'C' and resid 451 through 459 Processing sheet with id=AA9, first strand: chain 'B' and resid 211 through 220 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 260 through 264 current: chain 'F' and resid 158 through 164 removed outlier: 4.318A pdb=" N GLY F 159 " --> pdb=" O LEU F 174 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 169 through 174 current: chain 'F' and resid 202 through 207 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 202 through 207 current: chain 'G' and resid 153 through 162 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 167 through 172 current: chain 'G' and resid 200 through 206 removed outlier: 4.769A pdb=" N VAL G 221 " --> pdb=" O GLN G 203 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N ARG G 205 " --> pdb=" O VAL G 221 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 301 through 302 Processing sheet with id=AB2, first strand: chain 'E' and resid 35 through 36 Processing sheet with id=AB3, first strand: chain 'E' and resid 93 through 96 removed outlier: 6.548A pdb=" N LEU E 299 " --> pdb=" O ILE E 328 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N ALA E 330 " --> pdb=" O LEU E 299 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N VAL E 301 " --> pdb=" O ALA E 330 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 120 through 139 removed outlier: 6.460A pdb=" N GLY E 160 " --> pdb=" O THR E 136 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N LEU E 138 " --> pdb=" O ILE E 158 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ILE E 158 " --> pdb=" O LEU E 138 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 167 through 172 current: chain 'E' and resid 199 through 206 removed outlier: 5.822A pdb=" N VAL E 221 " --> pdb=" O GLN E 203 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N ARG E 205 " --> pdb=" O VAL E 221 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 336 through 337 Processing sheet with id=AB6, first strand: chain 'F' and resid 42 through 43 Processing sheet with id=AB7, first strand: chain 'F' and resid 100 through 104 removed outlier: 6.525A pdb=" N THR F 101 " --> pdb=" O PHE F 297 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N ASP F 299 " --> pdb=" O THR F 101 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ILE F 103 " --> pdb=" O ASP F 299 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N LEU F 296 " --> pdb=" O ILE F 325 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N ALA F 327 " --> pdb=" O LEU F 296 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ILE F 298 " --> pdb=" O ALA F 327 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLY F 77 " --> pdb=" O THR F 328 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ALA F 72 " --> pdb=" O LEU F 355 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N VAL F 357 " --> pdb=" O ALA F 72 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LEU F 74 " --> pdb=" O VAL F 357 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N THR F 359 " --> pdb=" O LEU F 74 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N ALA F 76 " --> pdb=" O THR F 359 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 332 through 334 Processing sheet with id=AB9, first strand: chain 'G' and resid 35 through 36 Processing sheet with id=AC1, first strand: chain 'G' and resid 93 through 97 Processing sheet with id=AC2, first strand: chain 'G' and resid 214 through 215 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 214 through 215 current: chain 'H' and resid 160 through 164 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 169 through 174 current: chain 'H' and resid 202 through 207 Processing sheet with id=AC3, first strand: chain 'G' and resid 336 through 337 Processing sheet with id=AC4, first strand: chain 'H' and resid 100 through 104 Processing sheet with id=AC5, first strand: chain 'H' and resid 238 through 243 Processing sheet with id=AC6, first strand: chain 'H' and resid 332 through 334 Processing sheet with id=AC7, first strand: chain 'I' and resid 35 through 36 Processing sheet with id=AC8, first strand: chain 'I' and resid 93 through 97 removed outlier: 6.377A pdb=" N CYS I 94 " --> pdb=" O PHE I 300 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N ASP I 302 " --> pdb=" O CYS I 94 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N MET I 96 " --> pdb=" O ASP I 302 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N VAL I 66 " --> pdb=" O PHE I 329 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N SER I 331 " --> pdb=" O VAL I 66 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N LEU I 68 " --> pdb=" O SER I 331 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 120 through 140 removed outlier: 6.154A pdb=" N GLY I 160 " --> pdb=" O THR I 136 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N LEU I 138 " --> pdb=" O ILE I 158 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ILE I 158 " --> pdb=" O LEU I 138 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 166 through 172 current: chain 'I' and resid 200 through 206 removed outlier: 4.946A pdb=" N VAL I 221 " --> pdb=" O GLN I 203 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N ARG I 205 " --> pdb=" O VAL I 221 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 336 through 337 Processing sheet with id=AD2, first strand: chain 'I' and resid 385 through 386 removed outlier: 7.495A pdb=" N ASN I 385 " --> pdb=" O ILE I 425 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'J' and resid 42 through 43 Processing sheet with id=AD4, first strand: chain 'J' and resid 100 through 104 removed outlier: 6.345A pdb=" N THR J 101 " --> pdb=" O PHE J 297 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N ASP J 299 " --> pdb=" O THR J 101 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE J 103 " --> pdb=" O ASP J 299 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU J 296 " --> pdb=" O ILE J 325 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N ALA J 327 " --> pdb=" O LEU J 296 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N ILE J 298 " --> pdb=" O ALA J 327 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLY J 77 " --> pdb=" O THR J 328 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ALA J 72 " --> pdb=" O LEU J 355 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N VAL J 357 " --> pdb=" O ALA J 72 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEU J 74 " --> pdb=" O VAL J 357 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N THR J 359 " --> pdb=" O LEU J 74 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ALA J 76 " --> pdb=" O THR J 359 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 127 through 146 removed outlier: 6.694A pdb=" N THR J 162 " --> pdb=" O VAL J 143 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ILE J 145 " --> pdb=" O LYS J 160 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LYS J 160 " --> pdb=" O ILE J 145 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 169 through 173 current: chain 'J' and resid 202 through 207 Processing sheet with id=AD6, first strand: chain 'J' and resid 333 through 334 Processing sheet with id=AD7, first strand: chain 'L' and resid 29 through 32 removed outlier: 6.572A pdb=" N LEU L 8 " --> pdb=" O LEU L 104 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N THR L 106 " --> pdb=" O LEU L 8 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N VAL L 10 " --> pdb=" O THR L 106 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'L' and resid 53 through 54 Processing sheet with id=AD9, first strand: chain 'L' and resid 71 through 72 Processing sheet with id=AE1, first strand: chain 'L' and resid 150 through 155 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 169 through 170 current: chain 'L' and resid 329 through 330 Processing sheet with id=AE2, first strand: chain 'L' and resid 238 through 241 Processing sheet with id=AE3, first strand: chain 'M' and resid 35 through 38 removed outlier: 6.262A pdb=" N LEU M 14 " --> pdb=" O LEU M 121 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N SER M 123 " --> pdb=" O LEU M 14 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N PHE M 16 " --> pdb=" O SER M 123 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'M' and resid 67 through 69 Processing sheet with id=AE5, first strand: chain 'M' and resid 88 through 89 Processing sheet with id=AE6, first strand: chain 'M' and resid 167 through 172 Processing sheet with id=AE7, first strand: chain 'M' and resid 223 through 227 removed outlier: 4.821A pdb=" N ASN M 236 " --> pdb=" O GLU M 227 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'M' and resid 286 through 288 Processing sheet with id=AE9, first strand: chain 'N' and resid 95 through 101 removed outlier: 3.619A pdb=" N PHE N 111 " --> pdb=" O PHE N 100 " (cutoff:3.500A) 1532 hydrogen bonds defined for protein. 4341 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: 7.21 Time building geometry restraints manager: 3.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 11469 1.36 - 1.51: 8889 1.51 - 1.66: 13928 1.66 - 1.80: 220 1.80 - 1.95: 73 Bond restraints: 34579 Sorted by residual: bond pdb=" CG ARG B 263 " pdb=" CD ARG B 263 " ideal model delta sigma weight residual 1.520 1.483 0.037 3.00e-02 1.11e+03 1.54e+00 bond pdb=" CG GLU F 300 " pdb=" CD GLU F 300 " ideal model delta sigma weight residual 1.516 1.490 0.026 2.50e-02 1.60e+03 1.07e+00 bond pdb=" CB VAL A 841 " pdb=" CG2 VAL A 841 " ideal model delta sigma weight residual 1.521 1.488 0.033 3.30e-02 9.18e+02 9.85e-01 bond pdb=" CB THR I 313 " pdb=" CG2 THR I 313 " ideal model delta sigma weight residual 1.521 1.489 0.032 3.30e-02 9.18e+02 9.14e-01 bond pdb=" CG1 ILE H 276 " pdb=" CD1 ILE H 276 " ideal model delta sigma weight residual 1.513 1.476 0.037 3.90e-02 6.57e+02 9.07e-01 ... (remaining 34574 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 45906 1.76 - 3.51: 753 3.51 - 5.27: 63 5.27 - 7.03: 10 7.03 - 8.79: 1 Bond angle restraints: 46733 Sorted by residual: angle pdb=" C MET A1923 " pdb=" N ILE A1924 " pdb=" CA ILE A1924 " ideal model delta sigma weight residual 120.46 124.75 -4.29 1.37e+00 5.33e-01 9.81e+00 angle pdb=" C MET I 264 " pdb=" N LYS I 265 " pdb=" CA LYS I 265 " ideal model delta sigma weight residual 121.69 127.27 -5.58 1.82e+00 3.02e-01 9.41e+00 angle pdb=" N THR G 411 " pdb=" CA THR G 411 " pdb=" C THR G 411 " ideal model delta sigma weight residual 109.81 116.37 -6.56 2.21e+00 2.05e-01 8.81e+00 angle pdb=" N GLY J 230 " pdb=" CA GLY J 230 " pdb=" C GLY J 230 " ideal model delta sigma weight residual 113.18 119.63 -6.45 2.37e+00 1.78e-01 7.41e+00 angle pdb=" N PRO J 343 " pdb=" CA PRO J 343 " pdb=" C PRO J 343 " ideal model delta sigma weight residual 112.47 117.75 -5.28 2.06e+00 2.36e-01 6.57e+00 ... (remaining 46728 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.09: 20830 34.09 - 68.18: 379 68.18 - 102.27: 38 102.27 - 136.36: 2 136.36 - 170.45: 3 Dihedral angle restraints: 21252 sinusoidal: 8861 harmonic: 12391 Sorted by residual: dihedral pdb=" CA THR G 399 " pdb=" C THR G 399 " pdb=" N LYS G 400 " pdb=" CA LYS G 400 " ideal model delta harmonic sigma weight residual 180.00 151.03 28.97 0 5.00e+00 4.00e-02 3.36e+01 dihedral pdb=" CA VAL A1847 " pdb=" C VAL A1847 " pdb=" N PRO A1848 " pdb=" CA PRO A1848 " ideal model delta harmonic sigma weight residual 180.00 151.97 28.03 0 5.00e+00 4.00e-02 3.14e+01 dihedral pdb=" CA HIS N 113 " pdb=" C HIS N 113 " pdb=" N TRP N 114 " pdb=" CA TRP N 114 " ideal model delta harmonic sigma weight residual 180.00 152.05 27.95 0 5.00e+00 4.00e-02 3.13e+01 ... (remaining 21249 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 4196 0.050 - 0.100: 945 0.100 - 0.150: 177 0.150 - 0.200: 7 0.200 - 0.250: 2 Chirality restraints: 5327 Sorted by residual: chirality pdb=" CA THR G 411 " pdb=" N THR G 411 " pdb=" C THR G 411 " pdb=" CB THR G 411 " both_signs ideal model delta sigma weight residual False 2.53 2.28 0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" PB AGS H 901 " pdb=" O2B AGS H 901 " pdb=" O3A AGS H 901 " pdb=" O3B AGS H 901 " both_signs ideal model delta sigma weight residual True 3.18 -2.97 0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA HIS A1937 " pdb=" N HIS A1937 " pdb=" C HIS A1937 " pdb=" CB HIS A1937 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.79e-01 ... (remaining 5324 not shown) Planarity restraints: 5974 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG F 284 " -0.200 9.50e-02 1.11e+02 9.06e-02 7.22e+00 pdb=" NE ARG F 284 " 0.021 2.00e-02 2.50e+03 pdb=" CZ ARG F 284 " -0.024 2.00e-02 2.50e+03 pdb=" NH1 ARG F 284 " 0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG F 284 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG J 21 " 0.204 9.50e-02 1.11e+02 9.24e-02 6.89e+00 pdb=" NE ARG J 21 " -0.020 2.00e-02 2.50e+03 pdb=" CZ ARG J 21 " 0.020 2.00e-02 2.50e+03 pdb=" NH1 ARG J 21 " -0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG J 21 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 469 " -0.208 9.50e-02 1.11e+02 9.37e-02 6.85e+00 pdb=" NE ARG C 469 " 0.020 2.00e-02 2.50e+03 pdb=" CZ ARG C 469 " -0.019 2.00e-02 2.50e+03 pdb=" NH1 ARG C 469 " 0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG C 469 " -0.000 2.00e-02 2.50e+03 ... (remaining 5971 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 64 2.43 - 3.05: 21413 3.05 - 3.67: 51272 3.67 - 4.28: 78779 4.28 - 4.90: 130237 Nonbonded interactions: 281765 Sorted by model distance: nonbonded pdb=" O2G AGS I 501 " pdb="MG MG I 502 " model vdw 1.815 2.170 nonbonded pdb=" O2B AGS G 501 " pdb="MG MG G 502 " model vdw 1.877 2.170 nonbonded pdb=" O3G AGS H 901 " pdb="MG MG H 902 " model vdw 1.888 2.170 nonbonded pdb=" O3G AGS J 901 " pdb="MG MG J 902 " model vdw 1.898 2.170 nonbonded pdb=" O2G AGS G 501 " pdb="MG MG G 502 " model vdw 1.935 2.170 ... (remaining 281760 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 'E' and (resid 12 through 251 or resid 256 through 502)) selection = (chain 'G' and (resid 12 through 140 or resid 156 through 448 or resid 501 throu \ gh 502)) selection = (chain 'I' and (resid 12 through 140 or resid 156 through 251 or resid 256 throu \ gh 448 or resid 501 through 502)) } ncs_group { reference = (chain 'F' and (resid 16 through 147 or resid 159 through 208 or resid 226 throu \ gh 902)) selection = (chain 'H' and (resid 16 through 147 or resid 159 through 208 or resid 226 throu \ gh 902)) selection = (chain 'J' and (resid 16 through 453 or resid 901 through 902)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.480 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: 0.010 Extract box with map and model: 0.740 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 29.600 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.070 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 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 : 0.003 0.042 34579 Z= 0.144 Angle : 0.548 8.786 46733 Z= 0.309 Chirality : 0.043 0.250 5327 Planarity : 0.007 0.094 5974 Dihedral : 13.625 170.452 13250 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.74 (0.12), residues: 4227 helix: 0.52 (0.11), residues: 1870 sheet: 0.43 (0.18), residues: 710 loop : 0.77 (0.16), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.002 ARG F 284 TYR 0.022 0.003 TYR H 362 PHE 0.011 0.001 PHE H 257 TRP 0.029 0.002 TRP A2196 HIS 0.013 0.001 HIS A1937 Details of bonding type rmsd covalent geometry : bond 0.00313 (34579) covalent geometry : angle 0.54830 (46733) hydrogen bonds : bond 0.15247 ( 1532) hydrogen bonds : angle 5.63397 ( 4341) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8454 Ramachandran restraints generated. 4227 Oldfield, 0 Emsley, 4227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8454 Ramachandran restraints generated. 4227 Oldfield, 0 Emsley, 4227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1369 residues out of total 3673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1369 time to evaluate : 1.080 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: A 789 ARG cc_start: 0.7973 (ttm170) cc_final: 0.7763 (ttm170) REVERT: A 809 LYS cc_start: 0.8140 (mtmt) cc_final: 0.7877 (mtmm) REVERT: A 813 ASP cc_start: 0.8612 (m-30) cc_final: 0.8410 (m-30) REVERT: A 814 TYR cc_start: 0.8321 (m-80) cc_final: 0.8074 (m-80) REVERT: A 831 ARG cc_start: 0.7700 (mmm-85) cc_final: 0.7229 (ttm170) REVERT: A 840 LEU cc_start: 0.8512 (mt) cc_final: 0.8307 (mm) REVERT: A 841 VAL cc_start: 0.8446 (t) cc_final: 0.8209 (p) REVERT: A 851 LYS cc_start: 0.7928 (tttt) cc_final: 0.7573 (tttt) REVERT: A 1361 LEU cc_start: 0.6952 (mp) cc_final: 0.6600 (mp) REVERT: A 1412 MET cc_start: 0.8119 (ptp) cc_final: 0.7763 (ptp) REVERT: A 1413 PHE cc_start: 0.8275 (m-80) cc_final: 0.7918 (m-10) REVERT: A 1459 LYS cc_start: 0.8280 (mtmm) cc_final: 0.8016 (mtmm) REVERT: A 1746 LEU cc_start: 0.7961 (tp) cc_final: 0.7747 (tp) REVERT: A 1752 GLN cc_start: 0.7007 (mt0) cc_final: 0.6769 (mt0) REVERT: A 1759 ARG cc_start: 0.7363 (mtm110) cc_final: 0.7111 (mtp85) REVERT: A 1769 ARG cc_start: 0.7942 (mtp-110) cc_final: 0.7612 (mtp-110) REVERT: A 1952 GLN cc_start: 0.6719 (mm-40) cc_final: 0.5465 (mm110) REVERT: A 2020 ARG cc_start: 0.6545 (mmt180) cc_final: 0.6325 (mmt180) REVERT: A 2052 MET cc_start: 0.6252 (mmp) cc_final: 0.5943 (mpp) REVERT: A 2226 GLU cc_start: 0.7171 (mp0) cc_final: 0.6814 (mp0) REVERT: A 2227 ASP cc_start: 0.7452 (m-30) cc_final: 0.7002 (m-30) REVERT: A 2233 TYR cc_start: 0.8011 (m-80) cc_final: 0.7566 (m-80) REVERT: A 2236 GLU cc_start: 0.6646 (mp0) cc_final: 0.6441 (mp0) REVERT: A 2261 TYR cc_start: 0.7513 (t80) cc_final: 0.7139 (t80) REVERT: A 2266 MET cc_start: 0.7824 (ttp) cc_final: 0.7567 (ttp) REVERT: A 2269 MET cc_start: 0.7871 (mmm) cc_final: 0.7425 (mmm) REVERT: C 406 ARG cc_start: 0.7865 (ttt-90) cc_final: 0.7445 (ttt-90) REVERT: C 426 THR cc_start: 0.8194 (p) cc_final: 0.7881 (t) REVERT: C 530 ARG cc_start: 0.7334 (ptp-110) cc_final: 0.7099 (ptp-170) REVERT: E 17 SER cc_start: 0.7833 (m) cc_final: 0.7430 (t) REVERT: E 190 VAL cc_start: 0.8630 (t) cc_final: 0.8362 (p) REVERT: E 264 MET cc_start: 0.6558 (mmm) cc_final: 0.6216 (mmm) REVERT: E 274 LYS cc_start: 0.8089 (tttm) cc_final: 0.7717 (tttm) REVERT: E 278 GLU cc_start: 0.7519 (mm-30) cc_final: 0.7217 (mm-30) REVERT: E 288 ASP cc_start: 0.7753 (t0) cc_final: 0.7523 (t0) REVERT: E 306 MET cc_start: 0.8023 (mmp) cc_final: 0.7631 (mmt) REVERT: E 364 MET cc_start: 0.7249 (mtm) cc_final: 0.6998 (mtm) REVERT: E 376 LYS cc_start: 0.8081 (tptm) cc_final: 0.7755 (tptm) REVERT: E 381 THR cc_start: 0.8194 (m) cc_final: 0.7606 (p) REVERT: E 392 ASN cc_start: 0.7748 (m-40) cc_final: 0.7435 (m-40) REVERT: E 396 GLU cc_start: 0.7381 (tm-30) cc_final: 0.7058 (tm-30) REVERT: E 408 GLN cc_start: 0.7477 (mt0) cc_final: 0.7264 (mt0) REVERT: E 416 LEU cc_start: 0.8002 (mt) cc_final: 0.7717 (mt) REVERT: F 22 ILE cc_start: 0.7736 (mt) cc_final: 0.7481 (mt) REVERT: F 65 GLU cc_start: 0.7288 (mm-30) cc_final: 0.7063 (mm-30) REVERT: F 78 GLN cc_start: 0.7332 (mm110) cc_final: 0.6920 (mm110) REVERT: F 90 MET cc_start: 0.7420 (mtp) cc_final: 0.7190 (mtm) REVERT: F 181 SER cc_start: 0.8701 (t) cc_final: 0.8378 (t) REVERT: F 202 ILE cc_start: 0.8436 (mt) cc_final: 0.8166 (mt) REVERT: F 210 THR cc_start: 0.8647 (t) cc_final: 0.8431 (p) REVERT: F 231 GLU cc_start: 0.7644 (mp0) cc_final: 0.7368 (mp0) REVERT: F 274 GLU cc_start: 0.7656 (mt-10) cc_final: 0.7427 (mt-10) REVERT: F 300 GLU cc_start: 0.7275 (pt0) cc_final: 0.6958 (pt0) REVERT: F 307 GLU cc_start: 0.7155 (mt-10) cc_final: 0.6952 (mt-10) REVERT: F 333 THR cc_start: 0.7992 (p) cc_final: 0.7608 (t) REVERT: F 352 ASP cc_start: 0.6769 (t0) cc_final: 0.6550 (t0) REVERT: F 365 LYS cc_start: 0.7460 (mttm) cc_final: 0.7256 (mttm) REVERT: F 381 GLU cc_start: 0.7190 (mm-30) cc_final: 0.6947 (mm-30) REVERT: F 410 SER cc_start: 0.8276 (t) cc_final: 0.7938 (t) REVERT: F 414 ARG cc_start: 0.7024 (mtm-85) cc_final: 0.6730 (mtm-85) REVERT: F 420 GLU cc_start: 0.6817 (tt0) cc_final: 0.6530 (tt0) REVERT: G 19 SER cc_start: 0.8071 (m) cc_final: 0.7785 (p) REVERT: G 64 ARG cc_start: 0.7302 (mmm160) cc_final: 0.6700 (mmm160) REVERT: G 180 LEU cc_start: 0.8654 (mt) cc_final: 0.8453 (mt) REVERT: G 186 GLU cc_start: 0.7859 (mt-10) cc_final: 0.7481 (mt-10) REVERT: G 267 LYS cc_start: 0.7948 (ptpt) cc_final: 0.7671 (ptpt) REVERT: G 285 LYS cc_start: 0.8155 (mtpt) cc_final: 0.7911 (mtpt) REVERT: G 357 ARG cc_start: 0.7806 (mtt90) cc_final: 0.7605 (mtt90) REVERT: G 359 MET cc_start: 0.7938 (mtm) cc_final: 0.7510 (mtm) REVERT: G 369 GLN cc_start: 0.7364 (mp10) cc_final: 0.6843 (mp10) REVERT: G 372 LYS cc_start: 0.7630 (mttp) cc_final: 0.7427 (mttp) REVERT: G 411 THR cc_start: 0.8267 (t) cc_final: 0.7974 (m) REVERT: G 418 LYS cc_start: 0.7956 (ttmt) cc_final: 0.7749 (ttmt) REVERT: H 20 GLU cc_start: 0.6827 (mp0) cc_final: 0.6584 (mp0) REVERT: H 88 MET cc_start: 0.7905 (mmm) cc_final: 0.7704 (mmm) REVERT: H 134 GLU cc_start: 0.7682 (mt-10) cc_final: 0.6903 (mt-10) REVERT: H 146 GLN cc_start: 0.7007 (mt0) cc_final: 0.6807 (mt0) REVERT: H 178 MET cc_start: 0.7292 (mmm) cc_final: 0.7089 (tpp) REVERT: H 180 GLU cc_start: 0.7602 (mm-30) cc_final: 0.7069 (mm-30) REVERT: H 184 LYS cc_start: 0.8094 (mmpt) cc_final: 0.7838 (mmpt) REVERT: H 188 GLN cc_start: 0.7729 (tt0) cc_final: 0.7473 (tt0) REVERT: H 191 ASP cc_start: 0.7512 (m-30) cc_final: 0.7288 (m-30) REVERT: H 233 GLN cc_start: 0.8434 (tt0) cc_final: 0.8192 (tt0) REVERT: H 235 ARG cc_start: 0.8018 (ttt180) cc_final: 0.7579 (ttt180) REVERT: H 282 GLU cc_start: 0.7745 (tt0) cc_final: 0.7500 (tt0) REVERT: H 305 ASP cc_start: 0.6968 (p0) cc_final: 0.6734 (p0) REVERT: H 350 LEU cc_start: 0.7832 (tt) cc_final: 0.7572 (tp) REVERT: H 368 LYS cc_start: 0.8286 (ttmt) cc_final: 0.8034 (ttmm) REVERT: H 391 THR cc_start: 0.7961 (m) cc_final: 0.7192 (p) REVERT: H 396 GLU cc_start: 0.7627 (mm-30) cc_final: 0.7421 (mm-30) REVERT: H 397 THR cc_start: 0.8171 (p) cc_final: 0.7863 (p) REVERT: H 435 ASP cc_start: 0.7608 (p0) cc_final: 0.7301 (p0) REVERT: H 438 ARG cc_start: 0.7287 (mtp180) cc_final: 0.7038 (mtm-85) REVERT: I 17 SER cc_start: 0.7974 (m) cc_final: 0.7689 (p) REVERT: I 31 LEU cc_start: 0.7435 (mt) cc_final: 0.7220 (mt) REVERT: I 60 LYS cc_start: 0.8036 (ttmt) cc_final: 0.7809 (ttmt) REVERT: I 113 MET cc_start: 0.7539 (tpp) cc_final: 0.7210 (tpp) REVERT: I 130 VAL cc_start: 0.8706 (t) cc_final: 0.8475 (m) REVERT: I 221 VAL cc_start: 0.8823 (t) cc_final: 0.8562 (m) REVERT: I 260 MET cc_start: 0.6734 (mtt) cc_final: 0.6227 (mtt) REVERT: I 280 ASN cc_start: 0.8469 (m-40) cc_final: 0.8107 (m-40) REVERT: I 281 LYS cc_start: 0.8437 (mttt) cc_final: 0.8140 (mttt) REVERT: I 372 LYS cc_start: 0.8114 (mtpt) cc_final: 0.7805 (mtpt) REVERT: I 396 GLU cc_start: 0.7170 (mt-10) cc_final: 0.6906 (mt-10) REVERT: J 38 GLU cc_start: 0.7599 (mm-30) cc_final: 0.7388 (mm-30) REVERT: J 112 GLU cc_start: 0.7223 (mm-30) cc_final: 0.6940 (mm-30) REVERT: J 115 LYS cc_start: 0.7921 (mtmt) cc_final: 0.7713 (mtmt) REVERT: J 161 LEU cc_start: 0.8053 (tp) cc_final: 0.7842 (mt) REVERT: J 305 ASP cc_start: 0.6802 (p0) cc_final: 0.6595 (p0) REVERT: J 334 ARG cc_start: 0.7227 (ptm-80) cc_final: 0.6961 (ptm160) REVERT: J 368 LYS cc_start: 0.7293 (ttmt) cc_final: 0.6991 (ttmt) REVERT: J 420 GLU cc_start: 0.7271 (mt-10) cc_final: 0.7069 (mt-10) REVERT: J 431 SER cc_start: 0.8040 (m) cc_final: 0.7778 (t) REVERT: J 436 GLU cc_start: 0.6791 (tm-30) cc_final: 0.6348 (tm-30) REVERT: J 441 GLN cc_start: 0.6711 (mm110) cc_final: 0.6306 (mm110) REVERT: L 53 TYR cc_start: 0.7085 (m-80) cc_final: 0.6875 (m-80) REVERT: L 68 LYS cc_start: 0.8251 (mtpt) cc_final: 0.7964 (mtpt) REVERT: L 81 ASP cc_start: 0.8095 (m-30) cc_final: 0.7817 (m-30) REVERT: L 123 MET cc_start: 0.8553 (mmp) cc_final: 0.8330 (mmp) REVERT: L 136 ILE cc_start: 0.8555 (tt) cc_final: 0.8232 (pt) REVERT: L 191 LYS cc_start: 0.8379 (ttmt) cc_final: 0.8083 (ttmt) REVERT: L 215 LYS cc_start: 0.8436 (mmtt) cc_final: 0.7807 (mmtt) REVERT: L 218 TYR cc_start: 0.8332 (p90) cc_final: 0.8123 (p90) REVERT: L 227 MET cc_start: 0.7025 (mmm) cc_final: 0.6799 (mmm) REVERT: L 255 PHE cc_start: 0.8333 (p90) cc_final: 0.8100 (p90) REVERT: L 259 GLU cc_start: 0.7704 (tp30) cc_final: 0.7499 (tp30) REVERT: L 283 MET cc_start: 0.8084 (mmm) cc_final: 0.7871 (mmm) REVERT: L 306 TYR cc_start: 0.8596 (m-80) cc_final: 0.8063 (m-80) REVERT: L 313 MET cc_start: 0.8105 (mmm) cc_final: 0.7754 (mmm) REVERT: M 21 TYR cc_start: 0.8000 (t80) cc_final: 0.7741 (t80) REVERT: M 22 THR cc_start: 0.8315 (p) cc_final: 0.8039 (p) REVERT: M 43 MET cc_start: 0.7483 (tmm) cc_final: 0.7022 (tmm) REVERT: M 44 VAL cc_start: 0.8736 (t) cc_final: 0.8465 (p) REVERT: M 95 ASP cc_start: 0.7516 (t0) cc_final: 0.7133 (t0) REVERT: M 100 GLN cc_start: 0.8028 (mt0) cc_final: 0.7772 (mt0) REVERT: M 142 GLU cc_start: 0.7486 (mm-30) cc_final: 0.7206 (mm-30) REVERT: M 200 ASP cc_start: 0.7868 (m-30) cc_final: 0.7615 (m-30) REVERT: M 345 TYR cc_start: 0.7940 (m-80) cc_final: 0.7716 (m-80) REVERT: M 354 ASN cc_start: 0.8571 (t0) cc_final: 0.8177 (t0) REVERT: M 413 LYS cc_start: 0.8358 (tttm) cc_final: 0.8079 (tttm) REVERT: N 65 LYS cc_start: 0.7856 (ptpp) cc_final: 0.7587 (ptpp) REVERT: N 66 LYS cc_start: 0.8098 (mtmt) cc_final: 0.7890 (mtmt) REVERT: N 81 ARG cc_start: 0.8183 (ttt-90) cc_final: 0.7943 (ttt-90) REVERT: N 106 LYS cc_start: 0.8549 (ptpt) cc_final: 0.8315 (ptpt) REVERT: N 128 ARG cc_start: 0.7689 (ttm170) cc_final: 0.7488 (ttm170) REVERT: N 138 TYR cc_start: 0.8294 (p90) cc_final: 0.8057 (p90) REVERT: N 158 ASP cc_start: 0.7898 (m-30) cc_final: 0.7635 (m-30) REVERT: N 193 GLU cc_start: 0.7669 (tp30) cc_final: 0.7307 (tp30) outliers start: 0 outliers final: 0 residues processed: 1369 average time/residue: 0.2617 time to fit residues: 534.6774 Evaluate side-chains 1298 residues out of total 3673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1298 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 2.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 4.9990 chunk 401 optimal weight: 3.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 0.5980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1425 HIS A1922 GLN E 115 ASN E 203 GLN E 241 HIS E 316 HIS F 251 ASN F 275 GLN F 313 ASN F 404 GLN G 115 ASN G 305 HIS G 380 GLN H 121 GLN H 226 GLN H 233 GLN H 369 GLN H 404 GLN ** I 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 229 HIS I 247 ASN I 373 GLN J 44 GLN J 121 GLN J 302 HIS L 252 ASN M 268 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.146804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.127790 restraints weight = 51454.914| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 2.10 r_work: 0.3422 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.1331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 34579 Z= 0.219 Angle : 0.576 10.245 46733 Z= 0.308 Chirality : 0.045 0.237 5327 Planarity : 0.004 0.046 5974 Dihedral : 9.204 166.499 4826 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.50 % Allowed : 9.12 % Favored : 89.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.15 (0.13), residues: 4227 helix: 1.09 (0.12), residues: 1893 sheet: 0.37 (0.19), residues: 695 loop : 0.79 (0.16), residues: 1639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 18 TYR 0.029 0.002 TYR A1336 PHE 0.024 0.002 PHE B 278 TRP 0.012 0.002 TRP L 79 HIS 0.010 0.001 HIS N 113 Details of bonding type rmsd covalent geometry : bond 0.00478 (34579) covalent geometry : angle 0.57552 (46733) hydrogen bonds : bond 0.05244 ( 1532) hydrogen bonds : angle 4.71435 ( 4341) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8454 Ramachandran restraints generated. 4227 Oldfield, 0 Emsley, 4227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8454 Ramachandran restraints generated. 4227 Oldfield, 0 Emsley, 4227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1376 residues out of total 3673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 1321 time to evaluate : 1.324 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: A 789 ARG cc_start: 0.8069 (ttm170) cc_final: 0.7813 (ttm170) REVERT: A 793 LEU cc_start: 0.8001 (mp) cc_final: 0.7699 (tp) REVERT: A 809 LYS cc_start: 0.8290 (mtmt) cc_final: 0.8006 (mtmm) REVERT: A 820 GLN cc_start: 0.8458 (tt0) cc_final: 0.8099 (tt0) REVERT: A 839 LYS cc_start: 0.8784 (mmmt) cc_final: 0.8569 (mmmt) REVERT: A 841 VAL cc_start: 0.8566 (t) cc_final: 0.8349 (p) REVERT: A 851 LYS cc_start: 0.8077 (tttt) cc_final: 0.7727 (tttt) REVERT: A 1346 GLN cc_start: 0.7900 (mm-40) cc_final: 0.7233 (mm-40) REVERT: A 1361 LEU cc_start: 0.7101 (mp) cc_final: 0.6773 (mt) REVERT: A 1412 MET cc_start: 0.8230 (ptp) cc_final: 0.8001 (ptp) REVERT: A 1413 PHE cc_start: 0.8532 (m-80) cc_final: 0.8142 (m-10) REVERT: A 1459 LYS cc_start: 0.8133 (mtmm) cc_final: 0.7878 (mtmm) REVERT: A 1746 LEU cc_start: 0.7996 (tp) cc_final: 0.7752 (tp) REVERT: A 1769 ARG cc_start: 0.7974 (mtp-110) cc_final: 0.7699 (mtp-110) REVERT: A 1894 GLN cc_start: 0.7850 (tt0) cc_final: 0.7550 (tt0) REVERT: A 1909 LYS cc_start: 0.8220 (tmmt) cc_final: 0.8011 (tmmt) REVERT: A 1941 TYR cc_start: 0.6938 (p90) cc_final: 0.6489 (p90) REVERT: A 1957 MET cc_start: 0.7782 (tpp) cc_final: 0.7522 (tpp) REVERT: A 1962 ARG cc_start: 0.7634 (ptp-170) cc_final: 0.7341 (ptp-170) REVERT: A 2052 MET cc_start: 0.6398 (mmp) cc_final: 0.6193 (mpp) REVERT: A 2198 PHE cc_start: 0.7885 (m-80) cc_final: 0.7607 (m-80) REVERT: A 2226 GLU cc_start: 0.7513 (mp0) cc_final: 0.7128 (mp0) REVERT: A 2227 ASP cc_start: 0.7864 (m-30) cc_final: 0.7549 (m-30) REVERT: A 2233 TYR cc_start: 0.8120 (m-80) cc_final: 0.7613 (m-80) REVERT: A 2236 GLU cc_start: 0.6906 (mp0) cc_final: 0.6660 (mp0) REVERT: A 2266 MET cc_start: 0.8173 (ttp) cc_final: 0.7918 (ttp) REVERT: A 2269 MET cc_start: 0.7988 (mmm) cc_final: 0.7497 (mmm) REVERT: B 302 ARG cc_start: 0.8418 (ptp-110) cc_final: 0.8046 (ttm-80) REVERT: C 406 ARG cc_start: 0.7859 (ttt-90) cc_final: 0.7400 (ttt-90) REVERT: C 426 THR cc_start: 0.8179 (p) cc_final: 0.7728 (t) REVERT: C 530 ARG cc_start: 0.7256 (ptp-110) cc_final: 0.6967 (ptp-110) REVERT: E 17 SER cc_start: 0.7870 (m) cc_final: 0.7344 (t) REVERT: E 110 GLU cc_start: 0.6938 (mm-30) cc_final: 0.6410 (tm-30) REVERT: E 114 GLU cc_start: 0.7546 (mt-10) cc_final: 0.7115 (mt-10) REVERT: E 190 VAL cc_start: 0.8724 (t) cc_final: 0.8415 (p) REVERT: E 236 GLN cc_start: 0.8073 (mm-40) cc_final: 0.7762 (mm-40) REVERT: E 264 MET cc_start: 0.6668 (mmm) cc_final: 0.6270 (mmm) REVERT: E 274 LYS cc_start: 0.8249 (tttm) cc_final: 0.7833 (tttt) REVERT: E 278 GLU cc_start: 0.7734 (mm-30) cc_final: 0.7203 (mm-30) REVERT: E 281 LYS cc_start: 0.7708 (mtmm) cc_final: 0.7457 (mtmm) REVERT: E 288 ASP cc_start: 0.8023 (t0) cc_final: 0.7771 (t0) REVERT: E 306 MET cc_start: 0.8099 (mmp) cc_final: 0.7638 (mmt) REVERT: E 352 LEU cc_start: 0.8005 (mt) cc_final: 0.7660 (mt) REVERT: E 364 MET cc_start: 0.7202 (mtm) cc_final: 0.6797 (mtm) REVERT: E 376 LYS cc_start: 0.8161 (tptm) cc_final: 0.7819 (tptm) REVERT: E 381 THR cc_start: 0.8300 (m) cc_final: 0.7658 (p) REVERT: E 392 ASN cc_start: 0.7837 (m-40) cc_final: 0.7503 (m-40) REVERT: E 416 LEU cc_start: 0.8032 (mt) cc_final: 0.7674 (mt) REVERT: E 435 GLU cc_start: 0.7218 (mt-10) cc_final: 0.6982 (mt-10) REVERT: E 438 TYR cc_start: 0.6883 (m-80) cc_final: 0.6655 (m-80) REVERT: F 20 GLU cc_start: 0.7654 (mp0) cc_final: 0.7259 (mp0) REVERT: F 65 GLU cc_start: 0.7398 (mm-30) cc_final: 0.6980 (mm-30) REVERT: F 67 LYS cc_start: 0.7976 (mttt) cc_final: 0.7745 (mttt) REVERT: F 117 GLU cc_start: 0.7617 (tp30) cc_final: 0.6915 (mm-30) REVERT: F 136 GLU cc_start: 0.6539 (mm-30) cc_final: 0.6123 (mm-30) REVERT: F 141 GLU cc_start: 0.7826 (pt0) cc_final: 0.7034 (pt0) REVERT: F 181 SER cc_start: 0.8784 (t) cc_final: 0.8491 (t) REVERT: F 202 ILE cc_start: 0.8574 (mt) cc_final: 0.8299 (mt) REVERT: F 210 THR cc_start: 0.8780 (t) cc_final: 0.8492 (p) REVERT: F 231 GLU cc_start: 0.7850 (mp0) cc_final: 0.7351 (mp0) REVERT: F 234 LYS cc_start: 0.8311 (mttp) cc_final: 0.8077 (mtmm) REVERT: F 274 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7620 (mt-10) REVERT: F 381 GLU cc_start: 0.7572 (mm-30) cc_final: 0.7256 (mm-30) REVERT: F 410 SER cc_start: 0.8099 (t) cc_final: 0.7755 (t) REVERT: F 414 ARG cc_start: 0.7173 (mtm-85) cc_final: 0.6926 (mtm-85) REVERT: F 420 GLU cc_start: 0.6951 (tt0) cc_final: 0.6559 (tt0) REVERT: G 19 SER cc_start: 0.8184 (m) cc_final: 0.7785 (p) REVERT: G 60 LYS cc_start: 0.7546 (mtpp) cc_final: 0.7231 (mtpp) REVERT: G 64 ARG cc_start: 0.7438 (mmm160) cc_final: 0.6761 (mmm160) REVERT: G 180 LEU cc_start: 0.8762 (mt) cc_final: 0.8438 (mt) REVERT: G 267 LYS cc_start: 0.7931 (ptpt) cc_final: 0.7630 (ptpt) REVERT: G 285 LYS cc_start: 0.8073 (mtpt) cc_final: 0.7789 (mtpt) REVERT: G 357 ARG cc_start: 0.7823 (mtt90) cc_final: 0.7616 (mtt90) REVERT: G 362 ARG cc_start: 0.8068 (ptm160) cc_final: 0.7630 (ttm170) REVERT: G 369 GLN cc_start: 0.7327 (mp10) cc_final: 0.6662 (mp10) REVERT: G 372 LYS cc_start: 0.7561 (mttp) cc_final: 0.7241 (mttp) REVERT: G 411 THR cc_start: 0.8102 (t) cc_final: 0.7822 (m) REVERT: G 414 ASN cc_start: 0.7710 (t0) cc_final: 0.7371 (t0) REVERT: G 418 LYS cc_start: 0.7787 (ttmt) cc_final: 0.7585 (ttmt) REVERT: H 18 ARG cc_start: 0.7174 (mtp85) cc_final: 0.6747 (mtp85) REVERT: H 46 MET cc_start: 0.8544 (mmm) cc_final: 0.8331 (mmm) REVERT: H 88 MET cc_start: 0.7906 (mmm) cc_final: 0.7660 (mmm) REVERT: H 124 ARG cc_start: 0.8060 (mtp85) cc_final: 0.7833 (mtp85) REVERT: H 134 GLU cc_start: 0.7909 (mt-10) cc_final: 0.7072 (mt-10) REVERT: H 144 GLU cc_start: 0.8093 (tt0) cc_final: 0.7884 (tt0) REVERT: H 178 MET cc_start: 0.7831 (mmm) cc_final: 0.7595 (tpp) REVERT: H 180 GLU cc_start: 0.8107 (mm-30) cc_final: 0.7662 (mm-30) REVERT: H 184 LYS cc_start: 0.8425 (mmpt) cc_final: 0.7974 (mmpt) REVERT: H 188 GLN cc_start: 0.8066 (tt0) cc_final: 0.7847 (tt0) REVERT: H 191 ASP cc_start: 0.7832 (m-30) cc_final: 0.7581 (m-30) REVERT: H 235 ARG cc_start: 0.7896 (ttt180) cc_final: 0.7434 (ttt180) REVERT: H 248 ASP cc_start: 0.7493 (m-30) cc_final: 0.7142 (m-30) REVERT: H 274 GLU cc_start: 0.7386 (mt-10) cc_final: 0.7002 (mt-10) REVERT: H 282 GLU cc_start: 0.7831 (tt0) cc_final: 0.7569 (tt0) REVERT: H 352 ASP cc_start: 0.7463 (m-30) cc_final: 0.7089 (m-30) REVERT: H 396 GLU cc_start: 0.7777 (mm-30) cc_final: 0.7536 (mm-30) REVERT: H 397 THR cc_start: 0.8115 (p) cc_final: 0.7889 (p) REVERT: H 435 ASP cc_start: 0.7703 (p0) cc_final: 0.7412 (p0) REVERT: H 438 ARG cc_start: 0.7357 (mtp180) cc_final: 0.7073 (mtm-85) REVERT: I 17 SER cc_start: 0.8018 (m) cc_final: 0.7684 (p) REVERT: I 47 GLU cc_start: 0.7110 (mt-10) cc_final: 0.6856 (mt-10) REVERT: I 60 LYS cc_start: 0.7969 (ttmt) cc_final: 0.7731 (ttmt) REVERT: I 113 MET cc_start: 0.7384 (tpp) cc_final: 0.6951 (tpp) REVERT: I 130 VAL cc_start: 0.8834 (t) cc_final: 0.8549 (m) REVERT: I 186 GLU cc_start: 0.6877 (mm-30) cc_final: 0.6676 (mm-30) REVERT: I 249 ARG cc_start: 0.7546 (tmm160) cc_final: 0.7131 (tmm160) REVERT: I 260 MET cc_start: 0.7007 (mtt) cc_final: 0.6118 (mtt) REVERT: I 264 MET cc_start: 0.6566 (ptp) cc_final: 0.6170 (ptp) REVERT: I 280 ASN cc_start: 0.8509 (m-40) cc_final: 0.8208 (m-40) REVERT: I 281 LYS cc_start: 0.8394 (mttt) cc_final: 0.8090 (mttt) REVERT: I 372 LYS cc_start: 0.8060 (mtpt) cc_final: 0.7735 (mtpt) REVERT: I 396 GLU cc_start: 0.7270 (mt-10) cc_final: 0.7021 (mt-10) REVERT: I 432 GLU cc_start: 0.7366 (tt0) cc_final: 0.7157 (tt0) REVERT: J 38 GLU cc_start: 0.7647 (mm-30) cc_final: 0.7354 (mm-30) REVERT: J 40 ARG cc_start: 0.7436 (mtt180) cc_final: 0.7198 (mtt-85) REVERT: J 44 GLN cc_start: 0.7855 (mt0) cc_final: 0.7647 (mt0) REVERT: J 115 LYS cc_start: 0.8038 (mtmt) cc_final: 0.7828 (mtmt) REVERT: J 164 LYS cc_start: 0.8235 (pttt) cc_final: 0.7707 (pttt) REVERT: J 169 GLU cc_start: 0.6517 (tt0) cc_final: 0.6175 (tt0) REVERT: J 178 MET cc_start: 0.6017 (tpp) cc_final: 0.5628 (tpp) REVERT: J 305 ASP cc_start: 0.7043 (p0) cc_final: 0.6740 (p0) REVERT: J 316 LEU cc_start: 0.7917 (mt) cc_final: 0.7533 (mm) REVERT: J 368 LYS cc_start: 0.7280 (ttmt) cc_final: 0.6922 (ttmt) REVERT: J 401 TYR cc_start: 0.7863 (t80) cc_final: 0.7573 (t80) REVERT: J 420 GLU cc_start: 0.7278 (mt-10) cc_final: 0.6961 (mt-10) REVERT: J 436 GLU cc_start: 0.6865 (tm-30) cc_final: 0.6663 (tm-30) REVERT: J 441 GLN cc_start: 0.6771 (mm110) cc_final: 0.6419 (mm110) REVERT: L 18 LYS cc_start: 0.8432 (mppt) cc_final: 0.8185 (mttp) REVERT: L 68 LYS cc_start: 0.8006 (mtpt) cc_final: 0.7743 (mtpt) REVERT: L 81 ASP cc_start: 0.8235 (m-30) cc_final: 0.8025 (m-30) REVERT: L 113 LYS cc_start: 0.8223 (ttpp) cc_final: 0.7729 (mtpt) REVERT: L 132 MET cc_start: 0.8419 (ttp) cc_final: 0.8167 (tmm) REVERT: L 191 LYS cc_start: 0.8426 (ttmt) cc_final: 0.8108 (ttmt) REVERT: L 215 LYS cc_start: 0.8417 (mmtt) cc_final: 0.7778 (mmtt) REVERT: L 221 LEU cc_start: 0.8124 (tp) cc_final: 0.7849 (tt) REVERT: L 222 ASP cc_start: 0.7708 (t0) cc_final: 0.7491 (t0) REVERT: L 227 MET cc_start: 0.7059 (mmm) cc_final: 0.6763 (mmm) REVERT: L 242 LEU cc_start: 0.8378 (mt) cc_final: 0.8169 (mm) REVERT: L 259 GLU cc_start: 0.7930 (tp30) cc_final: 0.7579 (tp30) REVERT: L 291 LYS cc_start: 0.8286 (ttpp) cc_final: 0.8023 (ttpp) REVERT: L 306 TYR cc_start: 0.8638 (m-80) cc_final: 0.8154 (m-80) REVERT: L 313 MET cc_start: 0.8195 (mmm) cc_final: 0.7913 (mmm) REVERT: L 317 ILE cc_start: 0.8331 (mm) cc_final: 0.8093 (mt) REVERT: M 21 TYR cc_start: 0.8213 (t80) cc_final: 0.7798 (t80) REVERT: M 30 GLU cc_start: 0.7977 (mm-30) cc_final: 0.7680 (mm-30) REVERT: M 43 MET cc_start: 0.7497 (tmm) cc_final: 0.7033 (tmm) REVERT: M 95 ASP cc_start: 0.7658 (t0) cc_final: 0.7054 (t0) REVERT: M 100 GLN cc_start: 0.8206 (mt0) cc_final: 0.7884 (mt0) REVERT: M 142 GLU cc_start: 0.7740 (mm-30) cc_final: 0.7450 (mm-30) REVERT: M 178 THR cc_start: 0.8593 (m) cc_final: 0.8369 (p) REVERT: M 200 ASP cc_start: 0.8045 (m-30) cc_final: 0.7720 (m-30) REVERT: M 345 TYR cc_start: 0.8053 (m-80) cc_final: 0.7662 (m-80) REVERT: M 354 ASN cc_start: 0.8605 (t0) cc_final: 0.8134 (t0) REVERT: M 358 GLN cc_start: 0.7880 (OUTLIER) cc_final: 0.7331 (tm-30) REVERT: M 379 LYS cc_start: 0.7918 (tptt) cc_final: 0.7646 (tptt) REVERT: M 413 LYS cc_start: 0.8278 (tttm) cc_final: 0.8004 (tttm) REVERT: N 65 LYS cc_start: 0.7928 (ptpp) cc_final: 0.7725 (ptpp) REVERT: N 66 LYS cc_start: 0.8133 (mtmt) cc_final: 0.7883 (mtmt) REVERT: N 81 ARG cc_start: 0.7914 (ttt-90) cc_final: 0.7692 (ttt-90) REVERT: N 106 LYS cc_start: 0.8486 (ptpt) cc_final: 0.8218 (ptpt) REVERT: N 128 ARG cc_start: 0.7574 (ttm170) cc_final: 0.7320 (ttm170) REVERT: N 138 TYR cc_start: 0.8412 (p90) cc_final: 0.7845 (p90) REVERT: N 142 GLU cc_start: 0.7790 (mt-10) cc_final: 0.7070 (mt-10) REVERT: N 149 ASP cc_start: 0.7703 (t0) cc_final: 0.7417 (t0) REVERT: N 158 ASP cc_start: 0.8024 (m-30) cc_final: 0.7713 (m-30) REVERT: N 170 ARG cc_start: 0.8370 (mtt-85) cc_final: 0.8113 (mtt-85) REVERT: N 176 ASP cc_start: 0.7754 (t70) cc_final: 0.7483 (t70) REVERT: N 190 ASP cc_start: 0.7312 (m-30) cc_final: 0.7012 (m-30) REVERT: N 193 GLU cc_start: 0.7684 (tp30) cc_final: 0.7280 (tp30) REVERT: N 195 TYR cc_start: 0.8042 (t80) cc_final: 0.7590 (t80) outliers start: 55 outliers final: 38 residues processed: 1334 average time/residue: 0.2560 time to fit residues: 509.6469 Evaluate side-chains 1339 residues out of total 3673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 1300 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1773 ARG Chi-restraints excluded: chain A residue 2201 LEU Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain C residue 444 THR Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 159 ILE Chi-restraints excluded: chain E residue 387 SER Chi-restraints excluded: chain F residue 168 MET Chi-restraints excluded: chain F residue 236 LYS Chi-restraints excluded: chain F residue 348 ILE Chi-restraints excluded: chain G residue 17 SER Chi-restraints excluded: chain G residue 139 THR Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 171 LYS Chi-restraints excluded: chain G residue 293 GLU Chi-restraints excluded: chain G residue 295 VAL Chi-restraints excluded: chain G residue 313 THR Chi-restraints excluded: chain G residue 341 THR Chi-restraints excluded: chain G residue 403 LEU Chi-restraints excluded: chain H residue 19 ILE Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain H residue 161 LEU Chi-restraints excluded: chain H residue 195 ILE Chi-restraints excluded: chain H residue 333 THR Chi-restraints excluded: chain H residue 360 THR Chi-restraints excluded: chain I residue 208 THR Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 405 LEU Chi-restraints excluded: chain L residue 100 GLU Chi-restraints excluded: chain L residue 186 THR Chi-restraints excluded: chain L residue 194 THR Chi-restraints excluded: chain L residue 315 LYS Chi-restraints excluded: chain L residue 334 GLU Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 85 ILE Chi-restraints excluded: chain M residue 304 ILE Chi-restraints excluded: chain M residue 358 GLN Chi-restraints excluded: chain M residue 359 SER Chi-restraints excluded: chain N residue 164 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 293 optimal weight: 0.6980 chunk 90 optimal weight: 3.9990 chunk 126 optimal weight: 0.0970 chunk 203 optimal weight: 7.9990 chunk 147 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 160 optimal weight: 1.9990 chunk 294 optimal weight: 2.9990 chunk 416 optimal weight: 2.9990 chunk 376 optimal weight: 0.9990 chunk 1 optimal weight: 0.0770 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1465 GLN ** A1922 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1974 HIS E 241 HIS E 289 GLN E 316 HIS E 348 HIS E 373 GLN F 44 GLN F 275 GLN G 115 ASN ** G 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 146 GLN H 226 GLN H 404 GLN ** I 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 408 GLN M 118 HIS M 407 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.148107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.129264 restraints weight = 51548.982| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 2.14 r_work: 0.3438 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 34579 Z= 0.121 Angle : 0.499 10.869 46733 Z= 0.265 Chirality : 0.042 0.199 5327 Planarity : 0.004 0.049 5974 Dihedral : 8.834 165.731 4826 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.63 % Allowed : 11.95 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.47 (0.13), residues: 4227 helix: 1.46 (0.12), residues: 1883 sheet: 0.40 (0.19), residues: 712 loop : 0.89 (0.16), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 317 TYR 0.031 0.001 TYR A1336 PHE 0.027 0.001 PHE E 177 TRP 0.034 0.002 TRP A2006 HIS 0.007 0.001 HIS E 241 Details of bonding type rmsd covalent geometry : bond 0.00266 (34579) covalent geometry : angle 0.49940 (46733) hydrogen bonds : bond 0.04153 ( 1532) hydrogen bonds : angle 4.35619 ( 4341) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8454 Ramachandran restraints generated. 4227 Oldfield, 0 Emsley, 4227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8454 Ramachandran restraints generated. 4227 Oldfield, 0 Emsley, 4227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1364 residues out of total 3673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 1304 time to evaluate : 1.353 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: A 793 LEU cc_start: 0.7935 (mp) cc_final: 0.7677 (tp) REVERT: A 798 ARG cc_start: 0.8471 (mtp180) cc_final: 0.8080 (mtp180) REVERT: A 807 ARG cc_start: 0.8571 (ptt90) cc_final: 0.8369 (ptt90) REVERT: A 809 LYS cc_start: 0.8227 (mtmt) cc_final: 0.8010 (mtmm) REVERT: A 828 GLN cc_start: 0.8820 (mm-40) cc_final: 0.8604 (mm-40) REVERT: A 841 VAL cc_start: 0.8519 (t) cc_final: 0.8247 (p) REVERT: A 851 LYS cc_start: 0.8125 (tttt) cc_final: 0.7786 (tttt) REVERT: A 1333 LYS cc_start: 0.7966 (tptt) cc_final: 0.7673 (tptt) REVERT: A 1337 GLU cc_start: 0.8156 (tp30) cc_final: 0.7798 (tp30) REVERT: A 1412 MET cc_start: 0.8128 (ptp) cc_final: 0.7919 (ptp) REVERT: A 1413 PHE cc_start: 0.8544 (m-80) cc_final: 0.8284 (m-80) REVERT: A 1459 LYS cc_start: 0.8062 (mtmm) cc_final: 0.7786 (mtmm) REVERT: A 1746 LEU cc_start: 0.7983 (tp) cc_final: 0.7753 (tp) REVERT: A 1909 LYS cc_start: 0.8310 (tmmt) cc_final: 0.8082 (tmmt) REVERT: A 1913 GLU cc_start: 0.7575 (mm-30) cc_final: 0.6087 (mt-10) REVERT: A 1917 VAL cc_start: 0.7664 (OUTLIER) cc_final: 0.7445 (t) REVERT: A 1941 TYR cc_start: 0.6823 (p90) cc_final: 0.6484 (p90) REVERT: A 1952 GLN cc_start: 0.7071 (mm-40) cc_final: 0.6755 (mm110) REVERT: A 1962 ARG cc_start: 0.7652 (ptp-170) cc_final: 0.7448 (ptp-170) REVERT: A 2225 ARG cc_start: 0.8215 (ttm-80) cc_final: 0.7497 (ttt90) REVERT: A 2226 GLU cc_start: 0.7566 (mp0) cc_final: 0.7154 (mp0) REVERT: A 2227 ASP cc_start: 0.7877 (m-30) cc_final: 0.7617 (m-30) REVERT: A 2233 TYR cc_start: 0.8131 (m-80) cc_final: 0.7670 (m-80) REVERT: A 2236 GLU cc_start: 0.6887 (mp0) cc_final: 0.6621 (mp0) REVERT: A 2254 PRO cc_start: 0.8416 (Cg_endo) cc_final: 0.8186 (Cg_exo) REVERT: A 2269 MET cc_start: 0.7967 (mmm) cc_final: 0.7408 (mmm) REVERT: B 302 ARG cc_start: 0.8375 (ptp-110) cc_final: 0.8002 (ttm-80) REVERT: C 406 ARG cc_start: 0.7841 (ttt-90) cc_final: 0.7426 (ttt-90) REVERT: C 426 THR cc_start: 0.8152 (p) cc_final: 0.7680 (t) REVERT: C 530 ARG cc_start: 0.7164 (ptp-110) cc_final: 0.6899 (ptp-170) REVERT: E 110 GLU cc_start: 0.6950 (mm-30) cc_final: 0.6504 (tm-30) REVERT: E 236 GLN cc_start: 0.8117 (mm-40) cc_final: 0.7784 (mm-40) REVERT: E 260 MET cc_start: 0.7571 (mmm) cc_final: 0.7276 (mmm) REVERT: E 264 MET cc_start: 0.6650 (mmm) cc_final: 0.6254 (mmm) REVERT: E 274 LYS cc_start: 0.8142 (tttm) cc_final: 0.7845 (tttp) REVERT: E 278 GLU cc_start: 0.7741 (mm-30) cc_final: 0.7284 (mm-30) REVERT: E 288 ASP cc_start: 0.8028 (t0) cc_final: 0.7774 (t0) REVERT: E 352 LEU cc_start: 0.7970 (mt) cc_final: 0.7659 (mt) REVERT: E 364 MET cc_start: 0.7171 (mtm) cc_final: 0.6757 (mtm) REVERT: E 376 LYS cc_start: 0.8201 (tptm) cc_final: 0.7863 (tptm) REVERT: E 381 THR cc_start: 0.8281 (m) cc_final: 0.7627 (p) REVERT: E 392 ASN cc_start: 0.7890 (m-40) cc_final: 0.7580 (m-40) REVERT: E 416 LEU cc_start: 0.8011 (mt) cc_final: 0.7663 (mt) REVERT: F 20 GLU cc_start: 0.7627 (mp0) cc_final: 0.7187 (mp0) REVERT: F 65 GLU cc_start: 0.7443 (mm-30) cc_final: 0.7039 (mm-30) REVERT: F 117 GLU cc_start: 0.7596 (tp30) cc_final: 0.6883 (mm-30) REVERT: F 136 GLU cc_start: 0.6587 (mm-30) cc_final: 0.6010 (mm-30) REVERT: F 181 SER cc_start: 0.8725 (t) cc_final: 0.8443 (t) REVERT: F 197 LYS cc_start: 0.8595 (ttpt) cc_final: 0.8338 (ttpt) REVERT: F 202 ILE cc_start: 0.8562 (mt) cc_final: 0.8295 (mt) REVERT: F 210 THR cc_start: 0.8763 (t) cc_final: 0.8516 (p) REVERT: F 231 GLU cc_start: 0.7753 (mp0) cc_final: 0.7308 (mp0) REVERT: F 234 LYS cc_start: 0.8280 (mttp) cc_final: 0.8031 (mtmm) REVERT: F 274 GLU cc_start: 0.7776 (mt-10) cc_final: 0.7556 (mt-10) REVERT: F 348 ILE cc_start: 0.7853 (tt) cc_final: 0.7590 (pt) REVERT: F 381 GLU cc_start: 0.7517 (mm-30) cc_final: 0.7186 (mm-30) REVERT: F 410 SER cc_start: 0.8110 (t) cc_final: 0.7822 (t) REVERT: F 414 ARG cc_start: 0.7198 (mtm-85) cc_final: 0.6982 (mtm-85) REVERT: F 420 GLU cc_start: 0.6929 (tt0) cc_final: 0.6535 (tt0) REVERT: G 19 SER cc_start: 0.8176 (m) cc_final: 0.7762 (p) REVERT: G 60 LYS cc_start: 0.7527 (mtpp) cc_final: 0.7218 (mtpp) REVERT: G 64 ARG cc_start: 0.7443 (mmm160) cc_final: 0.6721 (mmm160) REVERT: G 100 GLU cc_start: 0.7719 (mt-10) cc_final: 0.7485 (mt-10) REVERT: G 180 LEU cc_start: 0.8750 (mt) cc_final: 0.8406 (mt) REVERT: G 260 MET cc_start: 0.5413 (tmm) cc_final: 0.5176 (tmm) REVERT: G 267 LYS cc_start: 0.7922 (ptpt) cc_final: 0.7601 (ptpt) REVERT: G 285 LYS cc_start: 0.8138 (mtpt) cc_final: 0.7855 (mtpt) REVERT: G 357 ARG cc_start: 0.7888 (mtt90) cc_final: 0.7648 (mtt90) REVERT: G 362 ARG cc_start: 0.8076 (ptm160) cc_final: 0.7634 (ttm170) REVERT: G 369 GLN cc_start: 0.7286 (mp10) cc_final: 0.6617 (mp10) REVERT: G 372 LYS cc_start: 0.7587 (mttp) cc_final: 0.7253 (mttp) REVERT: G 411 THR cc_start: 0.8109 (t) cc_final: 0.7839 (m) REVERT: G 414 ASN cc_start: 0.7678 (t0) cc_final: 0.7349 (t0) REVERT: G 418 LYS cc_start: 0.7767 (ttmt) cc_final: 0.7549 (ttmt) REVERT: H 18 ARG cc_start: 0.7191 (mtp85) cc_final: 0.6712 (mtp85) REVERT: H 46 MET cc_start: 0.8541 (mmm) cc_final: 0.8328 (mmm) REVERT: H 88 MET cc_start: 0.7945 (mmm) cc_final: 0.7700 (mmm) REVERT: H 134 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7050 (mt-10) REVERT: H 177 LYS cc_start: 0.8051 (mttt) cc_final: 0.7846 (mttt) REVERT: H 178 MET cc_start: 0.7797 (mmm) cc_final: 0.7554 (tpp) REVERT: H 180 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7619 (mm-30) REVERT: H 184 LYS cc_start: 0.8390 (mmpt) cc_final: 0.7938 (mmpt) REVERT: H 191 ASP cc_start: 0.7770 (m-30) cc_final: 0.7569 (m-30) REVERT: H 235 ARG cc_start: 0.7816 (ttt180) cc_final: 0.7376 (ttt180) REVERT: H 248 ASP cc_start: 0.7439 (m-30) cc_final: 0.7192 (m-30) REVERT: H 274 GLU cc_start: 0.7409 (mt-10) cc_final: 0.7038 (mt-10) REVERT: H 282 GLU cc_start: 0.7801 (tt0) cc_final: 0.7526 (tt0) REVERT: H 352 ASP cc_start: 0.7370 (m-30) cc_final: 0.7006 (m-30) REVERT: H 358 SER cc_start: 0.7873 (m) cc_final: 0.7662 (t) REVERT: H 381 GLU cc_start: 0.7604 (mm-30) cc_final: 0.7242 (mm-30) REVERT: H 396 GLU cc_start: 0.7761 (mm-30) cc_final: 0.7520 (mm-30) REVERT: H 397 THR cc_start: 0.8111 (p) cc_final: 0.7897 (p) REVERT: H 435 ASP cc_start: 0.7704 (p0) cc_final: 0.7406 (p0) REVERT: I 17 SER cc_start: 0.8002 (m) cc_final: 0.7683 (p) REVERT: I 31 LEU cc_start: 0.7240 (mt) cc_final: 0.6926 (mt) REVERT: I 47 GLU cc_start: 0.7104 (mt-10) cc_final: 0.6810 (mt-10) REVERT: I 60 LYS cc_start: 0.7960 (ttmt) cc_final: 0.7704 (ttmt) REVERT: I 64 ARG cc_start: 0.7305 (mtp-110) cc_final: 0.6967 (mtp180) REVERT: I 113 MET cc_start: 0.7389 (tpp) cc_final: 0.6984 (tpp) REVERT: I 130 VAL cc_start: 0.8772 (t) cc_final: 0.8491 (m) REVERT: I 249 ARG cc_start: 0.7516 (tmm160) cc_final: 0.7098 (tmm160) REVERT: I 260 MET cc_start: 0.7010 (mtt) cc_final: 0.6085 (mtt) REVERT: I 264 MET cc_start: 0.6572 (ptp) cc_final: 0.6146 (ptp) REVERT: I 281 LYS cc_start: 0.8395 (mttt) cc_final: 0.8081 (mttt) REVERT: I 372 LYS cc_start: 0.8056 (mtpt) cc_final: 0.7718 (mtpt) REVERT: I 376 LYS cc_start: 0.8027 (tptt) cc_final: 0.7629 (tptt) REVERT: I 380 GLN cc_start: 0.7983 (mt0) cc_final: 0.7780 (mt0) REVERT: I 396 GLU cc_start: 0.7274 (mt-10) cc_final: 0.7037 (mt-10) REVERT: J 38 GLU cc_start: 0.7618 (mm-30) cc_final: 0.7345 (mm-30) REVERT: J 40 ARG cc_start: 0.7479 (mtt180) cc_final: 0.7230 (mtt-85) REVERT: J 44 GLN cc_start: 0.7856 (mt0) cc_final: 0.7655 (mt0) REVERT: J 68 ILE cc_start: 0.8203 (mm) cc_final: 0.7997 (mm) REVERT: J 115 LYS cc_start: 0.8004 (mtmt) cc_final: 0.7764 (mtmt) REVERT: J 164 LYS cc_start: 0.8177 (pttt) cc_final: 0.7655 (pttt) REVERT: J 169 GLU cc_start: 0.6421 (tt0) cc_final: 0.6100 (tt0) REVERT: J 178 MET cc_start: 0.5979 (tpp) cc_final: 0.5568 (tpp) REVERT: J 316 LEU cc_start: 0.7883 (mt) cc_final: 0.7497 (mm) REVERT: J 319 ASP cc_start: 0.7078 (p0) cc_final: 0.6781 (p0) REVERT: J 334 ARG cc_start: 0.7519 (ptm-80) cc_final: 0.7142 (ptm160) REVERT: J 368 LYS cc_start: 0.7294 (ttmt) cc_final: 0.6938 (ttmt) REVERT: J 420 GLU cc_start: 0.7278 (mt-10) cc_final: 0.6965 (mt-10) REVERT: J 436 GLU cc_start: 0.6827 (tm-30) cc_final: 0.6580 (tm-30) REVERT: J 441 GLN cc_start: 0.6759 (mm110) cc_final: 0.6392 (mm110) REVERT: L 18 LYS cc_start: 0.8413 (mppt) cc_final: 0.8046 (mttp) REVERT: L 68 LYS cc_start: 0.8028 (mtpt) cc_final: 0.7748 (mtpt) REVERT: L 81 ASP cc_start: 0.8165 (m-30) cc_final: 0.7800 (m-30) REVERT: L 113 LYS cc_start: 0.8222 (ttpp) cc_final: 0.7940 (mtpt) REVERT: L 123 MET cc_start: 0.8701 (mmp) cc_final: 0.8482 (mmm) REVERT: L 132 MET cc_start: 0.8384 (ttp) cc_final: 0.8122 (tmm) REVERT: L 191 LYS cc_start: 0.8405 (ttmt) cc_final: 0.8078 (ttmt) REVERT: L 221 LEU cc_start: 0.8108 (tp) cc_final: 0.7832 (tt) REVERT: L 227 MET cc_start: 0.6998 (mmm) cc_final: 0.6734 (mmm) REVERT: L 242 LEU cc_start: 0.8334 (mt) cc_final: 0.8119 (mm) REVERT: L 306 TYR cc_start: 0.8634 (m-80) cc_final: 0.8087 (m-80) REVERT: L 312 ARG cc_start: 0.8326 (tpt90) cc_final: 0.8078 (tpt90) REVERT: L 313 MET cc_start: 0.8130 (mmm) cc_final: 0.7833 (mmm) REVERT: L 364 GLU cc_start: 0.7611 (pt0) cc_final: 0.7286 (pt0) REVERT: M 21 TYR cc_start: 0.8250 (t80) cc_final: 0.7882 (t80) REVERT: M 30 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7678 (mm-30) REVERT: M 43 MET cc_start: 0.7437 (tmm) cc_final: 0.6952 (tmm) REVERT: M 95 ASP cc_start: 0.7650 (t0) cc_final: 0.7048 (t0) REVERT: M 100 GLN cc_start: 0.8195 (mt0) cc_final: 0.7870 (mt0) REVERT: M 142 GLU cc_start: 0.7738 (mm-30) cc_final: 0.7352 (mm-30) REVERT: M 164 ARG cc_start: 0.8244 (mmt90) cc_final: 0.8008 (mmt90) REVERT: M 178 THR cc_start: 0.8552 (m) cc_final: 0.8351 (p) REVERT: M 200 ASP cc_start: 0.7952 (m-30) cc_final: 0.7625 (m-30) REVERT: M 231 GLU cc_start: 0.7713 (pm20) cc_final: 0.7443 (pm20) REVERT: M 271 ASP cc_start: 0.7983 (t0) cc_final: 0.7564 (t0) REVERT: M 294 ASN cc_start: 0.8254 (p0) cc_final: 0.8029 (p0) REVERT: M 345 TYR cc_start: 0.8036 (m-80) cc_final: 0.7640 (m-80) REVERT: M 354 ASN cc_start: 0.8594 (t0) cc_final: 0.8116 (t0) REVERT: M 379 LYS cc_start: 0.7913 (tptt) cc_final: 0.7603 (tptt) REVERT: M 413 LYS cc_start: 0.8294 (tttm) cc_final: 0.8015 (tttm) REVERT: N 66 LYS cc_start: 0.8125 (mtmt) cc_final: 0.7828 (mtmt) REVERT: N 81 ARG cc_start: 0.7859 (ttt-90) cc_final: 0.7632 (ttt-90) REVERT: N 106 LYS cc_start: 0.8424 (ptpt) cc_final: 0.8159 (ptpt) REVERT: N 128 ARG cc_start: 0.7573 (ttm170) cc_final: 0.7278 (ttm170) REVERT: N 138 TYR cc_start: 0.8425 (p90) cc_final: 0.7870 (p90) REVERT: N 142 GLU cc_start: 0.7847 (mt-10) cc_final: 0.7107 (mt-10) REVERT: N 149 ASP cc_start: 0.7771 (t0) cc_final: 0.7485 (t0) REVERT: N 158 ASP cc_start: 0.8046 (m-30) cc_final: 0.7724 (m-30) REVERT: N 176 ASP cc_start: 0.7766 (t70) cc_final: 0.7550 (t70) REVERT: N 190 ASP cc_start: 0.7368 (m-30) cc_final: 0.7040 (m-30) REVERT: N 193 GLU cc_start: 0.7600 (tp30) cc_final: 0.7200 (tp30) REVERT: N 231 GLU cc_start: 0.7431 (mm-30) cc_final: 0.6974 (mm-30) outliers start: 60 outliers final: 31 residues processed: 1319 average time/residue: 0.2822 time to fit residues: 554.3958 Evaluate side-chains 1311 residues out of total 3673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 1279 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1773 ARG Chi-restraints excluded: chain A residue 1917 VAL Chi-restraints excluded: chain A residue 1968 CYS Chi-restraints excluded: chain C residue 444 THR Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain F residue 184 LYS Chi-restraints excluded: chain F residue 236 LYS Chi-restraints excluded: chain G residue 152 LYS Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 295 VAL Chi-restraints excluded: chain G residue 403 LEU Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 130 ARG Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain H residue 161 LEU Chi-restraints excluded: chain H residue 195 ILE Chi-restraints excluded: chain H residue 360 THR Chi-restraints excluded: chain I residue 97 VAL Chi-restraints excluded: chain I residue 208 THR Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 248 ASP Chi-restraints excluded: chain J residue 405 LEU Chi-restraints excluded: chain L residue 118 LYS Chi-restraints excluded: chain L residue 136 ILE Chi-restraints excluded: chain L residue 186 THR Chi-restraints excluded: chain L residue 315 LYS Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain M residue 304 ILE Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 164 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 296 optimal weight: 1.9990 chunk 226 optimal weight: 3.9990 chunk 392 optimal weight: 4.9990 chunk 128 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 414 optimal weight: 0.0370 chunk 152 optimal weight: 0.7980 chunk 313 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 chunk 250 optimal weight: 2.9990 overall best weight: 0.9260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1894 GLN E 241 HIS E 393 HIS F 44 GLN F 233 GLN ** F 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 313 ASN G 85 GLN G 115 ASN ** G 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 408 GLN L 280 ASN M 118 HIS M 128 ASN M 183 HIS M 407 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.147277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.128423 restraints weight = 51149.538| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 2.10 r_work: 0.3431 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 34579 Z= 0.168 Angle : 0.518 9.992 46733 Z= 0.273 Chirality : 0.043 0.174 5327 Planarity : 0.004 0.048 5974 Dihedral : 8.790 166.890 4826 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.37 % Allowed : 13.07 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.41 (0.13), residues: 4227 helix: 1.48 (0.12), residues: 1888 sheet: 0.38 (0.19), residues: 712 loop : 0.77 (0.16), residues: 1627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 205 TYR 0.041 0.002 TYR A1336 PHE 0.030 0.002 PHE A1960 TRP 0.032 0.002 TRP A2006 HIS 0.006 0.001 HIS E 241 Details of bonding type rmsd covalent geometry : bond 0.00370 (34579) covalent geometry : angle 0.51820 (46733) hydrogen bonds : bond 0.04402 ( 1532) hydrogen bonds : angle 4.35005 ( 4341) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8454 Ramachandran restraints generated. 4227 Oldfield, 0 Emsley, 4227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8454 Ramachandran restraints generated. 4227 Oldfield, 0 Emsley, 4227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1396 residues out of total 3673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 1309 time to evaluate : 0.931 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: A 793 LEU cc_start: 0.8002 (mp) cc_final: 0.7693 (tp) REVERT: A 828 GLN cc_start: 0.8835 (mm-40) cc_final: 0.8542 (mm110) REVERT: A 841 VAL cc_start: 0.8566 (t) cc_final: 0.8348 (p) REVERT: A 851 LYS cc_start: 0.8113 (tttt) cc_final: 0.7777 (tttt) REVERT: A 1389 GLU cc_start: 0.7934 (tt0) cc_final: 0.7688 (tm-30) REVERT: A 1413 PHE cc_start: 0.8545 (m-80) cc_final: 0.8236 (m-80) REVERT: A 1459 LYS cc_start: 0.8150 (mtmm) cc_final: 0.7878 (mtmm) REVERT: A 1746 LEU cc_start: 0.8005 (tp) cc_final: 0.7771 (tp) REVERT: A 1909 LYS cc_start: 0.8290 (tmmt) cc_final: 0.8045 (tmmt) REVERT: A 1913 GLU cc_start: 0.7644 (mm-30) cc_final: 0.6131 (mt-10) REVERT: A 1917 VAL cc_start: 0.7690 (m) cc_final: 0.7463 (t) REVERT: A 1941 TYR cc_start: 0.7027 (p90) cc_final: 0.6562 (p90) REVERT: A 1952 GLN cc_start: 0.7073 (mm-40) cc_final: 0.6714 (mm110) REVERT: A 1962 ARG cc_start: 0.7659 (ptp-170) cc_final: 0.7425 (ptp-170) REVERT: A 2198 PHE cc_start: 0.7853 (m-80) cc_final: 0.7556 (m-80) REVERT: A 2226 GLU cc_start: 0.7583 (mp0) cc_final: 0.7192 (mp0) REVERT: A 2227 ASP cc_start: 0.7889 (m-30) cc_final: 0.7635 (m-30) REVERT: A 2233 TYR cc_start: 0.8091 (m-80) cc_final: 0.7676 (m-80) REVERT: A 2236 GLU cc_start: 0.6912 (mp0) cc_final: 0.6662 (mp0) REVERT: A 2269 MET cc_start: 0.7933 (mmm) cc_final: 0.7427 (mmm) REVERT: C 426 THR cc_start: 0.8210 (p) cc_final: 0.7724 (t) REVERT: C 530 ARG cc_start: 0.7271 (ptp-110) cc_final: 0.7027 (ptp-170) REVERT: E 110 GLU cc_start: 0.6977 (mm-30) cc_final: 0.6562 (tm-30) REVERT: E 236 GLN cc_start: 0.8117 (mm-40) cc_final: 0.7749 (mm-40) REVERT: E 260 MET cc_start: 0.7550 (mmm) cc_final: 0.7235 (mmm) REVERT: E 264 MET cc_start: 0.6598 (mmm) cc_final: 0.6195 (mmm) REVERT: E 274 LYS cc_start: 0.8230 (tttm) cc_final: 0.7863 (tttp) REVERT: E 278 GLU cc_start: 0.7713 (mm-30) cc_final: 0.7203 (mm-30) REVERT: E 281 LYS cc_start: 0.7745 (mtmm) cc_final: 0.7519 (mtmm) REVERT: E 288 ASP cc_start: 0.7987 (t0) cc_final: 0.7739 (t0) REVERT: E 306 MET cc_start: 0.8115 (mmt) cc_final: 0.7767 (mmt) REVERT: E 364 MET cc_start: 0.7244 (mtm) cc_final: 0.6829 (mtm) REVERT: E 376 LYS cc_start: 0.8184 (tptm) cc_final: 0.7828 (tptm) REVERT: E 381 THR cc_start: 0.8271 (m) cc_final: 0.7628 (p) REVERT: E 392 ASN cc_start: 0.7844 (m-40) cc_final: 0.7521 (m-40) REVERT: E 408 GLN cc_start: 0.7553 (mt0) cc_final: 0.7301 (mt0) REVERT: E 416 LEU cc_start: 0.8011 (mt) cc_final: 0.7661 (mt) REVERT: E 438 TYR cc_start: 0.6843 (m-80) cc_final: 0.6607 (m-80) REVERT: F 20 GLU cc_start: 0.7641 (mp0) cc_final: 0.7211 (mp0) REVERT: F 65 GLU cc_start: 0.7351 (mm-30) cc_final: 0.6951 (mm-30) REVERT: F 67 LYS cc_start: 0.7933 (mttt) cc_final: 0.7679 (mttt) REVERT: F 101 THR cc_start: 0.8039 (m) cc_final: 0.7645 (p) REVERT: F 117 GLU cc_start: 0.7614 (tp30) cc_final: 0.6990 (mm-30) REVERT: F 136 GLU cc_start: 0.6706 (mm-30) cc_final: 0.6190 (mm-30) REVERT: F 181 SER cc_start: 0.8677 (t) cc_final: 0.8475 (t) REVERT: F 202 ILE cc_start: 0.8593 (mt) cc_final: 0.8350 (mt) REVERT: F 210 THR cc_start: 0.8750 (t) cc_final: 0.8451 (p) REVERT: F 231 GLU cc_start: 0.7571 (mp0) cc_final: 0.7082 (mp0) REVERT: F 274 GLU cc_start: 0.7753 (mt-10) cc_final: 0.7543 (mt-10) REVERT: F 333 THR cc_start: 0.7931 (p) cc_final: 0.7599 (t) REVERT: F 381 GLU cc_start: 0.7496 (mm-30) cc_final: 0.7168 (mm-30) REVERT: F 410 SER cc_start: 0.8059 (t) cc_final: 0.7754 (t) REVERT: F 414 ARG cc_start: 0.7193 (mtm-85) cc_final: 0.6954 (mtm-85) REVERT: F 420 GLU cc_start: 0.6923 (tt0) cc_final: 0.6541 (tt0) REVERT: G 19 SER cc_start: 0.8195 (m) cc_final: 0.7770 (p) REVERT: G 60 LYS cc_start: 0.7521 (mtpp) cc_final: 0.7249 (mtpp) REVERT: G 64 ARG cc_start: 0.7463 (mmm160) cc_final: 0.6766 (mmm160) REVERT: G 180 LEU cc_start: 0.8781 (mt) cc_final: 0.8442 (mt) REVERT: G 260 MET cc_start: 0.5388 (tmm) cc_final: 0.5069 (tmm) REVERT: G 267 LYS cc_start: 0.7929 (ptpt) cc_final: 0.7620 (ptpt) REVERT: G 285 LYS cc_start: 0.8107 (mtpt) cc_final: 0.7815 (mtpt) REVERT: G 357 ARG cc_start: 0.7893 (mtt90) cc_final: 0.7657 (mtt90) REVERT: G 362 ARG cc_start: 0.8068 (ptm160) cc_final: 0.7645 (ttm170) REVERT: G 369 GLN cc_start: 0.7301 (mp10) cc_final: 0.6630 (mp10) REVERT: G 370 GLU cc_start: 0.7608 (mt-10) cc_final: 0.7338 (mt-10) REVERT: G 372 LYS cc_start: 0.7549 (mttp) cc_final: 0.7230 (mttp) REVERT: G 411 THR cc_start: 0.8089 (t) cc_final: 0.7827 (m) REVERT: G 414 ASN cc_start: 0.7720 (t0) cc_final: 0.7393 (t0) REVERT: G 418 LYS cc_start: 0.7765 (ttmt) cc_final: 0.7549 (ttmt) REVERT: H 18 ARG cc_start: 0.7188 (mtp85) cc_final: 0.6713 (mtp85) REVERT: H 88 MET cc_start: 0.7929 (mmm) cc_final: 0.7664 (mmm) REVERT: H 132 LYS cc_start: 0.8354 (ptpp) cc_final: 0.8123 (ptpp) REVERT: H 134 GLU cc_start: 0.7872 (mt-10) cc_final: 0.7027 (mt-10) REVERT: H 178 MET cc_start: 0.7824 (mmm) cc_final: 0.7578 (tpp) REVERT: H 180 GLU cc_start: 0.8068 (mm-30) cc_final: 0.7641 (mm-30) REVERT: H 184 LYS cc_start: 0.8385 (mmpt) cc_final: 0.7953 (mmpt) REVERT: H 235 ARG cc_start: 0.7848 (ttt180) cc_final: 0.7416 (ttt180) REVERT: H 248 ASP cc_start: 0.7457 (m-30) cc_final: 0.7218 (m-30) REVERT: H 271 GLU cc_start: 0.7242 (mp0) cc_final: 0.6965 (mp0) REVERT: H 274 GLU cc_start: 0.7396 (mt-10) cc_final: 0.7009 (mt-10) REVERT: H 282 GLU cc_start: 0.7763 (tt0) cc_final: 0.7492 (tt0) REVERT: H 352 ASP cc_start: 0.7386 (m-30) cc_final: 0.7013 (m-30) REVERT: H 358 SER cc_start: 0.7899 (m) cc_final: 0.7684 (t) REVERT: H 381 GLU cc_start: 0.7610 (mm-30) cc_final: 0.7245 (mm-30) REVERT: H 389 VAL cc_start: 0.7947 (m) cc_final: 0.7632 (p) REVERT: H 396 GLU cc_start: 0.7722 (mm-30) cc_final: 0.7485 (mm-30) REVERT: H 397 THR cc_start: 0.8128 (p) cc_final: 0.7908 (p) REVERT: H 435 ASP cc_start: 0.7715 (p0) cc_final: 0.7442 (p0) REVERT: H 438 ARG cc_start: 0.7338 (mtm180) cc_final: 0.6859 (mtm-85) REVERT: I 17 SER cc_start: 0.8042 (m) cc_final: 0.7701 (p) REVERT: I 47 GLU cc_start: 0.7135 (mt-10) cc_final: 0.6880 (mt-10) REVERT: I 60 LYS cc_start: 0.7994 (ttmt) cc_final: 0.7719 (ttmt) REVERT: I 64 ARG cc_start: 0.7288 (mtp-110) cc_final: 0.6863 (mtp180) REVERT: I 113 MET cc_start: 0.7397 (tpp) cc_final: 0.6981 (tpp) REVERT: I 130 VAL cc_start: 0.8736 (t) cc_final: 0.8440 (m) REVERT: I 249 ARG cc_start: 0.7540 (tmm160) cc_final: 0.7124 (tmm160) REVERT: I 260 MET cc_start: 0.7001 (mtt) cc_final: 0.6057 (mtt) REVERT: I 264 MET cc_start: 0.6592 (ptp) cc_final: 0.6173 (ptp) REVERT: I 281 LYS cc_start: 0.8405 (mttt) cc_final: 0.8090 (mttt) REVERT: I 341 THR cc_start: 0.7637 (OUTLIER) cc_final: 0.7401 (p) REVERT: I 344 ILE cc_start: 0.6775 (mt) cc_final: 0.6565 (mp) REVERT: I 372 LYS cc_start: 0.8073 (mtpt) cc_final: 0.7738 (mtpt) REVERT: I 396 GLU cc_start: 0.7315 (mt-10) cc_final: 0.7055 (mt-10) REVERT: J 38 GLU cc_start: 0.7616 (mm-30) cc_final: 0.7323 (mm-30) REVERT: J 40 ARG cc_start: 0.7422 (mtt180) cc_final: 0.7189 (mtt-85) REVERT: J 68 ILE cc_start: 0.8211 (mm) cc_final: 0.8010 (mm) REVERT: J 115 LYS cc_start: 0.8023 (mtmt) cc_final: 0.7782 (mtmt) REVERT: J 130 ARG cc_start: 0.8282 (ttm-80) cc_final: 0.7977 (ttm-80) REVERT: J 164 LYS cc_start: 0.8201 (pttt) cc_final: 0.7683 (pttt) REVERT: J 169 GLU cc_start: 0.6547 (tt0) cc_final: 0.6151 (tt0) REVERT: J 332 ILE cc_start: 0.7860 (mt) cc_final: 0.7509 (tt) REVERT: J 368 LYS cc_start: 0.7307 (ttmt) cc_final: 0.6962 (ttmt) REVERT: J 420 GLU cc_start: 0.7295 (mt-10) cc_final: 0.6990 (mt-10) REVERT: J 436 GLU cc_start: 0.6832 (tm-30) cc_final: 0.6377 (tm-30) REVERT: J 441 GLN cc_start: 0.6736 (mm110) cc_final: 0.6386 (mm110) REVERT: L 37 ARG cc_start: 0.6270 (mtt90) cc_final: 0.5871 (mtt90) REVERT: L 68 LYS cc_start: 0.8079 (mtpt) cc_final: 0.7799 (mtpt) REVERT: L 81 ASP cc_start: 0.8206 (m-30) cc_final: 0.7684 (m-30) REVERT: L 113 LYS cc_start: 0.8209 (ttpp) cc_final: 0.7908 (mtpt) REVERT: L 123 MET cc_start: 0.8702 (mmp) cc_final: 0.8475 (mmm) REVERT: L 132 MET cc_start: 0.8403 (ttp) cc_final: 0.8176 (tmm) REVERT: L 191 LYS cc_start: 0.8406 (ttmt) cc_final: 0.8089 (ttmt) REVERT: L 210 ARG cc_start: 0.7885 (mtp-110) cc_final: 0.7618 (mtp85) REVERT: L 221 LEU cc_start: 0.8064 (tp) cc_final: 0.7793 (tt) REVERT: L 227 MET cc_start: 0.7046 (mmm) cc_final: 0.6756 (mmm) REVERT: L 242 LEU cc_start: 0.8366 (mt) cc_final: 0.8160 (mm) REVERT: L 306 TYR cc_start: 0.8640 (m-80) cc_final: 0.8048 (m-80) REVERT: L 312 ARG cc_start: 0.8351 (tpt90) cc_final: 0.8042 (tpt90) REVERT: L 315 LYS cc_start: 0.8559 (OUTLIER) cc_final: 0.8226 (ptmm) REVERT: L 317 ILE cc_start: 0.8232 (mm) cc_final: 0.7994 (mt) REVERT: L 364 GLU cc_start: 0.7617 (pt0) cc_final: 0.7403 (pt0) REVERT: M 21 TYR cc_start: 0.8284 (t80) cc_final: 0.7886 (t80) REVERT: M 30 GLU cc_start: 0.8025 (mm-30) cc_final: 0.7758 (mm-30) REVERT: M 43 MET cc_start: 0.7455 (tmm) cc_final: 0.6995 (tmm) REVERT: M 79 ARG cc_start: 0.8058 (ttm-80) cc_final: 0.7777 (ttm-80) REVERT: M 95 ASP cc_start: 0.7624 (t0) cc_final: 0.7027 (t0) REVERT: M 100 GLN cc_start: 0.8226 (mt0) cc_final: 0.7900 (mt0) REVERT: M 142 GLU cc_start: 0.7703 (mm-30) cc_final: 0.7349 (mm-30) REVERT: M 178 THR cc_start: 0.8540 (m) cc_final: 0.8334 (p) REVERT: M 200 ASP cc_start: 0.7984 (m-30) cc_final: 0.7657 (m-30) REVERT: M 231 GLU cc_start: 0.7720 (pm20) cc_final: 0.7447 (pm20) REVERT: M 271 ASP cc_start: 0.7979 (t0) cc_final: 0.7554 (t0) REVERT: M 294 ASN cc_start: 0.8262 (p0) cc_final: 0.8053 (p0) REVERT: M 354 ASN cc_start: 0.8596 (t0) cc_final: 0.8117 (t0) REVERT: M 379 LYS cc_start: 0.7948 (tptt) cc_final: 0.7615 (tptt) REVERT: M 413 LYS cc_start: 0.8335 (tttm) cc_final: 0.8031 (tttm) REVERT: N 66 LYS cc_start: 0.8103 (mtmt) cc_final: 0.7816 (mtmt) REVERT: N 81 ARG cc_start: 0.7824 (ttt-90) cc_final: 0.7611 (ttt-90) REVERT: N 106 LYS cc_start: 0.8429 (ptpt) cc_final: 0.8148 (ptpt) REVERT: N 128 ARG cc_start: 0.7561 (ttm170) cc_final: 0.7297 (ttm170) REVERT: N 138 TYR cc_start: 0.8458 (p90) cc_final: 0.7984 (p90) REVERT: N 142 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7123 (mt-10) REVERT: N 149 ASP cc_start: 0.7744 (t0) cc_final: 0.7497 (t0) REVERT: N 158 ASP cc_start: 0.8032 (m-30) cc_final: 0.7716 (m-30) REVERT: N 176 ASP cc_start: 0.7773 (t70) cc_final: 0.7509 (t70) REVERT: N 190 ASP cc_start: 0.7345 (m-30) cc_final: 0.7002 (m-30) REVERT: N 193 GLU cc_start: 0.7609 (tp30) cc_final: 0.7198 (tp30) REVERT: N 195 TYR cc_start: 0.7981 (t80) cc_final: 0.7586 (t80) REVERT: N 231 GLU cc_start: 0.7503 (mm-30) cc_final: 0.7104 (mm-30) outliers start: 87 outliers final: 58 residues processed: 1334 average time/residue: 0.2529 time to fit residues: 504.2690 Evaluate side-chains 1342 residues out of total 3673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 1282 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1384 VAL Chi-restraints excluded: chain A residue 1410 LEU Chi-restraints excluded: chain A residue 1419 GLU Chi-restraints excluded: chain A residue 1761 CYS Chi-restraints excluded: chain A residue 1773 ARG Chi-restraints excluded: chain A residue 1932 MET Chi-restraints excluded: chain A residue 1937 HIS Chi-restraints excluded: chain A residue 1968 CYS Chi-restraints excluded: chain A residue 2000 ASP Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain C residue 444 THR Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 159 ILE Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 356 ASP Chi-restraints excluded: chain E residue 387 SER Chi-restraints excluded: chain E residue 415 LEU Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 184 LYS Chi-restraints excluded: chain F residue 236 LYS Chi-restraints excluded: chain F residue 340 TYR Chi-restraints excluded: chain G residue 17 SER Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 293 GLU Chi-restraints excluded: chain G residue 295 VAL Chi-restraints excluded: chain G residue 313 THR Chi-restraints excluded: chain G residue 337 VAL Chi-restraints excluded: chain G residue 403 LEU Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 130 ARG Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain H residue 161 LEU Chi-restraints excluded: chain H residue 170 THR Chi-restraints excluded: chain H residue 195 ILE Chi-restraints excluded: chain H residue 333 THR Chi-restraints excluded: chain H residue 360 THR Chi-restraints excluded: chain I residue 97 VAL Chi-restraints excluded: chain I residue 168 LYS Chi-restraints excluded: chain I residue 208 THR Chi-restraints excluded: chain I residue 237 ASP Chi-restraints excluded: chain I residue 341 THR Chi-restraints excluded: chain I residue 439 ASP Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 248 ASP Chi-restraints excluded: chain J residue 252 SER Chi-restraints excluded: chain J residue 326 MET Chi-restraints excluded: chain J residue 405 LEU Chi-restraints excluded: chain L residue 100 GLU Chi-restraints excluded: chain L residue 118 LYS Chi-restraints excluded: chain L residue 186 THR Chi-restraints excluded: chain L residue 315 LYS Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 85 ILE Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain M residue 202 ILE Chi-restraints excluded: chain M residue 273 THR Chi-restraints excluded: chain M residue 304 ILE Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 164 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 145 optimal weight: 1.9990 chunk 167 optimal weight: 0.8980 chunk 187 optimal weight: 1.9990 chunk 125 optimal weight: 0.7980 chunk 137 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 368 optimal weight: 0.7980 chunk 400 optimal weight: 3.9990 chunk 237 optimal weight: 1.9990 chunk 179 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1894 GLN E 241 HIS E 247 ASN E 373 GLN E 393 HIS E 408 GLN F 44 GLN ** F 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 115 ASN G 156 HIS ** G 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 146 GLN H 404 GLN ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 156 HIS I 408 GLN J 44 GLN J 344 HIS M 118 HIS M 128 ASN M 407 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.147443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.128505 restraints weight = 51339.436| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 2.12 r_work: 0.3429 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 34579 Z= 0.160 Angle : 0.506 9.982 46733 Z= 0.267 Chirality : 0.042 0.173 5327 Planarity : 0.004 0.048 5974 Dihedral : 8.649 167.122 4826 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.48 % Allowed : 13.99 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.39 (0.13), residues: 4227 helix: 1.52 (0.12), residues: 1882 sheet: 0.27 (0.19), residues: 718 loop : 0.73 (0.16), residues: 1627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 205 TYR 0.038 0.001 TYR A1336 PHE 0.033 0.001 PHE A1960 TRP 0.018 0.002 TRP A2006 HIS 0.008 0.001 HIS E 241 Details of bonding type rmsd covalent geometry : bond 0.00351 (34579) covalent geometry : angle 0.50646 (46733) hydrogen bonds : bond 0.04211 ( 1532) hydrogen bonds : angle 4.29582 ( 4341) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8454 Ramachandran restraints generated. 4227 Oldfield, 0 Emsley, 4227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8454 Ramachandran restraints generated. 4227 Oldfield, 0 Emsley, 4227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1378 residues out of total 3673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 1287 time to evaluate : 1.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 793 LEU cc_start: 0.7996 (mp) cc_final: 0.7705 (tp) REVERT: A 818 GLU cc_start: 0.7819 (tt0) cc_final: 0.7264 (tt0) REVERT: A 841 VAL cc_start: 0.8565 (t) cc_final: 0.8347 (p) REVERT: A 851 LYS cc_start: 0.8126 (tttt) cc_final: 0.7775 (tttt) REVERT: A 1389 GLU cc_start: 0.7980 (tt0) cc_final: 0.7691 (tm-30) REVERT: A 1413 PHE cc_start: 0.8547 (m-80) cc_final: 0.8270 (m-80) REVERT: A 1459 LYS cc_start: 0.8137 (mtmm) cc_final: 0.7874 (mtmm) REVERT: A 1746 LEU cc_start: 0.8003 (tp) cc_final: 0.7797 (tp) REVERT: A 1909 LYS cc_start: 0.8277 (OUTLIER) cc_final: 0.8015 (tmmt) REVERT: A 1913 GLU cc_start: 0.7668 (mm-30) cc_final: 0.6151 (mt-10) REVERT: A 1917 VAL cc_start: 0.7615 (m) cc_final: 0.7391 (t) REVERT: A 1941 TYR cc_start: 0.7028 (p90) cc_final: 0.6585 (p90) REVERT: A 1952 GLN cc_start: 0.7092 (mm-40) cc_final: 0.6842 (mm-40) REVERT: A 1962 ARG cc_start: 0.7705 (ptp-170) cc_final: 0.7451 (ptp-170) REVERT: A 2225 ARG cc_start: 0.8231 (ttm-80) cc_final: 0.7524 (ttt90) REVERT: A 2226 GLU cc_start: 0.7578 (mp0) cc_final: 0.7163 (mp0) REVERT: A 2227 ASP cc_start: 0.7875 (m-30) cc_final: 0.7631 (m-30) REVERT: A 2233 TYR cc_start: 0.8059 (m-80) cc_final: 0.7644 (m-80) REVERT: A 2236 GLU cc_start: 0.6898 (mp0) cc_final: 0.6637 (mp0) REVERT: A 2269 MET cc_start: 0.7948 (mmm) cc_final: 0.7444 (mmm) REVERT: C 426 THR cc_start: 0.8167 (p) cc_final: 0.7653 (t) REVERT: C 530 ARG cc_start: 0.7312 (ptp-110) cc_final: 0.7027 (ptp-110) REVERT: E 110 GLU cc_start: 0.6967 (mm-30) cc_final: 0.6646 (tp30) REVERT: E 236 GLN cc_start: 0.8102 (mm-40) cc_final: 0.7641 (mm-40) REVERT: E 260 MET cc_start: 0.7571 (mmm) cc_final: 0.7211 (mmm) REVERT: E 264 MET cc_start: 0.6618 (mmm) cc_final: 0.6233 (mmm) REVERT: E 278 GLU cc_start: 0.7703 (mm-30) cc_final: 0.7458 (mm-30) REVERT: E 281 LYS cc_start: 0.7737 (mtmm) cc_final: 0.7481 (mtmm) REVERT: E 288 ASP cc_start: 0.7997 (t0) cc_final: 0.7749 (t0) REVERT: E 306 MET cc_start: 0.8103 (mmt) cc_final: 0.7779 (mmt) REVERT: E 364 MET cc_start: 0.7240 (mtm) cc_final: 0.6825 (mtm) REVERT: E 376 LYS cc_start: 0.8172 (tptm) cc_final: 0.7816 (tptm) REVERT: E 381 THR cc_start: 0.8271 (m) cc_final: 0.7629 (p) REVERT: E 392 ASN cc_start: 0.7857 (m-40) cc_final: 0.7540 (m-40) REVERT: E 408 GLN cc_start: 0.7534 (mt0) cc_final: 0.7283 (mt0) REVERT: E 416 LEU cc_start: 0.8042 (mt) cc_final: 0.7792 (mt) REVERT: F 20 GLU cc_start: 0.7648 (mp0) cc_final: 0.7201 (mp0) REVERT: F 65 GLU cc_start: 0.7379 (mm-30) cc_final: 0.7031 (mm-30) REVERT: F 67 LYS cc_start: 0.7924 (mttt) cc_final: 0.7706 (mttt) REVERT: F 101 THR cc_start: 0.8011 (m) cc_final: 0.7620 (p) REVERT: F 117 GLU cc_start: 0.7566 (tp30) cc_final: 0.6963 (mm-30) REVERT: F 136 GLU cc_start: 0.6710 (mm-30) cc_final: 0.6266 (mm-30) REVERT: F 231 GLU cc_start: 0.7599 (mp0) cc_final: 0.7236 (mp0) REVERT: F 242 VAL cc_start: 0.7807 (m) cc_final: 0.7476 (p) REVERT: F 274 GLU cc_start: 0.7749 (mt-10) cc_final: 0.7533 (mt-10) REVERT: F 333 THR cc_start: 0.7925 (p) cc_final: 0.7582 (t) REVERT: F 381 GLU cc_start: 0.7501 (mm-30) cc_final: 0.7157 (mm-30) REVERT: F 410 SER cc_start: 0.8138 (t) cc_final: 0.7791 (t) REVERT: F 414 ARG cc_start: 0.7203 (mtm-85) cc_final: 0.6835 (mtm-85) REVERT: F 420 GLU cc_start: 0.7022 (tt0) cc_final: 0.6606 (tt0) REVERT: G 19 SER cc_start: 0.8183 (m) cc_final: 0.7742 (p) REVERT: G 64 ARG cc_start: 0.7457 (mmm160) cc_final: 0.6747 (mmm160) REVERT: G 180 LEU cc_start: 0.8768 (mt) cc_final: 0.8434 (mt) REVERT: G 202 ARG cc_start: 0.7994 (ttt90) cc_final: 0.7780 (ttt90) REVERT: G 260 MET cc_start: 0.5447 (tmm) cc_final: 0.5098 (tmm) REVERT: G 267 LYS cc_start: 0.7938 (ptpt) cc_final: 0.7624 (ptpt) REVERT: G 285 LYS cc_start: 0.8119 (mtpt) cc_final: 0.7829 (mtpt) REVERT: G 357 ARG cc_start: 0.7903 (mtt90) cc_final: 0.7650 (mtt90) REVERT: G 362 ARG cc_start: 0.8072 (ptm160) cc_final: 0.7664 (ttm170) REVERT: G 369 GLN cc_start: 0.7296 (mp10) cc_final: 0.6626 (mp10) REVERT: G 372 LYS cc_start: 0.7550 (mttp) cc_final: 0.7215 (mttp) REVERT: G 381 THR cc_start: 0.7797 (t) cc_final: 0.7528 (p) REVERT: G 411 THR cc_start: 0.8095 (t) cc_final: 0.7830 (m) REVERT: G 414 ASN cc_start: 0.7721 (t0) cc_final: 0.7397 (t0) REVERT: G 418 LYS cc_start: 0.7788 (ttmt) cc_final: 0.7573 (ttmt) REVERT: H 18 ARG cc_start: 0.7174 (mtp85) cc_final: 0.6671 (mtp85) REVERT: H 88 MET cc_start: 0.7937 (mmm) cc_final: 0.7665 (mmm) REVERT: H 134 GLU cc_start: 0.7902 (mt-10) cc_final: 0.7071 (mt-10) REVERT: H 178 MET cc_start: 0.7915 (mmm) cc_final: 0.7644 (tpp) REVERT: H 180 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7653 (mm-30) REVERT: H 184 LYS cc_start: 0.8374 (mmpt) cc_final: 0.7949 (mmpt) REVERT: H 201 LYS cc_start: 0.7978 (mmmm) cc_final: 0.7671 (mmmm) REVERT: H 235 ARG cc_start: 0.7797 (ttt180) cc_final: 0.7346 (ttt180) REVERT: H 248 ASP cc_start: 0.7445 (m-30) cc_final: 0.7218 (m-30) REVERT: H 271 GLU cc_start: 0.7215 (mp0) cc_final: 0.6951 (mp0) REVERT: H 274 GLU cc_start: 0.7409 (mt-10) cc_final: 0.6979 (mt-10) REVERT: H 282 GLU cc_start: 0.7774 (tt0) cc_final: 0.7506 (tt0) REVERT: H 352 ASP cc_start: 0.7377 (m-30) cc_final: 0.6995 (m-30) REVERT: H 358 SER cc_start: 0.7911 (m) cc_final: 0.7697 (t) REVERT: H 381 GLU cc_start: 0.7579 (mm-30) cc_final: 0.7220 (mm-30) REVERT: H 389 VAL cc_start: 0.7894 (m) cc_final: 0.7589 (p) REVERT: H 392 ARG cc_start: 0.7510 (ttt180) cc_final: 0.7310 (ttt180) REVERT: H 396 GLU cc_start: 0.7704 (mm-30) cc_final: 0.7448 (mm-30) REVERT: H 397 THR cc_start: 0.8120 (p) cc_final: 0.7907 (p) REVERT: H 435 ASP cc_start: 0.7712 (p0) cc_final: 0.7417 (p0) REVERT: I 17 SER cc_start: 0.8042 (m) cc_final: 0.7705 (p) REVERT: I 47 GLU cc_start: 0.7152 (mt-10) cc_final: 0.6889 (mt-10) REVERT: I 60 LYS cc_start: 0.7976 (ttmt) cc_final: 0.7732 (ttmt) REVERT: I 113 MET cc_start: 0.7359 (tpp) cc_final: 0.6902 (tpp) REVERT: I 130 VAL cc_start: 0.8742 (t) cc_final: 0.8443 (m) REVERT: I 232 LYS cc_start: 0.8362 (mttt) cc_final: 0.8158 (ttmt) REVERT: I 249 ARG cc_start: 0.7551 (tmm160) cc_final: 0.7139 (tmm160) REVERT: I 260 MET cc_start: 0.7037 (mtt) cc_final: 0.6068 (mtt) REVERT: I 264 MET cc_start: 0.6576 (ptp) cc_final: 0.6161 (ptp) REVERT: I 281 LYS cc_start: 0.8378 (mttt) cc_final: 0.8065 (mttt) REVERT: I 341 THR cc_start: 0.7642 (OUTLIER) cc_final: 0.7405 (p) REVERT: I 344 ILE cc_start: 0.6809 (mt) cc_final: 0.6556 (mp) REVERT: I 372 LYS cc_start: 0.8081 (mtpt) cc_final: 0.7742 (mtpt) REVERT: I 396 GLU cc_start: 0.7314 (mt-10) cc_final: 0.7056 (mt-10) REVERT: J 38 GLU cc_start: 0.7639 (mm-30) cc_final: 0.7319 (mm-30) REVERT: J 40 ARG cc_start: 0.7434 (mtt180) cc_final: 0.7202 (mtt-85) REVERT: J 115 LYS cc_start: 0.8030 (mtmt) cc_final: 0.7779 (mtmt) REVERT: J 130 ARG cc_start: 0.8295 (ttm-80) cc_final: 0.8009 (ttm-80) REVERT: J 164 LYS cc_start: 0.8220 (pttt) cc_final: 0.7693 (pttt) REVERT: J 169 GLU cc_start: 0.6644 (tt0) cc_final: 0.6234 (tt0) REVERT: J 178 MET cc_start: 0.6011 (tpp) cc_final: 0.5557 (mpp) REVERT: J 368 LYS cc_start: 0.7311 (ttmt) cc_final: 0.6967 (ttmt) REVERT: J 420 GLU cc_start: 0.7292 (mt-10) cc_final: 0.6989 (mt-10) REVERT: J 436 GLU cc_start: 0.6787 (tm-30) cc_final: 0.6396 (tm-30) REVERT: J 441 GLN cc_start: 0.6752 (mm110) cc_final: 0.6380 (mm110) REVERT: L 18 LYS cc_start: 0.8391 (mppt) cc_final: 0.8125 (mttp) REVERT: L 37 ARG cc_start: 0.6265 (mtt90) cc_final: 0.5872 (mtt90) REVERT: L 68 LYS cc_start: 0.8083 (mtpt) cc_final: 0.7790 (mtpt) REVERT: L 81 ASP cc_start: 0.8198 (m-30) cc_final: 0.7685 (m-30) REVERT: L 113 LYS cc_start: 0.8221 (ttpp) cc_final: 0.7913 (mtpt) REVERT: L 132 MET cc_start: 0.8400 (ttp) cc_final: 0.8164 (tmm) REVERT: L 153 MET cc_start: 0.8146 (tmm) cc_final: 0.7704 (tmm) REVERT: L 191 LYS cc_start: 0.8430 (ttmt) cc_final: 0.8113 (ttmt) REVERT: L 221 LEU cc_start: 0.8119 (tp) cc_final: 0.7826 (tt) REVERT: L 227 MET cc_start: 0.7055 (mmm) cc_final: 0.6759 (mmm) REVERT: L 242 LEU cc_start: 0.8339 (mt) cc_final: 0.8138 (mm) REVERT: L 306 TYR cc_start: 0.8660 (m-80) cc_final: 0.8117 (m-80) REVERT: L 315 LYS cc_start: 0.8566 (OUTLIER) cc_final: 0.8215 (ptmm) REVERT: L 364 GLU cc_start: 0.7622 (pt0) cc_final: 0.7385 (pt0) REVERT: M 21 TYR cc_start: 0.8313 (t80) cc_final: 0.7885 (t80) REVERT: M 30 GLU cc_start: 0.8042 (mm-30) cc_final: 0.7779 (mm-30) REVERT: M 43 MET cc_start: 0.7480 (tmm) cc_final: 0.7023 (tmm) REVERT: M 79 ARG cc_start: 0.8048 (ttm-80) cc_final: 0.7785 (ttm-80) REVERT: M 95 ASP cc_start: 0.7645 (t0) cc_final: 0.7048 (t0) REVERT: M 100 GLN cc_start: 0.8242 (mt0) cc_final: 0.7917 (mt0) REVERT: M 142 GLU cc_start: 0.7737 (mm-30) cc_final: 0.7353 (mm-30) REVERT: M 178 THR cc_start: 0.8544 (m) cc_final: 0.8337 (p) REVERT: M 200 ASP cc_start: 0.7956 (m-30) cc_final: 0.7637 (m-30) REVERT: M 231 GLU cc_start: 0.7722 (pm20) cc_final: 0.7486 (pm20) REVERT: M 271 ASP cc_start: 0.7985 (t0) cc_final: 0.7556 (t0) REVERT: M 345 TYR cc_start: 0.8115 (m-80) cc_final: 0.7729 (m-80) REVERT: M 354 ASN cc_start: 0.8588 (t0) cc_final: 0.8107 (t0) REVERT: M 379 LYS cc_start: 0.7955 (tptt) cc_final: 0.7610 (tptt) REVERT: M 413 LYS cc_start: 0.8367 (tttm) cc_final: 0.8068 (tttm) REVERT: N 66 LYS cc_start: 0.8100 (mtmt) cc_final: 0.7814 (mtmt) REVERT: N 81 ARG cc_start: 0.7851 (ttt-90) cc_final: 0.7645 (ttt-90) REVERT: N 106 LYS cc_start: 0.8430 (ptpt) cc_final: 0.8152 (ptpt) REVERT: N 128 ARG cc_start: 0.7592 (ttm170) cc_final: 0.7317 (ttm170) REVERT: N 138 TYR cc_start: 0.8464 (p90) cc_final: 0.8013 (p90) REVERT: N 142 GLU cc_start: 0.7832 (mt-10) cc_final: 0.7120 (mt-10) REVERT: N 149 ASP cc_start: 0.7755 (t0) cc_final: 0.7517 (t0) REVERT: N 158 ASP cc_start: 0.8039 (m-30) cc_final: 0.7720 (m-30) REVERT: N 176 ASP cc_start: 0.7751 (t70) cc_final: 0.7478 (t70) REVERT: N 190 ASP cc_start: 0.7357 (m-30) cc_final: 0.6992 (m-30) REVERT: N 193 GLU cc_start: 0.7630 (tp30) cc_final: 0.7199 (tp30) REVERT: N 195 TYR cc_start: 0.7935 (t80) cc_final: 0.7513 (t80) REVERT: N 231 GLU cc_start: 0.7562 (mm-30) cc_final: 0.7144 (mm-30) outliers start: 91 outliers final: 69 residues processed: 1315 average time/residue: 0.2749 time to fit residues: 538.3127 Evaluate side-chains 1364 residues out of total 3673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 1292 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 842 ARG Chi-restraints excluded: chain A residue 1320 TYR Chi-restraints excluded: chain A residue 1410 LEU Chi-restraints excluded: chain A residue 1419 GLU Chi-restraints excluded: chain A residue 1773 ARG Chi-restraints excluded: chain A residue 1893 VAL Chi-restraints excluded: chain A residue 1909 LYS Chi-restraints excluded: chain A residue 1932 MET Chi-restraints excluded: chain A residue 1937 HIS Chi-restraints excluded: chain A residue 1968 CYS Chi-restraints excluded: chain A residue 2201 LEU Chi-restraints excluded: chain A residue 2223 TYR Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain C residue 444 THR Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 159 ILE Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 387 SER Chi-restraints excluded: chain E residue 415 LEU Chi-restraints excluded: chain F residue 134 GLU Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 184 LYS Chi-restraints excluded: chain F residue 236 LYS Chi-restraints excluded: chain F residue 319 ASP Chi-restraints excluded: chain F residue 382 MET Chi-restraints excluded: chain F residue 392 ARG Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 293 GLU Chi-restraints excluded: chain G residue 295 VAL Chi-restraints excluded: chain G residue 313 THR Chi-restraints excluded: chain G residue 337 VAL Chi-restraints excluded: chain G residue 341 THR Chi-restraints excluded: chain G residue 403 LEU Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 130 ARG Chi-restraints excluded: chain H residue 161 LEU Chi-restraints excluded: chain H residue 195 ILE Chi-restraints excluded: chain H residue 258 LEU Chi-restraints excluded: chain H residue 360 THR Chi-restraints excluded: chain H residue 407 THR Chi-restraints excluded: chain I residue 97 VAL Chi-restraints excluded: chain I residue 125 LYS Chi-restraints excluded: chain I residue 208 THR Chi-restraints excluded: chain I residue 237 ASP Chi-restraints excluded: chain I residue 341 THR Chi-restraints excluded: chain I residue 365 LEU Chi-restraints excluded: chain I residue 439 ASP Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 168 MET Chi-restraints excluded: chain J residue 248 ASP Chi-restraints excluded: chain J residue 252 SER Chi-restraints excluded: chain J residue 326 MET Chi-restraints excluded: chain J residue 342 SER Chi-restraints excluded: chain J residue 405 LEU Chi-restraints excluded: chain J residue 437 SER Chi-restraints excluded: chain L residue 100 GLU Chi-restraints excluded: chain L residue 118 LYS Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain L residue 186 THR Chi-restraints excluded: chain L residue 194 THR Chi-restraints excluded: chain L residue 315 LYS Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 85 ILE Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain M residue 202 ILE Chi-restraints excluded: chain M residue 273 THR Chi-restraints excluded: chain M residue 304 ILE Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 164 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 392 optimal weight: 3.9990 chunk 48 optimal weight: 7.9990 chunk 27 optimal weight: 0.9980 chunk 360 optimal weight: 0.0010 chunk 347 optimal weight: 4.9990 chunk 251 optimal weight: 3.9990 chunk 297 optimal weight: 0.0770 chunk 322 optimal weight: 0.9980 chunk 107 optimal weight: 0.6980 chunk 8 optimal weight: 6.9990 chunk 37 optimal weight: 0.6980 overall best weight: 0.4944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1894 GLN E 241 HIS E 373 GLN E 393 HIS F 44 GLN ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 121 GLN ** F 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 85 GLN G 115 ASN G 247 ASN ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 408 GLN J 44 GLN M 118 HIS M 128 ASN M 407 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.148579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.129783 restraints weight = 51165.862| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 2.12 r_work: 0.3447 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 34579 Z= 0.116 Angle : 0.483 10.262 46733 Z= 0.254 Chirality : 0.041 0.169 5327 Planarity : 0.004 0.047 5974 Dihedral : 8.385 164.116 4826 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.37 % Allowed : 14.81 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.53 (0.13), residues: 4227 helix: 1.68 (0.12), residues: 1882 sheet: 0.29 (0.19), residues: 732 loop : 0.77 (0.16), residues: 1613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 205 TYR 0.039 0.001 TYR A1336 PHE 0.034 0.001 PHE A1960 TRP 0.012 0.001 TRP A 821 HIS 0.007 0.001 HIS E 241 Details of bonding type rmsd covalent geometry : bond 0.00254 (34579) covalent geometry : angle 0.48305 (46733) hydrogen bonds : bond 0.03728 ( 1532) hydrogen bonds : angle 4.15716 ( 4341) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8454 Ramachandran restraints generated. 4227 Oldfield, 0 Emsley, 4227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8454 Ramachandran restraints generated. 4227 Oldfield, 0 Emsley, 4227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1379 residues out of total 3673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 1292 time to evaluate : 1.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 789 ARG cc_start: 0.8076 (ttm170) cc_final: 0.7815 (ttm170) REVERT: A 793 LEU cc_start: 0.7997 (mp) cc_final: 0.7713 (tp) REVERT: A 822 MET cc_start: 0.8698 (tpp) cc_final: 0.8491 (mmm) REVERT: A 841 VAL cc_start: 0.8550 (t) cc_final: 0.8345 (p) REVERT: A 851 LYS cc_start: 0.8141 (tttt) cc_final: 0.7795 (tttt) REVERT: A 1319 LYS cc_start: 0.7068 (tttt) cc_final: 0.6780 (tttt) REVERT: A 1337 GLU cc_start: 0.8188 (mm-30) cc_final: 0.7963 (mm-30) REVERT: A 1389 GLU cc_start: 0.7972 (tt0) cc_final: 0.7683 (tm-30) REVERT: A 1459 LYS cc_start: 0.8079 (mtmm) cc_final: 0.7813 (mtmm) REVERT: A 1746 LEU cc_start: 0.7988 (tp) cc_final: 0.7737 (tp) REVERT: A 1917 VAL cc_start: 0.7601 (m) cc_final: 0.7374 (t) REVERT: A 1941 TYR cc_start: 0.6957 (p90) cc_final: 0.6520 (p90) REVERT: A 1952 GLN cc_start: 0.7102 (mm-40) cc_final: 0.6777 (mm110) REVERT: A 1962 ARG cc_start: 0.7674 (ptp-170) cc_final: 0.7403 (ptp-170) REVERT: A 2225 ARG cc_start: 0.8215 (ttm-80) cc_final: 0.7493 (ttt90) REVERT: A 2226 GLU cc_start: 0.7582 (mp0) cc_final: 0.7212 (mp0) REVERT: A 2227 ASP cc_start: 0.7882 (m-30) cc_final: 0.7653 (m-30) REVERT: A 2233 TYR cc_start: 0.8064 (m-80) cc_final: 0.7664 (m-80) REVERT: A 2236 GLU cc_start: 0.6863 (mp0) cc_final: 0.6596 (mp0) REVERT: A 2269 MET cc_start: 0.7955 (mmm) cc_final: 0.7459 (mmm) REVERT: A 2271 GLU cc_start: 0.6676 (OUTLIER) cc_final: 0.6120 (pp20) REVERT: C 530 ARG cc_start: 0.7318 (ptp-110) cc_final: 0.7075 (ptp-170) REVERT: E 110 GLU cc_start: 0.6973 (mm-30) cc_final: 0.6480 (tm-30) REVERT: E 134 GLU cc_start: 0.7689 (tm-30) cc_final: 0.7404 (pp20) REVERT: E 236 GLN cc_start: 0.8081 (mm-40) cc_final: 0.7615 (mm-40) REVERT: E 259 MET cc_start: 0.7252 (OUTLIER) cc_final: 0.6839 (mmm) REVERT: E 260 MET cc_start: 0.7518 (mmm) cc_final: 0.7167 (mmm) REVERT: E 264 MET cc_start: 0.6533 (mmm) cc_final: 0.6109 (mmm) REVERT: E 278 GLU cc_start: 0.7728 (mm-30) cc_final: 0.7464 (mm-30) REVERT: E 281 LYS cc_start: 0.7747 (mtmm) cc_final: 0.7468 (mtmm) REVERT: E 288 ASP cc_start: 0.8012 (t0) cc_final: 0.7768 (t0) REVERT: E 306 MET cc_start: 0.8082 (mmt) cc_final: 0.7814 (mmm) REVERT: E 364 MET cc_start: 0.7256 (mtm) cc_final: 0.6837 (mtm) REVERT: E 376 LYS cc_start: 0.8185 (tptm) cc_final: 0.7824 (tptm) REVERT: E 381 THR cc_start: 0.8259 (m) cc_final: 0.7600 (p) REVERT: E 392 ASN cc_start: 0.7845 (m-40) cc_final: 0.7534 (m-40) REVERT: E 408 GLN cc_start: 0.7550 (mt0) cc_final: 0.7263 (mt0) REVERT: E 416 LEU cc_start: 0.8033 (mt) cc_final: 0.7806 (mt) REVERT: F 20 GLU cc_start: 0.7653 (mp0) cc_final: 0.7199 (mp0) REVERT: F 38 GLU cc_start: 0.7161 (tp30) cc_final: 0.6803 (mm-30) REVERT: F 65 GLU cc_start: 0.7400 (mm-30) cc_final: 0.7166 (tt0) REVERT: F 78 GLN cc_start: 0.7411 (mm110) cc_final: 0.6944 (mm110) REVERT: F 101 THR cc_start: 0.8024 (m) cc_final: 0.7695 (p) REVERT: F 180 GLU cc_start: 0.7945 (mt-10) cc_final: 0.7673 (tp30) REVERT: F 185 ASP cc_start: 0.7782 (t70) cc_final: 0.7467 (t0) REVERT: F 210 THR cc_start: 0.8742 (t) cc_final: 0.8411 (p) REVERT: F 234 LYS cc_start: 0.8261 (mtmm) cc_final: 0.7967 (mtmm) REVERT: F 242 VAL cc_start: 0.7789 (m) cc_final: 0.7497 (p) REVERT: F 333 THR cc_start: 0.7921 (p) cc_final: 0.7578 (t) REVERT: F 381 GLU cc_start: 0.7469 (mm-30) cc_final: 0.7129 (mm-30) REVERT: F 410 SER cc_start: 0.8151 (t) cc_final: 0.7850 (t) REVERT: F 414 ARG cc_start: 0.7179 (mtm-85) cc_final: 0.6819 (mtm-85) REVERT: F 420 GLU cc_start: 0.7008 (tt0) cc_final: 0.6588 (tt0) REVERT: G 19 SER cc_start: 0.8166 (m) cc_final: 0.7738 (p) REVERT: G 64 ARG cc_start: 0.7491 (mmm160) cc_final: 0.6819 (mmm160) REVERT: G 137 GLU cc_start: 0.7650 (pm20) cc_final: 0.7380 (pm20) REVERT: G 180 LEU cc_start: 0.8778 (mt) cc_final: 0.8442 (mt) REVERT: G 260 MET cc_start: 0.5437 (tmm) cc_final: 0.5101 (tmm) REVERT: G 267 LYS cc_start: 0.7930 (ptpt) cc_final: 0.7583 (ptpt) REVERT: G 285 LYS cc_start: 0.8092 (mtpt) cc_final: 0.7804 (mtpt) REVERT: G 357 ARG cc_start: 0.7898 (mtt90) cc_final: 0.7643 (mtt90) REVERT: G 362 ARG cc_start: 0.8102 (ptm160) cc_final: 0.7691 (ttm170) REVERT: G 369 GLN cc_start: 0.7276 (mp10) cc_final: 0.6609 (mp10) REVERT: G 372 LYS cc_start: 0.7506 (mttp) cc_final: 0.7183 (mttp) REVERT: G 381 THR cc_start: 0.7782 (t) cc_final: 0.7501 (p) REVERT: G 411 THR cc_start: 0.8104 (t) cc_final: 0.7838 (m) REVERT: G 414 ASN cc_start: 0.7706 (t0) cc_final: 0.7380 (t0) REVERT: G 418 LYS cc_start: 0.7775 (ttmt) cc_final: 0.7563 (ttmt) REVERT: H 18 ARG cc_start: 0.7157 (mtp85) cc_final: 0.6667 (mtp85) REVERT: H 88 MET cc_start: 0.7937 (mmm) cc_final: 0.7660 (mmm) REVERT: H 134 GLU cc_start: 0.7908 (mt-10) cc_final: 0.7105 (mt-10) REVERT: H 180 GLU cc_start: 0.8067 (mm-30) cc_final: 0.7595 (mm-30) REVERT: H 184 LYS cc_start: 0.8311 (mmpt) cc_final: 0.7893 (mmpt) REVERT: H 201 LYS cc_start: 0.8002 (mmmm) cc_final: 0.7683 (mmmm) REVERT: H 235 ARG cc_start: 0.7800 (ttt180) cc_final: 0.7367 (ttt180) REVERT: H 248 ASP cc_start: 0.7384 (m-30) cc_final: 0.7161 (m-30) REVERT: H 271 GLU cc_start: 0.7226 (mp0) cc_final: 0.6962 (mp0) REVERT: H 274 GLU cc_start: 0.7410 (mt-10) cc_final: 0.6999 (mt-10) REVERT: H 282 GLU cc_start: 0.7770 (tt0) cc_final: 0.7502 (tt0) REVERT: H 352 ASP cc_start: 0.7345 (m-30) cc_final: 0.6965 (m-30) REVERT: H 358 SER cc_start: 0.7893 (m) cc_final: 0.7676 (t) REVERT: H 381 GLU cc_start: 0.7627 (mm-30) cc_final: 0.7268 (mm-30) REVERT: H 389 VAL cc_start: 0.7902 (m) cc_final: 0.7593 (p) REVERT: H 396 GLU cc_start: 0.7725 (mm-30) cc_final: 0.7479 (mm-30) REVERT: H 397 THR cc_start: 0.8140 (p) cc_final: 0.7931 (p) REVERT: H 435 ASP cc_start: 0.7660 (p0) cc_final: 0.7438 (p0) REVERT: H 438 ARG cc_start: 0.7317 (mtm110) cc_final: 0.7048 (mtm-85) REVERT: I 17 SER cc_start: 0.8049 (m) cc_final: 0.7704 (p) REVERT: I 47 GLU cc_start: 0.7154 (mt-10) cc_final: 0.6846 (mt-10) REVERT: I 60 LYS cc_start: 0.7973 (ttmt) cc_final: 0.7715 (ttmt) REVERT: I 113 MET cc_start: 0.7334 (tpp) cc_final: 0.6957 (tpp) REVERT: I 130 VAL cc_start: 0.8687 (t) cc_final: 0.8401 (m) REVERT: I 132 GLU cc_start: 0.7318 (tt0) cc_final: 0.6906 (tt0) REVERT: I 249 ARG cc_start: 0.7536 (tmm160) cc_final: 0.7113 (tmm160) REVERT: I 260 MET cc_start: 0.6966 (mtt) cc_final: 0.6012 (mtt) REVERT: I 264 MET cc_start: 0.6593 (ptp) cc_final: 0.6163 (ptp) REVERT: I 281 LYS cc_start: 0.8371 (mttt) cc_final: 0.8064 (mttt) REVERT: I 303 GLU cc_start: 0.7212 (mm-30) cc_final: 0.6800 (mm-30) REVERT: I 372 LYS cc_start: 0.8086 (mtpt) cc_final: 0.7744 (mtpt) REVERT: I 376 LYS cc_start: 0.8017 (tptt) cc_final: 0.7683 (tptt) REVERT: I 396 GLU cc_start: 0.7316 (mt-10) cc_final: 0.7051 (mt-10) REVERT: J 38 GLU cc_start: 0.7615 (mm-30) cc_final: 0.7323 (mm-30) REVERT: J 40 ARG cc_start: 0.7412 (mtt180) cc_final: 0.7173 (mtt-85) REVERT: J 115 LYS cc_start: 0.8003 (mtmt) cc_final: 0.7767 (mtmt) REVERT: J 130 ARG cc_start: 0.8289 (ttm-80) cc_final: 0.8028 (ttm-80) REVERT: J 164 LYS cc_start: 0.8203 (pttt) cc_final: 0.7917 (pttt) REVERT: J 178 MET cc_start: 0.5965 (tpp) cc_final: 0.5600 (mpp) REVERT: J 246 GLU cc_start: 0.7436 (mt-10) cc_final: 0.7188 (mt-10) REVERT: J 420 GLU cc_start: 0.7292 (mt-10) cc_final: 0.6978 (mt-10) REVERT: J 436 GLU cc_start: 0.6786 (tm-30) cc_final: 0.6359 (tm-30) REVERT: J 441 GLN cc_start: 0.6716 (mm110) cc_final: 0.6336 (mm110) REVERT: L 37 ARG cc_start: 0.6277 (mtt90) cc_final: 0.5891 (mtt90) REVERT: L 68 LYS cc_start: 0.8068 (mtpt) cc_final: 0.7767 (mtpt) REVERT: L 81 ASP cc_start: 0.8201 (m-30) cc_final: 0.7693 (m-30) REVERT: L 123 MET cc_start: 0.8677 (mmp) cc_final: 0.8460 (mmp) REVERT: L 191 LYS cc_start: 0.8424 (ttmt) cc_final: 0.8108 (ttmt) REVERT: L 221 LEU cc_start: 0.8102 (tp) cc_final: 0.7827 (tt) REVERT: L 227 MET cc_start: 0.7025 (mmm) cc_final: 0.6744 (mmm) REVERT: L 242 LEU cc_start: 0.8321 (mt) cc_final: 0.8118 (mm) REVERT: L 283 MET cc_start: 0.8396 (mmm) cc_final: 0.8192 (mmm) REVERT: L 306 TYR cc_start: 0.8667 (m-80) cc_final: 0.8220 (m-80) REVERT: L 364 GLU cc_start: 0.7533 (pt0) cc_final: 0.7292 (pt0) REVERT: M 21 TYR cc_start: 0.8323 (t80) cc_final: 0.7945 (t80) REVERT: M 30 GLU cc_start: 0.8069 (mm-30) cc_final: 0.7843 (mm-30) REVERT: M 43 MET cc_start: 0.7436 (tmm) cc_final: 0.6976 (tmm) REVERT: M 95 ASP cc_start: 0.7662 (t0) cc_final: 0.7065 (t0) REVERT: M 100 GLN cc_start: 0.8228 (mt0) cc_final: 0.7904 (mt0) REVERT: M 142 GLU cc_start: 0.7703 (mm-30) cc_final: 0.7365 (mm-30) REVERT: M 200 ASP cc_start: 0.7961 (m-30) cc_final: 0.7634 (m-30) REVERT: M 231 GLU cc_start: 0.7734 (pm20) cc_final: 0.7489 (pm20) REVERT: M 271 ASP cc_start: 0.7983 (t0) cc_final: 0.7554 (t0) REVERT: M 354 ASN cc_start: 0.8606 (t0) cc_final: 0.8102 (t0) REVERT: M 379 LYS cc_start: 0.7964 (tptt) cc_final: 0.7645 (tptt) REVERT: M 413 LYS cc_start: 0.8354 (tttm) cc_final: 0.8060 (tttm) REVERT: N 66 LYS cc_start: 0.8087 (mtmt) cc_final: 0.7785 (mtmt) REVERT: N 81 ARG cc_start: 0.7850 (ttt-90) cc_final: 0.7642 (ttt-90) REVERT: N 106 LYS cc_start: 0.8450 (ptpt) cc_final: 0.8170 (ptpt) REVERT: N 119 GLU cc_start: 0.7726 (mt-10) cc_final: 0.7492 (tt0) REVERT: N 138 TYR cc_start: 0.8485 (p90) cc_final: 0.8016 (p90) REVERT: N 142 GLU cc_start: 0.7829 (mt-10) cc_final: 0.7143 (mt-10) REVERT: N 149 ASP cc_start: 0.7750 (t0) cc_final: 0.7516 (t0) REVERT: N 158 ASP cc_start: 0.8037 (m-30) cc_final: 0.7710 (m-30) REVERT: N 176 ASP cc_start: 0.7792 (t70) cc_final: 0.7407 (t70) REVERT: N 177 ARG cc_start: 0.7928 (mmt-90) cc_final: 0.7532 (mmt-90) REVERT: N 190 ASP cc_start: 0.7392 (m-30) cc_final: 0.7038 (m-30) REVERT: N 193 GLU cc_start: 0.7609 (tp30) cc_final: 0.7180 (tp30) REVERT: N 225 ARG cc_start: 0.7777 (OUTLIER) cc_final: 0.7462 (mtt90) REVERT: N 231 GLU cc_start: 0.7537 (mm-30) cc_final: 0.7124 (mm-30) outliers start: 87 outliers final: 57 residues processed: 1313 average time/residue: 0.2750 time to fit residues: 537.6993 Evaluate side-chains 1349 residues out of total 3673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 1289 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 842 ARG Chi-restraints excluded: chain A residue 1339 VAL Chi-restraints excluded: chain A residue 1384 VAL Chi-restraints excluded: chain A residue 1465 GLN Chi-restraints excluded: chain A residue 1773 ARG Chi-restraints excluded: chain A residue 1937 HIS Chi-restraints excluded: chain A residue 1968 CYS Chi-restraints excluded: chain A residue 2264 SER Chi-restraints excluded: chain A residue 2271 GLU Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain C residue 444 THR Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 159 ILE Chi-restraints excluded: chain E residue 259 MET Chi-restraints excluded: chain E residue 268 LYS Chi-restraints excluded: chain E residue 415 LEU Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 184 LYS Chi-restraints excluded: chain F residue 236 LYS Chi-restraints excluded: chain F residue 319 ASP Chi-restraints excluded: chain F residue 382 MET Chi-restraints excluded: chain F residue 392 ARG Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 295 VAL Chi-restraints excluded: chain G residue 313 THR Chi-restraints excluded: chain G residue 337 VAL Chi-restraints excluded: chain G residue 403 LEU Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 130 ARG Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain H residue 161 LEU Chi-restraints excluded: chain H residue 170 THR Chi-restraints excluded: chain H residue 177 LYS Chi-restraints excluded: chain H residue 195 ILE Chi-restraints excluded: chain H residue 258 LEU Chi-restraints excluded: chain H residue 326 MET Chi-restraints excluded: chain H residue 333 THR Chi-restraints excluded: chain H residue 360 THR Chi-restraints excluded: chain H residue 407 THR Chi-restraints excluded: chain I residue 97 VAL Chi-restraints excluded: chain I residue 125 LYS Chi-restraints excluded: chain I residue 208 THR Chi-restraints excluded: chain I residue 237 ASP Chi-restraints excluded: chain I residue 439 ASP Chi-restraints excluded: chain J residue 248 ASP Chi-restraints excluded: chain J residue 252 SER Chi-restraints excluded: chain J residue 326 MET Chi-restraints excluded: chain J residue 342 SER Chi-restraints excluded: chain J residue 405 LEU Chi-restraints excluded: chain J residue 437 SER Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain L residue 186 THR Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain M residue 202 ILE Chi-restraints excluded: chain M residue 213 MET Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 164 SER Chi-restraints excluded: chain N residue 225 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 308 optimal weight: 5.9990 chunk 343 optimal weight: 0.9980 chunk 406 optimal weight: 0.1980 chunk 346 optimal weight: 5.9990 chunk 207 optimal weight: 1.9990 chunk 136 optimal weight: 0.9980 chunk 331 optimal weight: 4.9990 chunk 250 optimal weight: 1.9990 chunk 401 optimal weight: 3.9990 chunk 184 optimal weight: 0.0370 chunk 215 optimal weight: 0.8980 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 828 GLN A1894 GLN E 241 HIS E 247 ASN E 373 GLN E 393 HIS F 44 GLN ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 233 GLN ** F 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 85 GLN G 115 ASN G 247 ASN H 25 HIS ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 408 GLN J 44 GLN L 280 ASN M 407 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.148384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.129523 restraints weight = 51297.171| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 2.13 r_work: 0.3443 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 34579 Z= 0.132 Angle : 0.494 9.777 46733 Z= 0.259 Chirality : 0.041 0.175 5327 Planarity : 0.004 0.047 5974 Dihedral : 8.331 162.187 4826 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.50 % Allowed : 15.14 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.53 (0.13), residues: 4227 helix: 1.67 (0.12), residues: 1888 sheet: 0.28 (0.19), residues: 724 loop : 0.77 (0.16), residues: 1615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 205 TYR 0.043 0.001 TYR A1336 PHE 0.034 0.001 PHE A1960 TRP 0.011 0.001 TRP A2006 HIS 0.007 0.001 HIS E 241 Details of bonding type rmsd covalent geometry : bond 0.00292 (34579) covalent geometry : angle 0.49388 (46733) hydrogen bonds : bond 0.03834 ( 1532) hydrogen bonds : angle 4.15564 ( 4341) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8454 Ramachandran restraints generated. 4227 Oldfield, 0 Emsley, 4227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8454 Ramachandran restraints generated. 4227 Oldfield, 0 Emsley, 4227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1383 residues out of total 3673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 1291 time to evaluate : 1.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 789 ARG cc_start: 0.8033 (ttm170) cc_final: 0.7760 (ttm170) REVERT: A 793 LEU cc_start: 0.8018 (mp) cc_final: 0.7757 (tp) REVERT: A 822 MET cc_start: 0.8710 (tpp) cc_final: 0.8483 (mmm) REVERT: A 841 VAL cc_start: 0.8569 (t) cc_final: 0.8348 (p) REVERT: A 851 LYS cc_start: 0.8155 (tttt) cc_final: 0.7804 (tttt) REVERT: A 1319 LYS cc_start: 0.7088 (tttt) cc_final: 0.6811 (tttt) REVERT: A 1389 GLU cc_start: 0.7963 (tt0) cc_final: 0.7600 (tm-30) REVERT: A 1409 ASP cc_start: 0.7789 (t0) cc_final: 0.7335 (t0) REVERT: A 1413 PHE cc_start: 0.8498 (m-80) cc_final: 0.8259 (m-80) REVERT: A 1419 GLU cc_start: 0.7375 (mm-30) cc_final: 0.7109 (mt-10) REVERT: A 1459 LYS cc_start: 0.8059 (mtmm) cc_final: 0.7789 (mtmm) REVERT: A 1746 LEU cc_start: 0.8003 (tp) cc_final: 0.7757 (tp) REVERT: A 1893 VAL cc_start: 0.8192 (OUTLIER) cc_final: 0.7798 (t) REVERT: A 1941 TYR cc_start: 0.7025 (p90) cc_final: 0.6534 (p90) REVERT: A 1952 GLN cc_start: 0.7129 (mm-40) cc_final: 0.6822 (mm110) REVERT: A 1962 ARG cc_start: 0.7663 (ptp-170) cc_final: 0.7448 (ptp-170) REVERT: A 2226 GLU cc_start: 0.7613 (mp0) cc_final: 0.7228 (mp0) REVERT: A 2227 ASP cc_start: 0.7867 (m-30) cc_final: 0.7624 (m-30) REVERT: A 2233 TYR cc_start: 0.8065 (m-80) cc_final: 0.7719 (m-80) REVERT: A 2236 GLU cc_start: 0.6869 (mp0) cc_final: 0.6280 (mm-30) REVERT: A 2243 GLU cc_start: 0.7229 (tt0) cc_final: 0.6879 (tt0) REVERT: A 2269 MET cc_start: 0.7975 (mmm) cc_final: 0.7486 (mmm) REVERT: A 2271 GLU cc_start: 0.6716 (OUTLIER) cc_final: 0.6137 (pp20) REVERT: C 530 ARG cc_start: 0.7344 (ptp-110) cc_final: 0.7079 (ptp-170) REVERT: E 100 GLU cc_start: 0.7320 (mt-10) cc_final: 0.7083 (mt-10) REVERT: E 110 GLU cc_start: 0.6985 (mm-30) cc_final: 0.6517 (tm-30) REVERT: E 134 GLU cc_start: 0.7646 (tm-30) cc_final: 0.7404 (pp20) REVERT: E 236 GLN cc_start: 0.8054 (mm-40) cc_final: 0.7622 (mm-40) REVERT: E 259 MET cc_start: 0.7286 (OUTLIER) cc_final: 0.6865 (mmm) REVERT: E 260 MET cc_start: 0.7525 (mmm) cc_final: 0.7166 (mmm) REVERT: E 264 MET cc_start: 0.6572 (mmm) cc_final: 0.6143 (mmm) REVERT: E 278 GLU cc_start: 0.7730 (mm-30) cc_final: 0.7470 (mm-30) REVERT: E 281 LYS cc_start: 0.7749 (mtmm) cc_final: 0.7473 (mtmm) REVERT: E 288 ASP cc_start: 0.7986 (t0) cc_final: 0.7744 (t0) REVERT: E 306 MET cc_start: 0.8076 (mmp) cc_final: 0.7819 (mmm) REVERT: E 364 MET cc_start: 0.7255 (mtm) cc_final: 0.6838 (mtm) REVERT: E 376 LYS cc_start: 0.8193 (tptm) cc_final: 0.7839 (tptm) REVERT: E 381 THR cc_start: 0.8263 (m) cc_final: 0.7613 (p) REVERT: E 392 ASN cc_start: 0.7862 (m-40) cc_final: 0.7550 (m-40) REVERT: E 416 LEU cc_start: 0.8038 (mt) cc_final: 0.7831 (mt) REVERT: F 20 GLU cc_start: 0.7661 (mp0) cc_final: 0.7202 (mp0) REVERT: F 38 GLU cc_start: 0.7174 (tp30) cc_final: 0.6807 (mm-30) REVERT: F 49 GLN cc_start: 0.8035 (mm110) cc_final: 0.7766 (mm110) REVERT: F 78 GLN cc_start: 0.7411 (mm110) cc_final: 0.6930 (mm110) REVERT: F 101 THR cc_start: 0.8024 (m) cc_final: 0.7681 (p) REVERT: F 180 GLU cc_start: 0.7992 (mt-10) cc_final: 0.7702 (tp30) REVERT: F 185 ASP cc_start: 0.7801 (t70) cc_final: 0.7456 (t0) REVERT: F 210 THR cc_start: 0.8732 (t) cc_final: 0.8397 (p) REVERT: F 242 VAL cc_start: 0.7781 (m) cc_final: 0.7491 (p) REVERT: F 274 GLU cc_start: 0.7677 (mt-10) cc_final: 0.7441 (mt-10) REVERT: F 326 MET cc_start: 0.8529 (OUTLIER) cc_final: 0.8240 (mtm) REVERT: F 333 THR cc_start: 0.7915 (p) cc_final: 0.7580 (t) REVERT: F 381 GLU cc_start: 0.7474 (mm-30) cc_final: 0.7136 (mm-30) REVERT: F 410 SER cc_start: 0.8148 (t) cc_final: 0.7811 (t) REVERT: F 414 ARG cc_start: 0.7190 (mtm-85) cc_final: 0.6815 (mtm-85) REVERT: F 420 GLU cc_start: 0.6993 (tt0) cc_final: 0.6578 (tt0) REVERT: G 19 SER cc_start: 0.8184 (m) cc_final: 0.7734 (p) REVERT: G 64 ARG cc_start: 0.7517 (mmm160) cc_final: 0.6841 (mmm160) REVERT: G 180 LEU cc_start: 0.8779 (mt) cc_final: 0.8429 (mt) REVERT: G 205 ARG cc_start: 0.7899 (mmm160) cc_final: 0.7531 (mtp-110) REVERT: G 260 MET cc_start: 0.5416 (tmm) cc_final: 0.5060 (tmm) REVERT: G 267 LYS cc_start: 0.7914 (ptpt) cc_final: 0.7554 (ptpt) REVERT: G 285 LYS cc_start: 0.8091 (mtpt) cc_final: 0.7798 (mtpt) REVERT: G 357 ARG cc_start: 0.7908 (mtt90) cc_final: 0.7611 (mtt90) REVERT: G 362 ARG cc_start: 0.8094 (ptm160) cc_final: 0.7683 (ttm170) REVERT: G 369 GLN cc_start: 0.7284 (mp10) cc_final: 0.6617 (mp10) REVERT: G 372 LYS cc_start: 0.7515 (mttp) cc_final: 0.7191 (mttp) REVERT: G 381 THR cc_start: 0.7774 (t) cc_final: 0.7494 (p) REVERT: G 411 THR cc_start: 0.8097 (t) cc_final: 0.7836 (m) REVERT: G 414 ASN cc_start: 0.7713 (t0) cc_final: 0.7385 (t0) REVERT: G 418 LYS cc_start: 0.7768 (ttmt) cc_final: 0.7551 (ttmt) REVERT: H 18 ARG cc_start: 0.7145 (mtp85) cc_final: 0.6661 (mtp85) REVERT: H 88 MET cc_start: 0.7945 (mmm) cc_final: 0.7646 (mmm) REVERT: H 134 GLU cc_start: 0.7911 (mt-10) cc_final: 0.7130 (mt-10) REVERT: H 178 MET cc_start: 0.7898 (mmm) cc_final: 0.7631 (tpp) REVERT: H 180 GLU cc_start: 0.8035 (mm-30) cc_final: 0.7561 (mm-30) REVERT: H 184 LYS cc_start: 0.8284 (mmpt) cc_final: 0.7895 (mmpt) REVERT: H 201 LYS cc_start: 0.8002 (mmmm) cc_final: 0.7698 (mmmm) REVERT: H 235 ARG cc_start: 0.7790 (ttt180) cc_final: 0.7356 (ttt180) REVERT: H 248 ASP cc_start: 0.7394 (m-30) cc_final: 0.7163 (m-30) REVERT: H 271 GLU cc_start: 0.7258 (mp0) cc_final: 0.6968 (mp0) REVERT: H 274 GLU cc_start: 0.7381 (mt-10) cc_final: 0.6957 (mt-10) REVERT: H 282 GLU cc_start: 0.7812 (tt0) cc_final: 0.7545 (tt0) REVERT: H 352 ASP cc_start: 0.7331 (m-30) cc_final: 0.6947 (m-30) REVERT: H 379 ASP cc_start: 0.7177 (t0) cc_final: 0.6957 (t0) REVERT: H 381 GLU cc_start: 0.7624 (mm-30) cc_final: 0.7264 (mm-30) REVERT: H 389 VAL cc_start: 0.7895 (m) cc_final: 0.7587 (p) REVERT: H 396 GLU cc_start: 0.7668 (mm-30) cc_final: 0.7421 (mm-30) REVERT: H 397 THR cc_start: 0.8143 (p) cc_final: 0.7918 (p) REVERT: H 435 ASP cc_start: 0.7675 (p0) cc_final: 0.7419 (p0) REVERT: I 17 SER cc_start: 0.8044 (m) cc_final: 0.7691 (p) REVERT: I 47 GLU cc_start: 0.7173 (mt-10) cc_final: 0.6871 (mt-10) REVERT: I 60 LYS cc_start: 0.7969 (ttmt) cc_final: 0.7737 (ttmt) REVERT: I 113 MET cc_start: 0.7346 (tpp) cc_final: 0.6925 (tpp) REVERT: I 130 VAL cc_start: 0.8705 (t) cc_final: 0.8392 (m) REVERT: I 249 ARG cc_start: 0.7566 (tmm160) cc_final: 0.7152 (tmm160) REVERT: I 260 MET cc_start: 0.6982 (mtt) cc_final: 0.6021 (mtt) REVERT: I 264 MET cc_start: 0.6594 (ptp) cc_final: 0.6167 (ptp) REVERT: I 346 SER cc_start: 0.7971 (t) cc_final: 0.7721 (t) REVERT: I 369 GLN cc_start: 0.7408 (mp10) cc_final: 0.7166 (mp10) REVERT: I 372 LYS cc_start: 0.8096 (mtpt) cc_final: 0.7754 (mtpt) REVERT: I 396 GLU cc_start: 0.7325 (mt-10) cc_final: 0.6923 (mt-10) REVERT: J 38 GLU cc_start: 0.7731 (mm-30) cc_final: 0.7370 (mm-30) REVERT: J 40 ARG cc_start: 0.7414 (mtt180) cc_final: 0.7175 (mtt-85) REVERT: J 115 LYS cc_start: 0.8011 (mtmt) cc_final: 0.7786 (mtmt) REVERT: J 130 ARG cc_start: 0.8268 (ttm-80) cc_final: 0.8042 (ttm-80) REVERT: J 164 LYS cc_start: 0.8128 (pttt) cc_final: 0.7867 (pttt) REVERT: J 178 MET cc_start: 0.6010 (tpp) cc_final: 0.5702 (mpp) REVERT: J 246 GLU cc_start: 0.7437 (mt-10) cc_final: 0.7183 (mt-10) REVERT: J 319 ASP cc_start: 0.7048 (p0) cc_final: 0.6814 (p0) REVERT: J 420 GLU cc_start: 0.7295 (mt-10) cc_final: 0.6987 (mt-10) REVERT: J 436 GLU cc_start: 0.6784 (tm-30) cc_final: 0.6354 (tm-30) REVERT: J 441 GLN cc_start: 0.6741 (mm110) cc_final: 0.6343 (mm110) REVERT: L 37 ARG cc_start: 0.6302 (mtt90) cc_final: 0.5942 (mtt90) REVERT: L 68 LYS cc_start: 0.8070 (mtpt) cc_final: 0.7769 (mtpt) REVERT: L 81 ASP cc_start: 0.8200 (m-30) cc_final: 0.7687 (m-30) REVERT: L 136 ILE cc_start: 0.8556 (tt) cc_final: 0.8212 (pt) REVERT: L 191 LYS cc_start: 0.8411 (ttmt) cc_final: 0.8093 (ttmt) REVERT: L 227 MET cc_start: 0.7044 (mmm) cc_final: 0.6756 (mmm) REVERT: L 306 TYR cc_start: 0.8668 (m-80) cc_final: 0.8215 (m-80) REVERT: L 313 MET cc_start: 0.8093 (mmm) cc_final: 0.7853 (mmm) REVERT: M 17 ASP cc_start: 0.7625 (t70) cc_final: 0.7392 (t0) REVERT: M 21 TYR cc_start: 0.8323 (t80) cc_final: 0.7885 (t80) REVERT: M 30 GLU cc_start: 0.8070 (mm-30) cc_final: 0.7840 (mm-30) REVERT: M 43 MET cc_start: 0.7416 (tmm) cc_final: 0.6963 (tmm) REVERT: M 95 ASP cc_start: 0.7648 (t0) cc_final: 0.7066 (t0) REVERT: M 96 TRP cc_start: 0.8484 (m100) cc_final: 0.8283 (m100) REVERT: M 100 GLN cc_start: 0.8242 (mt0) cc_final: 0.7923 (mt0) REVERT: M 142 GLU cc_start: 0.7710 (mm-30) cc_final: 0.7378 (mm-30) REVERT: M 200 ASP cc_start: 0.7966 (m-30) cc_final: 0.7616 (m-30) REVERT: M 231 GLU cc_start: 0.7690 (pm20) cc_final: 0.7437 (pm20) REVERT: M 271 ASP cc_start: 0.7999 (t0) cc_final: 0.7568 (t0) REVERT: M 354 ASN cc_start: 0.8596 (t0) cc_final: 0.8100 (t0) REVERT: M 379 LYS cc_start: 0.7945 (tptt) cc_final: 0.7605 (tptt) REVERT: M 413 LYS cc_start: 0.8397 (tttm) cc_final: 0.8097 (tttm) REVERT: N 66 LYS cc_start: 0.8068 (mtmt) cc_final: 0.7779 (mtmt) REVERT: N 106 LYS cc_start: 0.8441 (ptpt) cc_final: 0.8165 (ptpt) REVERT: N 128 ARG cc_start: 0.7410 (ttm170) cc_final: 0.7185 (ttm170) REVERT: N 138 TYR cc_start: 0.8488 (p90) cc_final: 0.8114 (p90) REVERT: N 149 ASP cc_start: 0.7758 (t0) cc_final: 0.7533 (t0) REVERT: N 158 ASP cc_start: 0.8040 (m-30) cc_final: 0.7717 (m-30) REVERT: N 176 ASP cc_start: 0.7772 (t70) cc_final: 0.7390 (t70) REVERT: N 177 ARG cc_start: 0.7926 (mmt-90) cc_final: 0.7525 (mmt-90) REVERT: N 190 ASP cc_start: 0.7408 (m-30) cc_final: 0.7054 (m-30) REVERT: N 193 GLU cc_start: 0.7605 (tp30) cc_final: 0.7166 (tp30) REVERT: N 225 ARG cc_start: 0.7764 (OUTLIER) cc_final: 0.7464 (mtt90) outliers start: 92 outliers final: 72 residues processed: 1315 average time/residue: 0.2821 time to fit residues: 551.7852 Evaluate side-chains 1345 residues out of total 3673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 1268 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 842 ARG Chi-restraints excluded: chain A residue 1339 VAL Chi-restraints excluded: chain A residue 1384 VAL Chi-restraints excluded: chain A residue 1465 GLN Chi-restraints excluded: chain A residue 1893 VAL Chi-restraints excluded: chain A residue 1937 HIS Chi-restraints excluded: chain A residue 1968 CYS Chi-restraints excluded: chain A residue 2201 LEU Chi-restraints excluded: chain A residue 2223 TYR Chi-restraints excluded: chain A residue 2271 GLU Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain C residue 444 THR Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 159 ILE Chi-restraints excluded: chain E residue 259 MET Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 356 ASP Chi-restraints excluded: chain E residue 387 SER Chi-restraints excluded: chain E residue 415 LEU Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 184 LYS Chi-restraints excluded: chain F residue 236 LYS Chi-restraints excluded: chain F residue 319 ASP Chi-restraints excluded: chain F residue 326 MET Chi-restraints excluded: chain F residue 382 MET Chi-restraints excluded: chain F residue 392 ARG Chi-restraints excluded: chain G residue 17 SER Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 293 GLU Chi-restraints excluded: chain G residue 295 VAL Chi-restraints excluded: chain G residue 313 THR Chi-restraints excluded: chain G residue 337 VAL Chi-restraints excluded: chain G residue 403 LEU Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 130 ARG Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain H residue 161 LEU Chi-restraints excluded: chain H residue 170 THR Chi-restraints excluded: chain H residue 177 LYS Chi-restraints excluded: chain H residue 195 ILE Chi-restraints excluded: chain H residue 258 LEU Chi-restraints excluded: chain H residue 326 MET Chi-restraints excluded: chain H residue 333 THR Chi-restraints excluded: chain H residue 360 THR Chi-restraints excluded: chain H residue 407 THR Chi-restraints excluded: chain I residue 97 VAL Chi-restraints excluded: chain I residue 125 LYS Chi-restraints excluded: chain I residue 208 THR Chi-restraints excluded: chain I residue 237 ASP Chi-restraints excluded: chain I residue 365 LEU Chi-restraints excluded: chain I residue 439 ASP Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 248 ASP Chi-restraints excluded: chain J residue 252 SER Chi-restraints excluded: chain J residue 326 MET Chi-restraints excluded: chain J residue 342 SER Chi-restraints excluded: chain J residue 359 THR Chi-restraints excluded: chain J residue 405 LEU Chi-restraints excluded: chain J residue 437 SER Chi-restraints excluded: chain L residue 118 LYS Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain L residue 186 THR Chi-restraints excluded: chain L residue 238 LYS Chi-restraints excluded: chain M residue 85 ILE Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain M residue 202 ILE Chi-restraints excluded: chain M residue 213 MET Chi-restraints excluded: chain M residue 222 MET Chi-restraints excluded: chain M residue 273 THR Chi-restraints excluded: chain M residue 304 ILE Chi-restraints excluded: chain M residue 385 THR Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 164 SER Chi-restraints excluded: chain N residue 225 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 152 optimal weight: 0.0020 chunk 171 optimal weight: 0.0980 chunk 276 optimal weight: 3.9990 chunk 158 optimal weight: 0.8980 chunk 234 optimal weight: 2.9990 chunk 392 optimal weight: 3.9990 chunk 157 optimal weight: 0.9990 chunk 396 optimal weight: 0.6980 chunk 174 optimal weight: 0.9990 chunk 410 optimal weight: 3.9990 chunk 411 optimal weight: 0.9980 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1894 GLN E 241 HIS E 373 GLN E 393 HIS F 44 GLN ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 233 GLN ** F 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 85 GLN G 115 ASN G 203 GLN H 25 HIS H 302 HIS ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 408 GLN J 44 GLN M 263 GLN M 407 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.148348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.129625 restraints weight = 51393.999| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 2.13 r_work: 0.3448 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 34579 Z= 0.123 Angle : 0.494 10.181 46733 Z= 0.257 Chirality : 0.041 0.172 5327 Planarity : 0.004 0.046 5974 Dihedral : 8.232 160.546 4826 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.59 % Allowed : 15.41 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.55 (0.13), residues: 4227 helix: 1.69 (0.12), residues: 1888 sheet: 0.29 (0.19), residues: 724 loop : 0.77 (0.16), residues: 1615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 205 TYR 0.040 0.001 TYR A1336 PHE 0.037 0.001 PHE E 177 TRP 0.014 0.001 TRP N 152 HIS 0.007 0.001 HIS E 241 Details of bonding type rmsd covalent geometry : bond 0.00272 (34579) covalent geometry : angle 0.49446 (46733) hydrogen bonds : bond 0.03698 ( 1532) hydrogen bonds : angle 4.12537 ( 4341) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8454 Ramachandran restraints generated. 4227 Oldfield, 0 Emsley, 4227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8454 Ramachandran restraints generated. 4227 Oldfield, 0 Emsley, 4227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1388 residues out of total 3673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 1293 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 789 ARG cc_start: 0.7983 (ttm170) cc_final: 0.7719 (ttm170) REVERT: A 793 LEU cc_start: 0.8010 (mp) cc_final: 0.7726 (tp) REVERT: A 822 MET cc_start: 0.8704 (tpp) cc_final: 0.8503 (mmm) REVERT: A 841 VAL cc_start: 0.8569 (t) cc_final: 0.8355 (p) REVERT: A 851 LYS cc_start: 0.8164 (tttt) cc_final: 0.7823 (tttt) REVERT: A 1319 LYS cc_start: 0.7095 (tttt) cc_final: 0.6811 (tttt) REVERT: A 1389 GLU cc_start: 0.8039 (tt0) cc_final: 0.7645 (tm-30) REVERT: A 1390 TYR cc_start: 0.7624 (t80) cc_final: 0.7293 (t80) REVERT: A 1409 ASP cc_start: 0.7864 (t0) cc_final: 0.7428 (t0) REVERT: A 1413 PHE cc_start: 0.8508 (m-80) cc_final: 0.7940 (m-80) REVERT: A 1442 GLU cc_start: 0.7849 (mt-10) cc_final: 0.7396 (mt-10) REVERT: A 1746 LEU cc_start: 0.8002 (tp) cc_final: 0.7773 (tp) REVERT: A 1896 ASP cc_start: 0.7364 (m-30) cc_final: 0.6909 (m-30) REVERT: A 1941 TYR cc_start: 0.7032 (p90) cc_final: 0.6488 (p90) REVERT: A 1952 GLN cc_start: 0.7123 (mm-40) cc_final: 0.6846 (mm110) REVERT: A 1957 MET cc_start: 0.7730 (tpp) cc_final: 0.7464 (tpp) REVERT: A 2225 ARG cc_start: 0.8088 (ttm-80) cc_final: 0.7546 (ttt90) REVERT: A 2226 GLU cc_start: 0.7587 (mp0) cc_final: 0.7191 (mp0) REVERT: A 2227 ASP cc_start: 0.7865 (m-30) cc_final: 0.7653 (m-30) REVERT: A 2236 GLU cc_start: 0.6838 (mp0) cc_final: 0.6574 (mp0) REVERT: A 2243 GLU cc_start: 0.7257 (tt0) cc_final: 0.6873 (tt0) REVERT: A 2269 MET cc_start: 0.7948 (mmm) cc_final: 0.7475 (mmm) REVERT: A 2271 GLU cc_start: 0.6737 (OUTLIER) cc_final: 0.6110 (pp20) REVERT: C 530 ARG cc_start: 0.7317 (ptp-110) cc_final: 0.7060 (ptp-170) REVERT: E 100 GLU cc_start: 0.7316 (mt-10) cc_final: 0.7078 (mt-10) REVERT: E 134 GLU cc_start: 0.7617 (tm-30) cc_final: 0.7363 (pp20) REVERT: E 259 MET cc_start: 0.7272 (OUTLIER) cc_final: 0.6873 (mmm) REVERT: E 260 MET cc_start: 0.7528 (mmm) cc_final: 0.7161 (mmm) REVERT: E 264 MET cc_start: 0.6561 (mmm) cc_final: 0.6150 (mmm) REVERT: E 278 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7497 (mm-30) REVERT: E 281 LYS cc_start: 0.7767 (mtmm) cc_final: 0.7490 (mtmm) REVERT: E 288 ASP cc_start: 0.8012 (t0) cc_final: 0.7779 (t0) REVERT: E 306 MET cc_start: 0.8087 (mmp) cc_final: 0.7834 (mmm) REVERT: E 364 MET cc_start: 0.7235 (mtm) cc_final: 0.6817 (mtm) REVERT: E 376 LYS cc_start: 0.8205 (tptm) cc_final: 0.7857 (tptm) REVERT: E 381 THR cc_start: 0.8284 (m) cc_final: 0.7630 (p) REVERT: E 392 ASN cc_start: 0.7884 (m-40) cc_final: 0.7577 (m-40) REVERT: F 20 GLU cc_start: 0.7595 (mp0) cc_final: 0.7141 (mp0) REVERT: F 38 GLU cc_start: 0.7160 (tp30) cc_final: 0.6874 (mm-30) REVERT: F 49 GLN cc_start: 0.8056 (mm110) cc_final: 0.7809 (mm110) REVERT: F 78 GLN cc_start: 0.7412 (mm110) cc_final: 0.6929 (mm110) REVERT: F 101 THR cc_start: 0.8014 (m) cc_final: 0.7673 (p) REVERT: F 167 GLU cc_start: 0.7891 (mm-30) cc_final: 0.7656 (mm-30) REVERT: F 180 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7701 (tp30) REVERT: F 185 ASP cc_start: 0.7819 (t70) cc_final: 0.7464 (t0) REVERT: F 242 VAL cc_start: 0.7788 (m) cc_final: 0.7506 (p) REVERT: F 274 GLU cc_start: 0.7646 (mt-10) cc_final: 0.7439 (mt-10) REVERT: F 326 MET cc_start: 0.8513 (OUTLIER) cc_final: 0.8239 (mtm) REVERT: F 348 ILE cc_start: 0.7883 (tt) cc_final: 0.7621 (pt) REVERT: F 381 GLU cc_start: 0.7469 (mm-30) cc_final: 0.7141 (mm-30) REVERT: F 410 SER cc_start: 0.8142 (t) cc_final: 0.7831 (t) REVERT: F 414 ARG cc_start: 0.7162 (mtm-85) cc_final: 0.6791 (mtm-85) REVERT: F 420 GLU cc_start: 0.6987 (tt0) cc_final: 0.6576 (tt0) REVERT: G 19 SER cc_start: 0.8190 (m) cc_final: 0.7747 (p) REVERT: G 64 ARG cc_start: 0.7484 (mmm160) cc_final: 0.6820 (mmm160) REVERT: G 110 GLU cc_start: 0.7855 (tp30) cc_final: 0.7539 (tp30) REVERT: G 180 LEU cc_start: 0.8763 (mt) cc_final: 0.8422 (mt) REVERT: G 205 ARG cc_start: 0.7932 (mmm160) cc_final: 0.7552 (mtp-110) REVERT: G 260 MET cc_start: 0.5463 (tmm) cc_final: 0.5076 (tmm) REVERT: G 267 LYS cc_start: 0.7844 (ptpt) cc_final: 0.7509 (ptpt) REVERT: G 285 LYS cc_start: 0.8095 (mtpt) cc_final: 0.7803 (mtpt) REVERT: G 357 ARG cc_start: 0.7908 (mtt90) cc_final: 0.7621 (mtt90) REVERT: G 362 ARG cc_start: 0.8073 (ptm160) cc_final: 0.7660 (ttm170) REVERT: G 369 GLN cc_start: 0.7247 (mp10) cc_final: 0.6591 (mp10) REVERT: G 372 LYS cc_start: 0.7500 (mttp) cc_final: 0.7171 (mttp) REVERT: G 411 THR cc_start: 0.8098 (t) cc_final: 0.7835 (m) REVERT: G 414 ASN cc_start: 0.7725 (t0) cc_final: 0.7393 (t0) REVERT: G 418 LYS cc_start: 0.7752 (ttmt) cc_final: 0.7530 (ttmt) REVERT: H 18 ARG cc_start: 0.7187 (mtp85) cc_final: 0.6860 (mtp85) REVERT: H 88 MET cc_start: 0.7982 (mmm) cc_final: 0.7686 (mmm) REVERT: H 134 GLU cc_start: 0.7878 (mt-10) cc_final: 0.7128 (mt-10) REVERT: H 178 MET cc_start: 0.7842 (mmm) cc_final: 0.7555 (tpp) REVERT: H 180 GLU cc_start: 0.8038 (mm-30) cc_final: 0.7556 (mm-30) REVERT: H 184 LYS cc_start: 0.8310 (mmpt) cc_final: 0.7909 (mmpt) REVERT: H 201 LYS cc_start: 0.8019 (mmmm) cc_final: 0.7716 (mmmm) REVERT: H 235 ARG cc_start: 0.7799 (ttt180) cc_final: 0.7372 (ttt180) REVERT: H 248 ASP cc_start: 0.7388 (m-30) cc_final: 0.7125 (m-30) REVERT: H 271 GLU cc_start: 0.7247 (mp0) cc_final: 0.6933 (mp0) REVERT: H 274 GLU cc_start: 0.7404 (mt-10) cc_final: 0.6993 (mt-10) REVERT: H 282 GLU cc_start: 0.7765 (tt0) cc_final: 0.7498 (tt0) REVERT: H 352 ASP cc_start: 0.7333 (m-30) cc_final: 0.6954 (m-30) REVERT: H 379 ASP cc_start: 0.7178 (t0) cc_final: 0.6959 (t0) REVERT: H 381 GLU cc_start: 0.7629 (mm-30) cc_final: 0.7273 (mm-30) REVERT: H 389 VAL cc_start: 0.7889 (m) cc_final: 0.7579 (p) REVERT: H 396 GLU cc_start: 0.7681 (mm-30) cc_final: 0.7438 (mm-30) REVERT: H 397 THR cc_start: 0.8114 (p) cc_final: 0.7892 (p) REVERT: H 435 ASP cc_start: 0.7667 (p0) cc_final: 0.7418 (p0) REVERT: I 17 SER cc_start: 0.8022 (m) cc_final: 0.7668 (p) REVERT: I 47 GLU cc_start: 0.7175 (mt-10) cc_final: 0.6851 (mt-10) REVERT: I 60 LYS cc_start: 0.7934 (ttmt) cc_final: 0.7677 (ttmt) REVERT: I 113 MET cc_start: 0.7363 (tpp) cc_final: 0.6943 (tpp) REVERT: I 130 VAL cc_start: 0.8735 (t) cc_final: 0.8400 (m) REVERT: I 249 ARG cc_start: 0.7569 (tmm160) cc_final: 0.7155 (tmm160) REVERT: I 260 MET cc_start: 0.6914 (mtt) cc_final: 0.5985 (mtt) REVERT: I 264 MET cc_start: 0.6580 (ptp) cc_final: 0.6168 (ptp) REVERT: I 284 ASN cc_start: 0.8261 (m-40) cc_final: 0.7588 (m110) REVERT: I 344 ILE cc_start: 0.6735 (mt) cc_final: 0.6521 (mp) REVERT: I 346 SER cc_start: 0.7991 (t) cc_final: 0.7755 (t) REVERT: I 372 LYS cc_start: 0.8100 (mtpt) cc_final: 0.7752 (mtpt) REVERT: I 392 ASN cc_start: 0.7623 (m-40) cc_final: 0.7416 (m-40) REVERT: I 396 GLU cc_start: 0.7377 (mt-10) cc_final: 0.7046 (mt-10) REVERT: I 414 ASN cc_start: 0.7824 (t0) cc_final: 0.7599 (t0) REVERT: J 38 GLU cc_start: 0.7738 (mm-30) cc_final: 0.7384 (mm-30) REVERT: J 40 ARG cc_start: 0.7430 (mtt180) cc_final: 0.7200 (mtt-85) REVERT: J 115 LYS cc_start: 0.7995 (mtmt) cc_final: 0.7766 (mtmt) REVERT: J 130 ARG cc_start: 0.8241 (ttm-80) cc_final: 0.8015 (ttm-80) REVERT: J 164 LYS cc_start: 0.8078 (pttt) cc_final: 0.7817 (pttt) REVERT: J 178 MET cc_start: 0.5982 (tpp) cc_final: 0.5744 (mpp) REVERT: J 246 GLU cc_start: 0.7433 (mt-10) cc_final: 0.7222 (mt-10) REVERT: J 319 ASP cc_start: 0.7042 (p0) cc_final: 0.6804 (p0) REVERT: J 420 GLU cc_start: 0.7270 (mt-10) cc_final: 0.6968 (mt-10) REVERT: J 441 GLN cc_start: 0.6749 (mm110) cc_final: 0.6348 (mm110) REVERT: L 37 ARG cc_start: 0.6328 (mtt90) cc_final: 0.5981 (mtt90) REVERT: L 68 LYS cc_start: 0.8061 (mtpt) cc_final: 0.7754 (mtpt) REVERT: L 81 ASP cc_start: 0.8211 (m-30) cc_final: 0.7763 (m-30) REVERT: L 133 TYR cc_start: 0.8597 (t80) cc_final: 0.8291 (t80) REVERT: L 136 ILE cc_start: 0.8552 (tt) cc_final: 0.8236 (pt) REVERT: L 191 LYS cc_start: 0.8408 (ttmt) cc_final: 0.8090 (ttmt) REVERT: L 227 MET cc_start: 0.7039 (mmm) cc_final: 0.6766 (mmm) REVERT: L 306 TYR cc_start: 0.8659 (m-80) cc_final: 0.8199 (m-80) REVERT: L 315 LYS cc_start: 0.8540 (OUTLIER) cc_final: 0.8265 (ptmm) REVERT: M 9 ASP cc_start: 0.7009 (t0) cc_final: 0.6671 (t0) REVERT: M 21 TYR cc_start: 0.8302 (t80) cc_final: 0.7875 (t80) REVERT: M 30 GLU cc_start: 0.8083 (mm-30) cc_final: 0.7871 (mm-30) REVERT: M 43 MET cc_start: 0.7396 (tmm) cc_final: 0.6945 (tmm) REVERT: M 79 ARG cc_start: 0.8004 (ttm-80) cc_final: 0.7751 (ttm-80) REVERT: M 95 ASP cc_start: 0.7629 (t0) cc_final: 0.7031 (t0) REVERT: M 96 TRP cc_start: 0.8469 (m100) cc_final: 0.8265 (m100) REVERT: M 100 GLN cc_start: 0.8224 (mt0) cc_final: 0.7897 (mt0) REVERT: M 142 GLU cc_start: 0.7674 (mm-30) cc_final: 0.7321 (mm-30) REVERT: M 200 ASP cc_start: 0.7894 (m-30) cc_final: 0.7551 (m-30) REVERT: M 222 MET cc_start: 0.8242 (mtm) cc_final: 0.8037 (mtm) REVERT: M 231 GLU cc_start: 0.7691 (pm20) cc_final: 0.7432 (pm20) REVERT: M 354 ASN cc_start: 0.8609 (t0) cc_final: 0.8100 (t0) REVERT: M 379 LYS cc_start: 0.7982 (tptt) cc_final: 0.7637 (tptt) REVERT: M 413 LYS cc_start: 0.8391 (tttm) cc_final: 0.8080 (tttm) REVERT: N 66 LYS cc_start: 0.8053 (mtmt) cc_final: 0.7842 (mtmt) REVERT: N 106 LYS cc_start: 0.8439 (ptpt) cc_final: 0.8166 (ptpt) REVERT: N 128 ARG cc_start: 0.7427 (ttm170) cc_final: 0.7188 (ttm170) REVERT: N 138 TYR cc_start: 0.8509 (p90) cc_final: 0.8140 (p90) REVERT: N 149 ASP cc_start: 0.7737 (t0) cc_final: 0.7534 (t0) REVERT: N 158 ASP cc_start: 0.8047 (m-30) cc_final: 0.7722 (m-30) REVERT: N 176 ASP cc_start: 0.7743 (t70) cc_final: 0.7433 (t70) REVERT: N 190 ASP cc_start: 0.7380 (m-30) cc_final: 0.7068 (m-30) REVERT: N 193 GLU cc_start: 0.7539 (tp30) cc_final: 0.7087 (tp30) REVERT: N 201 LYS cc_start: 0.8600 (tptm) cc_final: 0.8369 (tptm) REVERT: N 225 ARG cc_start: 0.7769 (mtp85) cc_final: 0.7494 (mtt90) outliers start: 95 outliers final: 68 residues processed: 1319 average time/residue: 0.2683 time to fit residues: 529.5266 Evaluate side-chains 1351 residues out of total 3673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 1279 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 842 ARG Chi-restraints excluded: chain A residue 1339 VAL Chi-restraints excluded: chain A residue 1465 GLN Chi-restraints excluded: chain A residue 1893 VAL Chi-restraints excluded: chain A residue 1937 HIS Chi-restraints excluded: chain A residue 1968 CYS Chi-restraints excluded: chain A residue 2201 LEU Chi-restraints excluded: chain A residue 2223 TYR Chi-restraints excluded: chain A residue 2264 SER Chi-restraints excluded: chain A residue 2271 GLU Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain C residue 426 THR Chi-restraints excluded: chain C residue 444 THR Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 159 ILE Chi-restraints excluded: chain E residue 212 GLU Chi-restraints excluded: chain E residue 259 MET Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 415 LEU Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 184 LYS Chi-restraints excluded: chain F residue 195 ILE Chi-restraints excluded: chain F residue 233 GLN Chi-restraints excluded: chain F residue 236 LYS Chi-restraints excluded: chain F residue 291 ILE Chi-restraints excluded: chain F residue 319 ASP Chi-restraints excluded: chain F residue 326 MET Chi-restraints excluded: chain F residue 382 MET Chi-restraints excluded: chain F residue 392 ARG Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 295 VAL Chi-restraints excluded: chain G residue 313 THR Chi-restraints excluded: chain G residue 337 VAL Chi-restraints excluded: chain G residue 403 LEU Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 130 ARG Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain H residue 161 LEU Chi-restraints excluded: chain H residue 170 THR Chi-restraints excluded: chain H residue 177 LYS Chi-restraints excluded: chain H residue 195 ILE Chi-restraints excluded: chain H residue 258 LEU Chi-restraints excluded: chain H residue 326 MET Chi-restraints excluded: chain H residue 333 THR Chi-restraints excluded: chain H residue 360 THR Chi-restraints excluded: chain H residue 407 THR Chi-restraints excluded: chain I residue 97 VAL Chi-restraints excluded: chain I residue 208 THR Chi-restraints excluded: chain I residue 365 LEU Chi-restraints excluded: chain I residue 439 ASP Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 248 ASP Chi-restraints excluded: chain J residue 252 SER Chi-restraints excluded: chain J residue 326 MET Chi-restraints excluded: chain J residue 342 SER Chi-restraints excluded: chain J residue 359 THR Chi-restraints excluded: chain J residue 405 LEU Chi-restraints excluded: chain J residue 437 SER Chi-restraints excluded: chain L residue 118 LYS Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain L residue 186 THR Chi-restraints excluded: chain L residue 238 LYS Chi-restraints excluded: chain L residue 315 LYS Chi-restraints excluded: chain M residue 85 ILE Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain M residue 385 THR Chi-restraints excluded: chain M residue 408 GLN Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 164 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 419 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 244 optimal weight: 1.9990 chunk 313 optimal weight: 0.9980 chunk 346 optimal weight: 2.9990 chunk 287 optimal weight: 0.7980 chunk 421 optimal weight: 5.9990 chunk 213 optimal weight: 0.7980 chunk 408 optimal weight: 5.9990 chunk 252 optimal weight: 3.9990 chunk 88 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 241 HIS E 247 ASN E 373 GLN E 393 HIS E 408 GLN ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 121 GLN F 233 GLN ** F 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 85 GLN G 115 ASN ** G 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 25 HIS ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 44 GLN M 263 GLN M 407 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.147837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.128997 restraints weight = 51097.930| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 2.13 r_work: 0.3433 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3252 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 34579 Z= 0.160 Angle : 0.523 8.991 46733 Z= 0.272 Chirality : 0.042 0.175 5327 Planarity : 0.004 0.050 5974 Dihedral : 8.325 162.045 4826 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.26 % Allowed : 16.04 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.47 (0.13), residues: 4227 helix: 1.63 (0.12), residues: 1889 sheet: 0.28 (0.19), residues: 720 loop : 0.72 (0.16), residues: 1618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 317 TYR 0.037 0.001 TYR A1336 PHE 0.039 0.002 PHE E 177 TRP 0.012 0.001 TRP A1405 HIS 0.008 0.001 HIS E 241 Details of bonding type rmsd covalent geometry : bond 0.00355 (34579) covalent geometry : angle 0.52282 (46733) hydrogen bonds : bond 0.04053 ( 1532) hydrogen bonds : angle 4.19442 ( 4341) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8454 Ramachandran restraints generated. 4227 Oldfield, 0 Emsley, 4227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8454 Ramachandran restraints generated. 4227 Oldfield, 0 Emsley, 4227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1380 residues out of total 3673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 1297 time to evaluate : 1.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 789 ARG cc_start: 0.7993 (ttm170) cc_final: 0.7731 (ttm170) REVERT: A 793 LEU cc_start: 0.8018 (mp) cc_final: 0.7728 (tp) REVERT: A 822 MET cc_start: 0.8713 (tpp) cc_final: 0.8489 (mmm) REVERT: A 841 VAL cc_start: 0.8588 (t) cc_final: 0.8363 (p) REVERT: A 851 LYS cc_start: 0.8138 (tttt) cc_final: 0.7785 (tttt) REVERT: A 1319 LYS cc_start: 0.7190 (tttt) cc_final: 0.6885 (tttt) REVERT: A 1389 GLU cc_start: 0.8053 (tt0) cc_final: 0.7766 (tm-30) REVERT: A 1390 TYR cc_start: 0.7609 (t80) cc_final: 0.7361 (t80) REVERT: A 1409 ASP cc_start: 0.8005 (t0) cc_final: 0.7592 (t0) REVERT: A 1413 PHE cc_start: 0.8500 (m-80) cc_final: 0.7971 (m-80) REVERT: A 1746 LEU cc_start: 0.8040 (tp) cc_final: 0.7810 (tp) REVERT: A 1767 TYR cc_start: 0.8060 (m-80) cc_final: 0.7819 (m-80) REVERT: A 1896 ASP cc_start: 0.7382 (m-30) cc_final: 0.6960 (m-30) REVERT: A 1941 TYR cc_start: 0.7116 (p90) cc_final: 0.6560 (p90) REVERT: A 1952 GLN cc_start: 0.7157 (mm-40) cc_final: 0.6885 (mm110) REVERT: A 1957 MET cc_start: 0.7734 (tpp) cc_final: 0.7488 (tpp) REVERT: A 2225 ARG cc_start: 0.8133 (ttm-80) cc_final: 0.7871 (ttt90) REVERT: A 2226 GLU cc_start: 0.7571 (mp0) cc_final: 0.7182 (mp0) REVERT: A 2236 GLU cc_start: 0.6844 (mp0) cc_final: 0.6563 (mp0) REVERT: A 2243 GLU cc_start: 0.7260 (tt0) cc_final: 0.6878 (tt0) REVERT: A 2269 MET cc_start: 0.7961 (mmm) cc_final: 0.7467 (mmm) REVERT: A 2271 GLU cc_start: 0.6761 (OUTLIER) cc_final: 0.6111 (pp20) REVERT: C 530 ARG cc_start: 0.7332 (ptp-110) cc_final: 0.7050 (ptp-170) REVERT: C 532 ARG cc_start: 0.6988 (ptt180) cc_final: 0.6592 (ppt170) REVERT: E 134 GLU cc_start: 0.7627 (tm-30) cc_final: 0.7361 (pp20) REVERT: E 259 MET cc_start: 0.7314 (OUTLIER) cc_final: 0.6883 (mmm) REVERT: E 260 MET cc_start: 0.7550 (mmm) cc_final: 0.7172 (mmm) REVERT: E 264 MET cc_start: 0.6598 (mmm) cc_final: 0.6180 (mmm) REVERT: E 278 GLU cc_start: 0.7727 (mm-30) cc_final: 0.7467 (mm-30) REVERT: E 281 LYS cc_start: 0.7771 (mtmm) cc_final: 0.7499 (mtmm) REVERT: E 288 ASP cc_start: 0.7988 (t0) cc_final: 0.7750 (t0) REVERT: E 306 MET cc_start: 0.8072 (mmp) cc_final: 0.7812 (mmm) REVERT: E 364 MET cc_start: 0.7263 (mtm) cc_final: 0.6838 (mtm) REVERT: E 376 LYS cc_start: 0.8193 (tptm) cc_final: 0.7833 (tptm) REVERT: E 381 THR cc_start: 0.8290 (m) cc_final: 0.7656 (p) REVERT: E 392 ASN cc_start: 0.7863 (m-40) cc_final: 0.7555 (m-40) REVERT: F 20 GLU cc_start: 0.7636 (mp0) cc_final: 0.7178 (mp0) REVERT: F 38 GLU cc_start: 0.7174 (tp30) cc_final: 0.6882 (mm-30) REVERT: F 49 GLN cc_start: 0.8038 (mm110) cc_final: 0.7792 (mm110) REVERT: F 78 GLN cc_start: 0.7372 (mm110) cc_final: 0.6874 (mm110) REVERT: F 101 THR cc_start: 0.8033 (m) cc_final: 0.7617 (p) REVERT: F 166 THR cc_start: 0.8014 (p) cc_final: 0.6858 (m) REVERT: F 167 GLU cc_start: 0.7875 (mm-30) cc_final: 0.7540 (mm-30) REVERT: F 180 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7717 (tp30) REVERT: F 185 ASP cc_start: 0.7819 (t70) cc_final: 0.7469 (t0) REVERT: F 197 LYS cc_start: 0.8464 (mtmt) cc_final: 0.8255 (mtmt) REVERT: F 242 VAL cc_start: 0.7820 (m) cc_final: 0.7482 (p) REVERT: F 274 GLU cc_start: 0.7684 (mt-10) cc_final: 0.7474 (mt-10) REVERT: F 381 GLU cc_start: 0.7437 (mm-30) cc_final: 0.7104 (mm-30) REVERT: F 410 SER cc_start: 0.8141 (t) cc_final: 0.7774 (t) REVERT: F 414 ARG cc_start: 0.7177 (mtm-85) cc_final: 0.6797 (mtm-85) REVERT: F 420 GLU cc_start: 0.7007 (tt0) cc_final: 0.6595 (tt0) REVERT: G 19 SER cc_start: 0.8186 (m) cc_final: 0.7735 (p) REVERT: G 64 ARG cc_start: 0.7504 (mmm160) cc_final: 0.6830 (mmm160) REVERT: G 180 LEU cc_start: 0.8761 (mt) cc_final: 0.8435 (mt) REVERT: G 205 ARG cc_start: 0.8034 (mmm160) cc_final: 0.7675 (mtp-110) REVERT: G 260 MET cc_start: 0.5464 (tmm) cc_final: 0.5067 (tmm) REVERT: G 267 LYS cc_start: 0.7880 (ptpt) cc_final: 0.7530 (ptpt) REVERT: G 285 LYS cc_start: 0.8094 (mtpt) cc_final: 0.7801 (mtpt) REVERT: G 357 ARG cc_start: 0.7901 (mtt90) cc_final: 0.7627 (mtt90) REVERT: G 362 ARG cc_start: 0.8111 (ptm160) cc_final: 0.7693 (ttm170) REVERT: G 369 GLN cc_start: 0.7250 (mp10) cc_final: 0.6577 (mp10) REVERT: G 372 LYS cc_start: 0.7477 (mttp) cc_final: 0.7159 (mttp) REVERT: G 411 THR cc_start: 0.8107 (t) cc_final: 0.7851 (m) REVERT: G 414 ASN cc_start: 0.7722 (t0) cc_final: 0.7402 (t0) REVERT: G 418 LYS cc_start: 0.7764 (ttmt) cc_final: 0.7545 (ttmt) REVERT: H 18 ARG cc_start: 0.7158 (mtp85) cc_final: 0.6850 (mtp85) REVERT: H 88 MET cc_start: 0.7966 (mmm) cc_final: 0.7661 (mmm) REVERT: H 134 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7190 (mt-10) REVERT: H 178 MET cc_start: 0.7819 (mmm) cc_final: 0.7535 (tpp) REVERT: H 180 GLU cc_start: 0.8054 (mm-30) cc_final: 0.7584 (mm-30) REVERT: H 184 LYS cc_start: 0.8316 (mmpt) cc_final: 0.7924 (mmpt) REVERT: H 201 LYS cc_start: 0.8050 (mmmm) cc_final: 0.7744 (mmmm) REVERT: H 235 ARG cc_start: 0.7736 (ttt180) cc_final: 0.7320 (ttt180) REVERT: H 248 ASP cc_start: 0.7389 (m-30) cc_final: 0.7151 (m-30) REVERT: H 271 GLU cc_start: 0.7265 (mp0) cc_final: 0.6894 (mp0) REVERT: H 274 GLU cc_start: 0.7409 (mt-10) cc_final: 0.6999 (mt-10) REVERT: H 282 GLU cc_start: 0.7757 (tt0) cc_final: 0.7486 (tt0) REVERT: H 352 ASP cc_start: 0.7391 (m-30) cc_final: 0.7011 (m-30) REVERT: H 379 ASP cc_start: 0.7194 (t0) cc_final: 0.6976 (t0) REVERT: H 381 GLU cc_start: 0.7598 (mm-30) cc_final: 0.7248 (mm-30) REVERT: H 389 VAL cc_start: 0.7889 (m) cc_final: 0.7586 (p) REVERT: H 396 GLU cc_start: 0.7687 (mm-30) cc_final: 0.7445 (mm-30) REVERT: H 397 THR cc_start: 0.8129 (p) cc_final: 0.7904 (p) REVERT: H 435 ASP cc_start: 0.7686 (p0) cc_final: 0.7409 (p0) REVERT: I 17 SER cc_start: 0.8026 (m) cc_final: 0.7673 (p) REVERT: I 42 GLN cc_start: 0.8217 (mm-40) cc_final: 0.8010 (mm-40) REVERT: I 47 GLU cc_start: 0.7148 (mt-10) cc_final: 0.6851 (mt-10) REVERT: I 60 LYS cc_start: 0.7982 (ttmt) cc_final: 0.7717 (ttmt) REVERT: I 113 MET cc_start: 0.7358 (tpp) cc_final: 0.6928 (tpp) REVERT: I 130 VAL cc_start: 0.8777 (t) cc_final: 0.8438 (m) REVERT: I 249 ARG cc_start: 0.7566 (tmm160) cc_final: 0.7162 (tmm160) REVERT: I 260 MET cc_start: 0.6974 (mtt) cc_final: 0.6035 (mtt) REVERT: I 264 MET cc_start: 0.6632 (ptp) cc_final: 0.6208 (ptp) REVERT: I 284 ASN cc_start: 0.8263 (m-40) cc_final: 0.7653 (m-40) REVERT: I 346 SER cc_start: 0.7970 (t) cc_final: 0.7716 (t) REVERT: I 372 LYS cc_start: 0.8097 (mtpt) cc_final: 0.7750 (mtpt) REVERT: I 376 LYS cc_start: 0.7962 (tptt) cc_final: 0.7699 (tptt) REVERT: I 392 ASN cc_start: 0.7639 (m-40) cc_final: 0.7417 (m-40) REVERT: I 396 GLU cc_start: 0.7271 (mt-10) cc_final: 0.6994 (mt-10) REVERT: I 414 ASN cc_start: 0.7792 (t0) cc_final: 0.7570 (t0) REVERT: I 429 HIS cc_start: 0.8101 (m90) cc_final: 0.7813 (m90) REVERT: J 38 GLU cc_start: 0.7756 (mm-30) cc_final: 0.7386 (mm-30) REVERT: J 40 ARG cc_start: 0.7395 (mtt180) cc_final: 0.7165 (mtt-85) REVERT: J 115 LYS cc_start: 0.8020 (mtmt) cc_final: 0.7754 (mtmt) REVERT: J 130 ARG cc_start: 0.8221 (ttm-80) cc_final: 0.8008 (ttm-80) REVERT: J 164 LYS cc_start: 0.8126 (pttt) cc_final: 0.7857 (pttt) REVERT: J 246 GLU cc_start: 0.7457 (mt-10) cc_final: 0.7236 (mt-10) REVERT: J 319 ASP cc_start: 0.7039 (p0) cc_final: 0.6788 (p0) REVERT: J 420 GLU cc_start: 0.7290 (mt-10) cc_final: 0.6984 (mt-10) REVERT: J 441 GLN cc_start: 0.6734 (mm110) cc_final: 0.6357 (mm110) REVERT: L 37 ARG cc_start: 0.6318 (mtt90) cc_final: 0.5955 (mtt90) REVERT: L 68 LYS cc_start: 0.8055 (mtpt) cc_final: 0.7746 (mtpt) REVERT: L 81 ASP cc_start: 0.8224 (m-30) cc_final: 0.7745 (m-30) REVERT: L 136 ILE cc_start: 0.8542 (tt) cc_final: 0.8221 (pt) REVERT: L 191 LYS cc_start: 0.8412 (ttmt) cc_final: 0.8099 (ttmt) REVERT: L 227 MET cc_start: 0.7089 (mmm) cc_final: 0.6775 (mmm) REVERT: L 306 TYR cc_start: 0.8661 (m-80) cc_final: 0.8203 (m-80) REVERT: L 315 LYS cc_start: 0.8539 (OUTLIER) cc_final: 0.8267 (ptmm) REVERT: M 9 ASP cc_start: 0.7015 (t0) cc_final: 0.6650 (t0) REVERT: M 21 TYR cc_start: 0.8319 (t80) cc_final: 0.7827 (t80) REVERT: M 30 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7879 (mm-30) REVERT: M 43 MET cc_start: 0.7471 (tmm) cc_final: 0.7009 (tmm) REVERT: M 79 ARG cc_start: 0.8036 (ttm-80) cc_final: 0.7782 (ttm-80) REVERT: M 95 ASP cc_start: 0.7650 (t0) cc_final: 0.7043 (t0) REVERT: M 100 GLN cc_start: 0.8254 (mt0) cc_final: 0.7927 (mt0) REVERT: M 142 GLU cc_start: 0.7704 (mm-30) cc_final: 0.7350 (mm-30) REVERT: M 200 ASP cc_start: 0.7928 (m-30) cc_final: 0.7583 (m-30) REVERT: M 231 GLU cc_start: 0.7650 (pm20) cc_final: 0.7387 (pm20) REVERT: M 265 SER cc_start: 0.8570 (p) cc_final: 0.8359 (p) REVERT: M 354 ASN cc_start: 0.8596 (t0) cc_final: 0.8093 (t0) REVERT: M 379 LYS cc_start: 0.7985 (tptt) cc_final: 0.7651 (tptt) REVERT: M 413 LYS cc_start: 0.8414 (tttm) cc_final: 0.8106 (tttm) REVERT: N 66 LYS cc_start: 0.8036 (mtmt) cc_final: 0.7829 (mtmt) REVERT: N 106 LYS cc_start: 0.8451 (ptpt) cc_final: 0.8171 (ptpt) REVERT: N 128 ARG cc_start: 0.7442 (ttm170) cc_final: 0.7204 (ttm170) REVERT: N 138 TYR cc_start: 0.8492 (p90) cc_final: 0.8099 (p90) REVERT: N 149 ASP cc_start: 0.7741 (t0) cc_final: 0.7534 (t0) REVERT: N 158 ASP cc_start: 0.8024 (m-30) cc_final: 0.7703 (m-30) REVERT: N 176 ASP cc_start: 0.7731 (t70) cc_final: 0.7424 (t70) REVERT: N 190 ASP cc_start: 0.7370 (m-30) cc_final: 0.7044 (m-30) REVERT: N 193 GLU cc_start: 0.7590 (tp30) cc_final: 0.7138 (tp30) REVERT: N 225 ARG cc_start: 0.7762 (mtp85) cc_final: 0.7458 (mtt90) outliers start: 83 outliers final: 71 residues processed: 1316 average time/residue: 0.2578 time to fit residues: 508.4814 Evaluate side-chains 1355 residues out of total 3673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 1281 time to evaluate : 1.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 842 ARG Chi-restraints excluded: chain A residue 1339 VAL Chi-restraints excluded: chain A residue 1465 GLN Chi-restraints excluded: chain A residue 1761 CYS Chi-restraints excluded: chain A residue 1773 ARG Chi-restraints excluded: chain A residue 1893 VAL Chi-restraints excluded: chain A residue 1937 HIS Chi-restraints excluded: chain A residue 1968 CYS Chi-restraints excluded: chain A residue 2201 LEU Chi-restraints excluded: chain A residue 2223 TYR Chi-restraints excluded: chain A residue 2264 SER Chi-restraints excluded: chain A residue 2271 GLU Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain C residue 426 THR Chi-restraints excluded: chain C residue 444 THR Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 159 ILE Chi-restraints excluded: chain E residue 212 GLU Chi-restraints excluded: chain E residue 259 MET Chi-restraints excluded: chain E residue 268 LYS Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 415 LEU Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 184 LYS Chi-restraints excluded: chain F residue 195 ILE Chi-restraints excluded: chain F residue 236 LYS Chi-restraints excluded: chain F residue 291 ILE Chi-restraints excluded: chain F residue 382 MET Chi-restraints excluded: chain F residue 392 ARG Chi-restraints excluded: chain G residue 17 SER Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 293 GLU Chi-restraints excluded: chain G residue 295 VAL Chi-restraints excluded: chain G residue 313 THR Chi-restraints excluded: chain G residue 337 VAL Chi-restraints excluded: chain G residue 403 LEU Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 130 ARG Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain H residue 170 THR Chi-restraints excluded: chain H residue 177 LYS Chi-restraints excluded: chain H residue 195 ILE Chi-restraints excluded: chain H residue 258 LEU Chi-restraints excluded: chain H residue 326 MET Chi-restraints excluded: chain H residue 333 THR Chi-restraints excluded: chain H residue 360 THR Chi-restraints excluded: chain H residue 407 THR Chi-restraints excluded: chain I residue 97 VAL Chi-restraints excluded: chain I residue 208 THR Chi-restraints excluded: chain I residue 365 LEU Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 90 MET Chi-restraints excluded: chain J residue 248 ASP Chi-restraints excluded: chain J residue 252 SER Chi-restraints excluded: chain J residue 326 MET Chi-restraints excluded: chain J residue 342 SER Chi-restraints excluded: chain J residue 359 THR Chi-restraints excluded: chain J residue 405 LEU Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain L residue 186 THR Chi-restraints excluded: chain L residue 238 LYS Chi-restraints excluded: chain L residue 315 LYS Chi-restraints excluded: chain M residue 85 ILE Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain M residue 128 ASN Chi-restraints excluded: chain M residue 273 THR Chi-restraints excluded: chain M residue 385 THR Chi-restraints excluded: chain M residue 408 GLN Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 164 SER Chi-restraints excluded: chain N residue 233 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 132 optimal weight: 2.9990 chunk 362 optimal weight: 2.9990 chunk 168 optimal weight: 0.6980 chunk 3 optimal weight: 0.7980 chunk 149 optimal weight: 2.9990 chunk 254 optimal weight: 1.9990 chunk 323 optimal weight: 0.9990 chunk 210 optimal weight: 0.9990 chunk 415 optimal weight: 3.9990 chunk 318 optimal weight: 0.1980 chunk 51 optimal weight: 0.7980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 241 HIS E 373 GLN E 393 HIS ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 121 GLN F 233 GLN ** F 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 115 ASN H 25 HIS ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 408 GLN J 44 GLN M 263 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.148242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.129413 restraints weight = 51418.863| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 2.13 r_work: 0.3438 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 34579 Z= 0.142 Angle : 0.517 9.257 46733 Z= 0.270 Chirality : 0.042 0.173 5327 Planarity : 0.004 0.089 5974 Dihedral : 8.271 162.354 4826 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.07 % Allowed : 16.61 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.48 (0.13), residues: 4227 helix: 1.65 (0.12), residues: 1881 sheet: 0.24 (0.19), residues: 722 loop : 0.74 (0.16), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 830 TYR 0.037 0.001 TYR A1336 PHE 0.040 0.001 PHE E 177 TRP 0.013 0.001 TRP A1405 HIS 0.008 0.001 HIS E 241 Details of bonding type rmsd covalent geometry : bond 0.00316 (34579) covalent geometry : angle 0.51696 (46733) hydrogen bonds : bond 0.03873 ( 1532) hydrogen bonds : angle 4.17253 ( 4341) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8454 Ramachandran restraints generated. 4227 Oldfield, 0 Emsley, 4227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8454 Ramachandran restraints generated. 4227 Oldfield, 0 Emsley, 4227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1354 residues out of total 3673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 1278 time to evaluate : 1.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 789 ARG cc_start: 0.7985 (ttm170) cc_final: 0.7718 (ttm170) REVERT: A 793 LEU cc_start: 0.8001 (mp) cc_final: 0.7707 (tp) REVERT: A 822 MET cc_start: 0.8705 (tpp) cc_final: 0.8493 (mmm) REVERT: A 841 VAL cc_start: 0.8578 (t) cc_final: 0.8363 (p) REVERT: A 851 LYS cc_start: 0.8141 (tttt) cc_final: 0.7786 (tttt) REVERT: A 1319 LYS cc_start: 0.7193 (tttt) cc_final: 0.6889 (tttt) REVERT: A 1389 GLU cc_start: 0.8045 (tt0) cc_final: 0.7766 (tm-30) REVERT: A 1390 TYR cc_start: 0.7609 (t80) cc_final: 0.7317 (t80) REVERT: A 1409 ASP cc_start: 0.7954 (t0) cc_final: 0.7511 (t0) REVERT: A 1413 PHE cc_start: 0.8452 (m-80) cc_final: 0.7977 (m-80) REVERT: A 1746 LEU cc_start: 0.8036 (tp) cc_final: 0.7825 (tp) REVERT: A 1896 ASP cc_start: 0.7348 (m-30) cc_final: 0.6932 (m-30) REVERT: A 1952 GLN cc_start: 0.7160 (mm-40) cc_final: 0.6892 (mm110) REVERT: A 1957 MET cc_start: 0.7759 (tpp) cc_final: 0.7529 (tpp) REVERT: A 1962 ARG cc_start: 0.7542 (ptp-170) cc_final: 0.7331 (ptp-170) REVERT: A 2225 ARG cc_start: 0.8122 (ttm-80) cc_final: 0.7863 (ttt90) REVERT: A 2226 GLU cc_start: 0.7558 (mp0) cc_final: 0.7164 (mp0) REVERT: A 2236 GLU cc_start: 0.6849 (mp0) cc_final: 0.6578 (mp0) REVERT: A 2243 GLU cc_start: 0.7267 (tt0) cc_final: 0.6890 (tt0) REVERT: A 2269 MET cc_start: 0.7957 (mmm) cc_final: 0.7462 (mmm) REVERT: A 2271 GLU cc_start: 0.6753 (OUTLIER) cc_final: 0.6092 (pp20) REVERT: C 530 ARG cc_start: 0.7309 (ptp-110) cc_final: 0.7031 (ptp-170) REVERT: C 532 ARG cc_start: 0.6990 (ptt180) cc_final: 0.6357 (ppt170) REVERT: E 134 GLU cc_start: 0.7613 (tm-30) cc_final: 0.7340 (pp20) REVERT: E 259 MET cc_start: 0.7301 (OUTLIER) cc_final: 0.6891 (mmm) REVERT: E 260 MET cc_start: 0.7549 (mmm) cc_final: 0.7167 (mmm) REVERT: E 264 MET cc_start: 0.6601 (mmm) cc_final: 0.6182 (mmm) REVERT: E 278 GLU cc_start: 0.7713 (mm-30) cc_final: 0.7441 (mm-30) REVERT: E 281 LYS cc_start: 0.7753 (mtmm) cc_final: 0.7473 (mtmm) REVERT: E 288 ASP cc_start: 0.7984 (t0) cc_final: 0.7744 (t0) REVERT: E 306 MET cc_start: 0.8081 (mmp) cc_final: 0.7748 (mmt) REVERT: E 364 MET cc_start: 0.7286 (mtm) cc_final: 0.6864 (mtm) REVERT: E 376 LYS cc_start: 0.8187 (tptm) cc_final: 0.7829 (tptm) REVERT: E 381 THR cc_start: 0.8286 (m) cc_final: 0.7645 (p) REVERT: E 392 ASN cc_start: 0.7861 (m-40) cc_final: 0.7550 (m-40) REVERT: F 20 GLU cc_start: 0.7652 (mp0) cc_final: 0.7194 (mp0) REVERT: F 38 GLU cc_start: 0.7160 (tp30) cc_final: 0.6871 (mm-30) REVERT: F 49 GLN cc_start: 0.8045 (mm110) cc_final: 0.7800 (mm110) REVERT: F 78 GLN cc_start: 0.7375 (mm110) cc_final: 0.6877 (mm110) REVERT: F 101 THR cc_start: 0.8030 (m) cc_final: 0.7646 (p) REVERT: F 166 THR cc_start: 0.7995 (p) cc_final: 0.6832 (m) REVERT: F 167 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7548 (mm-30) REVERT: F 180 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7722 (tp30) REVERT: F 185 ASP cc_start: 0.7804 (t70) cc_final: 0.7442 (t0) REVERT: F 242 VAL cc_start: 0.7809 (m) cc_final: 0.7491 (p) REVERT: F 274 GLU cc_start: 0.7668 (mt-10) cc_final: 0.7459 (mt-10) REVERT: F 381 GLU cc_start: 0.7430 (mm-30) cc_final: 0.7124 (mm-30) REVERT: F 410 SER cc_start: 0.8134 (t) cc_final: 0.7771 (t) REVERT: F 414 ARG cc_start: 0.7171 (mtm-85) cc_final: 0.6803 (mtm-85) REVERT: F 420 GLU cc_start: 0.7004 (tt0) cc_final: 0.6600 (tt0) REVERT: G 19 SER cc_start: 0.8185 (m) cc_final: 0.7728 (p) REVERT: G 64 ARG cc_start: 0.7514 (mmm160) cc_final: 0.6835 (mmm160) REVERT: G 152 LYS cc_start: 0.8028 (mtpt) cc_final: 0.7688 (mmtm) REVERT: G 180 LEU cc_start: 0.8762 (mt) cc_final: 0.8439 (mt) REVERT: G 205 ARG cc_start: 0.8040 (mmm160) cc_final: 0.7710 (mtp-110) REVERT: G 260 MET cc_start: 0.5444 (tmm) cc_final: 0.5046 (tmm) REVERT: G 267 LYS cc_start: 0.7850 (ptpt) cc_final: 0.7515 (ptpt) REVERT: G 285 LYS cc_start: 0.8116 (mtpt) cc_final: 0.7828 (mtpt) REVERT: G 357 ARG cc_start: 0.7908 (mtt90) cc_final: 0.7630 (mtt90) REVERT: G 362 ARG cc_start: 0.8118 (ptm160) cc_final: 0.7701 (ttm170) REVERT: G 369 GLN cc_start: 0.7250 (mp10) cc_final: 0.6585 (mp10) REVERT: G 372 LYS cc_start: 0.7504 (mttp) cc_final: 0.7182 (mttp) REVERT: G 411 THR cc_start: 0.8104 (t) cc_final: 0.7836 (m) REVERT: G 414 ASN cc_start: 0.7718 (t0) cc_final: 0.7411 (t0) REVERT: G 418 LYS cc_start: 0.7768 (ttmt) cc_final: 0.7544 (ttmt) REVERT: H 18 ARG cc_start: 0.7137 (mtp85) cc_final: 0.6823 (mtp85) REVERT: H 88 MET cc_start: 0.7964 (mmm) cc_final: 0.7662 (mmm) REVERT: H 134 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7186 (mt-10) REVERT: H 178 MET cc_start: 0.7818 (mmm) cc_final: 0.7531 (tpp) REVERT: H 180 GLU cc_start: 0.8069 (mm-30) cc_final: 0.7588 (mm-30) REVERT: H 184 LYS cc_start: 0.8321 (mmpt) cc_final: 0.7930 (mmpt) REVERT: H 201 LYS cc_start: 0.8060 (mmmm) cc_final: 0.7762 (mmmm) REVERT: H 235 ARG cc_start: 0.7745 (ttt180) cc_final: 0.7326 (ttt180) REVERT: H 248 ASP cc_start: 0.7392 (m-30) cc_final: 0.7189 (m-30) REVERT: H 271 GLU cc_start: 0.7245 (mp0) cc_final: 0.6873 (mp0) REVERT: H 274 GLU cc_start: 0.7407 (mt-10) cc_final: 0.6998 (mt-10) REVERT: H 282 GLU cc_start: 0.7765 (tt0) cc_final: 0.7496 (tt0) REVERT: H 352 ASP cc_start: 0.7338 (m-30) cc_final: 0.6956 (m-30) REVERT: H 379 ASP cc_start: 0.7195 (t0) cc_final: 0.6978 (t0) REVERT: H 381 GLU cc_start: 0.7598 (mm-30) cc_final: 0.7236 (mm-30) REVERT: H 389 VAL cc_start: 0.7890 (m) cc_final: 0.7581 (p) REVERT: H 396 GLU cc_start: 0.7695 (mm-30) cc_final: 0.7438 (mm-30) REVERT: H 397 THR cc_start: 0.8114 (p) cc_final: 0.7904 (p) REVERT: H 435 ASP cc_start: 0.7685 (p0) cc_final: 0.7421 (p0) REVERT: I 17 SER cc_start: 0.8032 (m) cc_final: 0.7689 (p) REVERT: I 47 GLU cc_start: 0.7164 (mt-10) cc_final: 0.6850 (mt-10) REVERT: I 60 LYS cc_start: 0.7989 (ttmt) cc_final: 0.7723 (ttmt) REVERT: I 64 ARG cc_start: 0.7623 (mmm-85) cc_final: 0.6835 (mmm-85) REVERT: I 113 MET cc_start: 0.7389 (tpp) cc_final: 0.6965 (tpp) REVERT: I 130 VAL cc_start: 0.8796 (t) cc_final: 0.8459 (m) REVERT: I 249 ARG cc_start: 0.7570 (tmm160) cc_final: 0.7157 (tmm160) REVERT: I 260 MET cc_start: 0.6899 (mtt) cc_final: 0.6001 (mtt) REVERT: I 264 MET cc_start: 0.6624 (ptp) cc_final: 0.6202 (ptp) REVERT: I 284 ASN cc_start: 0.8257 (m-40) cc_final: 0.7594 (m110) REVERT: I 346 SER cc_start: 0.7973 (t) cc_final: 0.7722 (t) REVERT: I 372 LYS cc_start: 0.8091 (mtpt) cc_final: 0.7750 (mtpt) REVERT: I 376 LYS cc_start: 0.7965 (tptt) cc_final: 0.7707 (tptt) REVERT: I 392 ASN cc_start: 0.7635 (m-40) cc_final: 0.7416 (m-40) REVERT: I 396 GLU cc_start: 0.7275 (mt-10) cc_final: 0.7000 (mt-10) REVERT: I 414 ASN cc_start: 0.7785 (t0) cc_final: 0.7562 (t0) REVERT: I 429 HIS cc_start: 0.8082 (m90) cc_final: 0.7790 (m90) REVERT: J 38 GLU cc_start: 0.7745 (mm-30) cc_final: 0.7393 (mm-30) REVERT: J 40 ARG cc_start: 0.7408 (mtt180) cc_final: 0.7179 (mtt-85) REVERT: J 115 LYS cc_start: 0.8009 (mtmt) cc_final: 0.7740 (mtmt) REVERT: J 130 ARG cc_start: 0.8260 (ttm-80) cc_final: 0.8041 (ttm-80) REVERT: J 164 LYS cc_start: 0.8119 (pttt) cc_final: 0.7847 (pttt) REVERT: J 246 GLU cc_start: 0.7460 (mt-10) cc_final: 0.7200 (mt-10) REVERT: J 319 ASP cc_start: 0.7054 (p0) cc_final: 0.6799 (p0) REVERT: J 420 GLU cc_start: 0.7278 (mt-10) cc_final: 0.6978 (mt-10) REVERT: J 436 GLU cc_start: 0.6791 (tm-30) cc_final: 0.6337 (tm-30) REVERT: J 441 GLN cc_start: 0.6732 (mm110) cc_final: 0.6352 (mm110) REVERT: L 37 ARG cc_start: 0.6324 (mtt90) cc_final: 0.5965 (mtt90) REVERT: L 68 LYS cc_start: 0.8065 (mtpt) cc_final: 0.7747 (mtpt) REVERT: L 81 ASP cc_start: 0.8220 (m-30) cc_final: 0.7742 (m-30) REVERT: L 136 ILE cc_start: 0.8543 (tt) cc_final: 0.8231 (pt) REVERT: L 191 LYS cc_start: 0.8412 (ttmt) cc_final: 0.8100 (ttmt) REVERT: L 227 MET cc_start: 0.7075 (mmm) cc_final: 0.6788 (mmm) REVERT: L 306 TYR cc_start: 0.8658 (m-80) cc_final: 0.8204 (m-80) REVERT: L 315 LYS cc_start: 0.8535 (OUTLIER) cc_final: 0.8247 (ptmm) REVERT: M 9 ASP cc_start: 0.7011 (t0) cc_final: 0.6692 (t0) REVERT: M 21 TYR cc_start: 0.8348 (t80) cc_final: 0.7853 (t80) REVERT: M 30 GLU cc_start: 0.8100 (mm-30) cc_final: 0.7897 (mm-30) REVERT: M 43 MET cc_start: 0.7462 (tmm) cc_final: 0.6995 (tmm) REVERT: M 95 ASP cc_start: 0.7656 (t0) cc_final: 0.7038 (t0) REVERT: M 100 GLN cc_start: 0.8248 (mt0) cc_final: 0.7918 (mt0) REVERT: M 142 GLU cc_start: 0.7714 (mm-30) cc_final: 0.7354 (mm-30) REVERT: M 200 ASP cc_start: 0.7904 (m-30) cc_final: 0.7568 (m-30) REVERT: M 231 GLU cc_start: 0.7653 (pm20) cc_final: 0.7423 (pm20) REVERT: M 265 SER cc_start: 0.8559 (p) cc_final: 0.8356 (p) REVERT: M 300 GLU cc_start: 0.7811 (mp0) cc_final: 0.7286 (mp0) REVERT: M 354 ASN cc_start: 0.8584 (t0) cc_final: 0.8083 (t0) REVERT: M 379 LYS cc_start: 0.8008 (tptt) cc_final: 0.7681 (tptt) REVERT: M 413 LYS cc_start: 0.8415 (tttm) cc_final: 0.8100 (tttm) REVERT: N 66 LYS cc_start: 0.8016 (mtmt) cc_final: 0.7810 (mtmt) REVERT: N 106 LYS cc_start: 0.8428 (ptpt) cc_final: 0.8145 (ptpt) REVERT: N 128 ARG cc_start: 0.7449 (ttm170) cc_final: 0.7212 (ttm170) REVERT: N 138 TYR cc_start: 0.8487 (p90) cc_final: 0.8023 (p90) REVERT: N 149 ASP cc_start: 0.7754 (t0) cc_final: 0.7543 (t0) REVERT: N 158 ASP cc_start: 0.8046 (m-30) cc_final: 0.7712 (m-30) REVERT: N 176 ASP cc_start: 0.7763 (t70) cc_final: 0.7513 (t70) REVERT: N 190 ASP cc_start: 0.7383 (m-30) cc_final: 0.7059 (m-30) REVERT: N 193 GLU cc_start: 0.7577 (tp30) cc_final: 0.7121 (tp30) REVERT: N 201 LYS cc_start: 0.8591 (tptm) cc_final: 0.8368 (tptm) REVERT: N 225 ARG cc_start: 0.7758 (mtp85) cc_final: 0.7475 (mtt90) outliers start: 76 outliers final: 67 residues processed: 1296 average time/residue: 0.2598 time to fit residues: 501.2992 Evaluate side-chains 1341 residues out of total 3673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 1271 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 842 ARG Chi-restraints excluded: chain A residue 1339 VAL Chi-restraints excluded: chain A residue 1465 GLN Chi-restraints excluded: chain A residue 1773 ARG Chi-restraints excluded: chain A residue 1893 VAL Chi-restraints excluded: chain A residue 1937 HIS Chi-restraints excluded: chain A residue 1968 CYS Chi-restraints excluded: chain A residue 2201 LEU Chi-restraints excluded: chain A residue 2223 TYR Chi-restraints excluded: chain A residue 2264 SER Chi-restraints excluded: chain A residue 2271 GLU Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain C residue 426 THR Chi-restraints excluded: chain C residue 444 THR Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 159 ILE Chi-restraints excluded: chain E residue 212 GLU Chi-restraints excluded: chain E residue 259 MET Chi-restraints excluded: chain E residue 268 LYS Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 415 LEU Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 184 LYS Chi-restraints excluded: chain F residue 195 ILE Chi-restraints excluded: chain F residue 233 GLN Chi-restraints excluded: chain F residue 291 ILE Chi-restraints excluded: chain F residue 382 MET Chi-restraints excluded: chain F residue 392 ARG Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 295 VAL Chi-restraints excluded: chain G residue 313 THR Chi-restraints excluded: chain G residue 337 VAL Chi-restraints excluded: chain G residue 403 LEU Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain H residue 170 THR Chi-restraints excluded: chain H residue 177 LYS Chi-restraints excluded: chain H residue 195 ILE Chi-restraints excluded: chain H residue 258 LEU Chi-restraints excluded: chain H residue 326 MET Chi-restraints excluded: chain H residue 333 THR Chi-restraints excluded: chain H residue 360 THR Chi-restraints excluded: chain H residue 407 THR Chi-restraints excluded: chain I residue 97 VAL Chi-restraints excluded: chain I residue 365 LEU Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 90 MET Chi-restraints excluded: chain J residue 248 ASP Chi-restraints excluded: chain J residue 252 SER Chi-restraints excluded: chain J residue 326 MET Chi-restraints excluded: chain J residue 342 SER Chi-restraints excluded: chain J residue 359 THR Chi-restraints excluded: chain J residue 405 LEU Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain L residue 186 THR Chi-restraints excluded: chain L residue 238 LYS Chi-restraints excluded: chain L residue 315 LYS Chi-restraints excluded: chain M residue 85 ILE Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain M residue 128 ASN Chi-restraints excluded: chain M residue 132 LYS Chi-restraints excluded: chain M residue 273 THR Chi-restraints excluded: chain M residue 385 THR Chi-restraints excluded: chain M residue 408 GLN Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 164 SER Chi-restraints excluded: chain N residue 233 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 5 optimal weight: 0.8980 chunk 315 optimal weight: 0.7980 chunk 10 optimal weight: 0.4980 chunk 87 optimal weight: 0.7980 chunk 122 optimal weight: 0.2980 chunk 78 optimal weight: 3.9990 chunk 181 optimal weight: 2.9990 chunk 117 optimal weight: 0.6980 chunk 297 optimal weight: 0.0970 chunk 90 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 241 HIS E 373 GLN E 393 HIS ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 233 GLN ** F 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 115 ASN H 25 HIS ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 115 ASN I 408 GLN J 44 GLN M 407 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.148591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.129819 restraints weight = 51058.777| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 2.12 r_work: 0.3447 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 34579 Z= 0.123 Angle : 0.516 9.534 46733 Z= 0.268 Chirality : 0.041 0.188 5327 Planarity : 0.004 0.077 5974 Dihedral : 8.225 161.079 4826 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.96 % Allowed : 17.10 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.52 (0.13), residues: 4227 helix: 1.69 (0.12), residues: 1880 sheet: 0.24 (0.19), residues: 722 loop : 0.76 (0.16), residues: 1625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 317 TYR 0.036 0.001 TYR A1336 PHE 0.040 0.001 PHE E 177 TRP 0.013 0.001 TRP A1405 HIS 0.008 0.001 HIS E 241 Details of bonding type rmsd covalent geometry : bond 0.00277 (34579) covalent geometry : angle 0.51624 (46733) hydrogen bonds : bond 0.03733 ( 1532) hydrogen bonds : angle 4.15258 ( 4341) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14149.31 seconds wall clock time: 240 minutes 53.18 seconds (14453.18 seconds total)