Starting phenix.real_space_refine on Thu Mar 5 09:22:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6l31_0816/03_2026/6l31_0816.cif Found real_map, /net/cci-nas-00/data/ceres_data/6l31_0816/03_2026/6l31_0816.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6l31_0816/03_2026/6l31_0816.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6l31_0816/03_2026/6l31_0816.map" model { file = "/net/cci-nas-00/data/ceres_data/6l31_0816/03_2026/6l31_0816.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6l31_0816/03_2026/6l31_0816.cif" } resolution = 4.18 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= 0.005 sd= 1.105 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 126 5.16 5 C 13247 2.51 5 N 3516 2.21 5 O 4016 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20905 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3477 Classifications: {'peptide': 444} Link IDs: {'CIS': 1, 'PTRANS': 30, 'TRANS': 412} Chain: "B" Number of atoms: 3497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3497 Classifications: {'peptide': 447} Link IDs: {'CIS': 1, 'PTRANS': 30, 'TRANS': 415} Chain: "C" Number of atoms: 3497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3497 Classifications: {'peptide': 447} Link IDs: {'PTRANS': 30, 'TRANS': 416} Chain: "D" Number of atoms: 3485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3485 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 30, 'TRANS': 414} Chain: "E" Number of atoms: 3472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3472 Classifications: {'peptide': 443} Link IDs: {'PTRANS': 30, 'TRANS': 412} Chain: "F" Number of atoms: 3477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3477 Classifications: {'peptide': 444} Link IDs: {'PTRANS': 30, 'TRANS': 413} Time building chain proxies: 4.74, per 1000 atoms: 0.23 Number of scatterers: 20905 At special positions: 0 Unit cell: (221.76, 154.56, 108.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 126 16.00 O 4016 8.00 N 3516 7.00 C 13247 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 423 " - pdb=" SG CYS B 171 " distance=2.04 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: 1.65 Conformation dependent library (CDL) restraints added in 838.6 milliseconds 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4908 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 45 sheets defined 12.4% alpha, 21.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 217 through 223 Processing helix chain 'A' and resid 229 through 236 removed outlier: 3.920A pdb=" N ASP A 236 " --> pdb=" O GLN A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 388 removed outlier: 3.779A pdb=" N TYR A 385 " --> pdb=" O GLU A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 395 removed outlier: 4.068A pdb=" N LEU A 394 " --> pdb=" O ASN A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 415 removed outlier: 3.837A pdb=" N TYR A 415 " --> pdb=" O THR A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 439 removed outlier: 3.992A pdb=" N ASN A 438 " --> pdb=" O PRO A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 450 removed outlier: 4.122A pdb=" N PHE A 450 " --> pdb=" O LYS A 447 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 447 through 450' Processing helix chain 'A' and resid 457 through 468 removed outlier: 4.114A pdb=" N ARG A 461 " --> pdb=" O TYR A 457 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYS A 462 " --> pdb=" O PRO A 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 26 removed outlier: 3.843A pdb=" N ALA B 25 " --> pdb=" O ALA B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 221 Processing helix chain 'B' and resid 230 through 236 Processing helix chain 'B' and resid 268 through 272 removed outlier: 3.592A pdb=" N LEU B 271 " --> pdb=" O PRO B 268 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE B 272 " --> pdb=" O ASP B 269 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 268 through 272' Processing helix chain 'B' and resid 276 through 281 removed outlier: 3.591A pdb=" N THR B 280 " --> pdb=" O GLY B 277 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER B 281 " --> pdb=" O ASN B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 322 No H-bonds generated for 'chain 'B' and resid 320 through 322' Processing helix chain 'B' and resid 381 through 390 removed outlier: 4.036A pdb=" N TYR B 385 " --> pdb=" O GLU B 381 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ILE B 386 " --> pdb=" O VAL B 382 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASN B 390 " --> pdb=" O ILE B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 397 removed outlier: 4.701A pdb=" N LEU B 394 " --> pdb=" O ASN B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 438 removed outlier: 4.142A pdb=" N LYS B 437 " --> pdb=" O ASP B 434 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ASN B 438 " --> pdb=" O PRO B 435 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 434 through 438' Processing helix chain 'B' and resid 453 through 457 removed outlier: 4.256A pdb=" N GLN B 456 " --> pdb=" O GLU B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 468 Processing helix chain 'C' and resid 22 through 26 removed outlier: 4.167A pdb=" N ALA C 25 " --> pdb=" O ALA C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 210 Processing helix chain 'C' and resid 217 through 222 removed outlier: 3.635A pdb=" N CYS C 221 " --> pdb=" O PRO C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 235 removed outlier: 3.525A pdb=" N MET C 233 " --> pdb=" O ASP C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 390 removed outlier: 3.847A pdb=" N HIS C 387 " --> pdb=" O MET C 383 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N THR C 388 " --> pdb=" O ALA C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 397 removed outlier: 4.132A pdb=" N ASP C 396 " --> pdb=" O SER C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 457 through 468 removed outlier: 4.129A pdb=" N ARG C 461 " --> pdb=" O TYR C 457 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS C 462 " --> pdb=" O PRO C 458 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 210 Processing helix chain 'D' and resid 229 through 234 Processing helix chain 'D' and resid 276 through 280 removed outlier: 4.076A pdb=" N THR D 280 " --> pdb=" O GLY D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 301 removed outlier: 3.768A pdb=" N GLN D 301 " --> pdb=" O SER D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 379 through 390 removed outlier: 3.797A pdb=" N HIS D 387 " --> pdb=" O MET D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 394 removed outlier: 4.012A pdb=" N LEU D 394 " --> pdb=" O PRO D 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 391 through 394' Processing helix chain 'D' and resid 420 through 424 removed outlier: 3.855A pdb=" N CYS D 423 " --> pdb=" O ALA D 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 453 through 457 removed outlier: 4.261A pdb=" N GLN D 456 " --> pdb=" O GLU D 453 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 468 removed outlier: 3.778A pdb=" N LEU D 465 " --> pdb=" O ARG D 461 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLN D 466 " --> pdb=" O LYS D 462 " (cutoff:3.500A) Processing helix chain 'E' and resid 217 through 222 removed outlier: 4.633A pdb=" N GLY E 222 " --> pdb=" O ILE E 218 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 234 Processing helix chain 'E' and resid 276 through 281 Processing helix chain 'E' and resid 379 through 390 removed outlier: 3.877A pdb=" N HIS E 387 " --> pdb=" O MET E 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 392 through 396 Processing helix chain 'E' and resid 457 through 468 removed outlier: 3.550A pdb=" N GLN E 466 " --> pdb=" O LYS E 462 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 210 Processing helix chain 'F' and resid 217 through 221 Processing helix chain 'F' and resid 230 through 236 Processing helix chain 'F' and resid 276 through 281 removed outlier: 3.624A pdb=" N SER F 281 " --> pdb=" O ASN F 278 " (cutoff:3.500A) Processing helix chain 'F' and resid 379 through 390 removed outlier: 3.527A pdb=" N MET F 389 " --> pdb=" O TYR F 385 " (cutoff:3.500A) Processing helix chain 'F' and resid 457 through 467 removed outlier: 3.525A pdb=" N LYS F 462 " --> pdb=" O PRO F 458 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LEU F 465 " --> pdb=" O ARG F 461 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN F 466 " --> pdb=" O LYS F 462 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 34 removed outlier: 6.664A pdb=" N ILE A 370 " --> pdb=" O THR A 100 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU A 102 " --> pdb=" O TYR A 307 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TYR A 307 " --> pdb=" O LEU A 102 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 247 through 250 removed outlier: 7.706A pdb=" N VAL A 444 " --> pdb=" O VAL A 69 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N LYS A 71 " --> pdb=" O VAL A 444 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 161 through 166 removed outlier: 3.993A pdb=" N GLY A 166 " --> pdb=" O GLU A 185 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLU A 185 " --> pdb=" O GLY A 166 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 338 through 340 removed outlier: 3.664A pdb=" N MET A 338 " --> pdb=" O ARG A 360 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ARG A 360 " --> pdb=" O MET A 338 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 33 through 37 removed outlier: 3.673A pdb=" N PHE B 371 " --> pdb=" O TYR B 34 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA B 36 " --> pdb=" O PHE B 369 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE B 369 " --> pdb=" O ALA B 36 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N GLN B 368 " --> pdb=" O LEU B 102 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LEU B 102 " --> pdb=" O GLN B 368 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ILE B 370 " --> pdb=" O THR B 100 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LEU B 102 " --> pdb=" O TYR B 307 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N TYR B 307 " --> pdb=" O LEU B 102 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 44 through 45 Processing sheet with id=AA7, first strand: chain 'B' and resid 51 through 52 Processing sheet with id=AA8, first strand: chain 'B' and resid 151 through 156 removed outlier: 3.578A pdb=" N LEU B 325 " --> pdb=" O VAL B 72 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 111 through 112 removed outlier: 6.264A pdb=" N GLY B 111 " --> pdb=" O SER B 335 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 115 through 120 removed outlier: 5.005A pdb=" N GLY B 116 " --> pdb=" O MET B 145 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N MET B 145 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N VAL B 143 " --> pdb=" O PRO B 118 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 161 through 167 Processing sheet with id=AB3, first strand: chain 'B' and resid 196 through 197 removed outlier: 5.917A pdb=" N MET B 196 " --> pdb=" O LYS B 226 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 252 through 257 removed outlier: 5.172A pdb=" N ALA B 253 " --> pdb=" O SER B 292 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N SER B 292 " --> pdb=" O ALA B 253 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N HIS B 255 " --> pdb=" O THR B 290 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 296 through 297 removed outlier: 3.804A pdb=" N PHE C 252 " --> pdb=" O SER C 292 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N THR C 290 " --> pdb=" O ARG C 254 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N PHE C 256 " --> pdb=" O VAL C 288 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL C 288 " --> pdb=" O PHE C 256 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 296 through 297 removed outlier: 4.033A pdb=" N LEU C 246 " --> pdb=" O CYS C 153 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N CYS C 153 " --> pdb=" O LEU C 246 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN C 250 " --> pdb=" O GLN C 149 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN C 149 " --> pdb=" O GLN C 250 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLY C 156 " --> pdb=" O PHE C 326 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE C 326 " --> pdb=" O GLY C 156 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N VAL C 69 " --> pdb=" O TRP C 442 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N VAL C 444 " --> pdb=" O VAL C 69 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LYS C 71 " --> pdb=" O VAL C 444 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 341 through 343 Processing sheet with id=AB8, first strand: chain 'C' and resid 28 through 36 removed outlier: 8.456A pdb=" N THR C 28 " --> pdb=" O THR C 377 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N THR C 377 " --> pdb=" O THR C 28 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N THR C 30 " --> pdb=" O SER C 375 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N SER C 375 " --> pdb=" O THR C 30 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N ILE C 32 " --> pdb=" O LEU C 373 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ILE C 370 " --> pdb=" O THR C 100 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARG C 94 " --> pdb=" O ILE C 376 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU C 102 " --> pdb=" O TYR C 307 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR C 307 " --> pdb=" O LEU C 102 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 104 through 105 Processing sheet with id=AC1, first strand: chain 'C' and resid 115 through 121 removed outlier: 3.556A pdb=" N SER C 115 " --> pdb=" O MET C 145 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N VAL C 141 " --> pdb=" O PHE C 119 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 161 through 167 Processing sheet with id=AC3, first strand: chain 'C' and resid 337 through 343 Processing sheet with id=AC4, first strand: chain 'D' and resid 28 through 37 removed outlier: 6.856A pdb=" N THR D 30 " --> pdb=" O SER D 375 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N SER D 375 " --> pdb=" O THR D 30 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N ILE D 32 " --> pdb=" O LEU D 373 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N PHE D 371 " --> pdb=" O TYR D 34 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N GLN D 368 " --> pdb=" O LEU D 102 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N LEU D 102 " --> pdb=" O GLN D 368 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N ILE D 370 " --> pdb=" O THR D 100 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 42 through 45 removed outlier: 4.112A pdb=" N ALA D 43 " --> pdb=" O GLU D 363 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N TYR D 358 " --> pdb=" O LEU D 340 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU D 340 " --> pdb=" O TYR D 358 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 42 through 45 removed outlier: 4.112A pdb=" N ALA D 43 " --> pdb=" O GLU D 363 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N TYR D 355 " --> pdb=" O GLU E 262 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 72 through 73 removed outlier: 3.592A pdb=" N GLN D 149 " --> pdb=" O GLN D 250 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN D 250 " --> pdb=" O GLN D 149 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU D 246 " --> pdb=" O CYS D 153 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N VAL D 155 " --> pdb=" O PHE D 244 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N PHE D 244 " --> pdb=" O VAL D 155 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 115 through 120 removed outlier: 4.825A pdb=" N GLY D 116 " --> pdb=" O MET D 145 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N MET D 145 " --> pdb=" O GLY D 116 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N VAL D 143 " --> pdb=" O PRO D 118 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 184 through 190 Processing sheet with id=AD1, first strand: chain 'D' and resid 252 through 257 removed outlier: 5.043A pdb=" N ALA D 253 " --> pdb=" O SER D 292 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N SER D 292 " --> pdb=" O ALA D 253 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N HIS D 255 " --> pdb=" O THR D 290 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 35 through 37 removed outlier: 6.569A pdb=" N ASP E 366 " --> pdb=" O VAL E 104 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N VAL E 104 " --> pdb=" O ASP E 366 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N GLN E 368 " --> pdb=" O LEU E 102 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N LEU E 102 " --> pdb=" O GLN E 368 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ILE E 370 " --> pdb=" O THR E 100 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 44 through 45 Processing sheet with id=AD4, first strand: chain 'E' and resid 51 through 52 removed outlier: 3.515A pdb=" N ILE E 51 " --> pdb=" O VAL E 59 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL E 59 " --> pdb=" O ILE E 51 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'E' and resid 244 through 247 removed outlier: 4.542A pdb=" N PHE E 244 " --> pdb=" O VAL E 155 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL E 155 " --> pdb=" O PHE E 244 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU E 246 " --> pdb=" O CYS E 153 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU E 325 " --> pdb=" O VAL E 72 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL E 72 " --> pdb=" O LEU E 325 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N TRP E 442 " --> pdb=" O VAL E 69 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS E 71 " --> pdb=" O TRP E 442 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 117 through 120 removed outlier: 4.929A pdb=" N VAL E 141 " --> pdb=" O PHE E 119 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 161 through 167 Processing sheet with id=AD8, first strand: chain 'E' and resid 252 through 253 Processing sheet with id=AD9, first strand: chain 'F' and resid 338 through 343 removed outlier: 3.837A pdb=" N MET F 338 " --> pdb=" O ARG F 360 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG F 360 " --> pdb=" O MET F 338 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N GLN F 372 " --> pdb=" O CYS F 99 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N CYS F 99 " --> pdb=" O GLN F 372 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N CYS F 374 " --> pdb=" O TRP F 97 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N TRP F 97 " --> pdb=" O CYS F 374 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU F 102 " --> pdb=" O TYR F 307 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 28 through 33 removed outlier: 3.522A pdb=" N THR F 30 " --> pdb=" O LEU F 373 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N LEU F 373 " --> pdb=" O THR F 30 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N ILE F 32 " --> pdb=" O PHE F 371 " (cutoff:3.500A) removed outlier: 8.386A pdb=" N PHE F 371 " --> pdb=" O ILE F 32 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE F 369 " --> pdb=" O ALA F 36 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ALA F 36 " --> pdb=" O PHE F 369 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 41 through 45 removed outlier: 4.060A pdb=" N ALA F 43 " --> pdb=" O GLU F 363 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'F' and resid 51 through 52 removed outlier: 3.658A pdb=" N VAL F 59 " --> pdb=" O ILE F 51 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 324 through 327 removed outlier: 6.747A pdb=" N LYS F 71 " --> pdb=" O VAL F 444 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 111 through 112 removed outlier: 7.036A pdb=" N GLY F 111 " --> pdb=" O SER F 335 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'F' and resid 115 through 117 removed outlier: 4.305A pdb=" N SER F 115 " --> pdb=" O MET F 145 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 149 through 152 removed outlier: 3.561A pdb=" N GLN F 250 " --> pdb=" O GLN F 149 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 161 through 167 Processing sheet with id=AE9, first strand: chain 'F' and resid 252 through 257 removed outlier: 6.831A pdb=" N THR F 290 " --> pdb=" O ARG F 254 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N PHE F 256 " --> pdb=" O VAL F 288 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N VAL F 288 " --> pdb=" O PHE F 256 " (cutoff:3.500A) 342 hydrogen bonds defined for protein. 870 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: 3.10 Time building geometry restraints manager: 2.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 6670 1.34 - 1.46: 5142 1.46 - 1.59: 9457 1.59 - 1.71: 2 1.71 - 1.83: 186 Bond restraints: 21457 Sorted by residual: bond pdb=" CA ARG B 414 " pdb=" C ARG B 414 " ideal model delta sigma weight residual 1.524 1.606 -0.081 1.28e-02 6.10e+03 4.05e+01 bond pdb=" C LYS A 226 " pdb=" N TYR A 227 " ideal model delta sigma weight residual 1.329 1.261 0.068 1.21e-02 6.83e+03 3.12e+01 bond pdb=" CA GLN B 417 " pdb=" C GLN B 417 " ideal model delta sigma weight residual 1.523 1.597 -0.075 1.45e-02 4.76e+03 2.65e+01 bond pdb=" C THR A 427 " pdb=" N PRO A 428 " ideal model delta sigma weight residual 1.331 1.386 -0.054 1.21e-02 6.83e+03 2.03e+01 bond pdb=" C PRO C 404 " pdb=" N PRO C 405 " ideal model delta sigma weight residual 1.329 1.377 -0.048 1.20e-02 6.94e+03 1.62e+01 ... (remaining 21452 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.52: 28885 4.52 - 9.03: 263 9.03 - 13.55: 36 13.55 - 18.06: 3 18.06 - 22.58: 3 Bond angle restraints: 29190 Sorted by residual: angle pdb=" N VAL A 27 " pdb=" CA VAL A 27 " pdb=" C VAL A 27 " ideal model delta sigma weight residual 111.62 123.71 -12.09 7.90e-01 1.60e+00 2.34e+02 angle pdb=" N LYS C 169 " pdb=" CA LYS C 169 " pdb=" C LYS C 169 " ideal model delta sigma weight residual 109.24 131.50 -22.26 1.63e+00 3.76e-01 1.86e+02 angle pdb=" N SER B 418 " pdb=" CA SER B 418 " pdb=" CB SER B 418 " ideal model delta sigma weight residual 110.49 133.07 -22.58 1.69e+00 3.50e-01 1.79e+02 angle pdb=" CA GLN B 417 " pdb=" C GLN B 417 " pdb=" N SER B 418 " ideal model delta sigma weight residual 117.74 102.17 15.57 1.58e+00 4.01e-01 9.72e+01 angle pdb=" CA GLN B 417 " pdb=" C GLN B 417 " pdb=" O GLN B 417 " ideal model delta sigma weight residual 120.12 130.16 -10.04 1.15e+00 7.56e-01 7.62e+01 ... (remaining 29185 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.27: 10984 17.27 - 34.54: 1412 34.54 - 51.81: 271 51.81 - 69.08: 63 69.08 - 86.34: 25 Dihedral angle restraints: 12755 sinusoidal: 5057 harmonic: 7698 Sorted by residual: dihedral pdb=" CA THR C 422 " pdb=" C THR C 422 " pdb=" N CYS C 423 " pdb=" CA CYS C 423 " ideal model delta harmonic sigma weight residual -180.00 -121.53 -58.47 0 5.00e+00 4.00e-02 1.37e+02 dihedral pdb=" CA VAL A 267 " pdb=" C VAL A 267 " pdb=" N PRO A 268 " pdb=" CA PRO A 268 " ideal model delta harmonic sigma weight residual -180.00 -127.74 -52.26 0 5.00e+00 4.00e-02 1.09e+02 dihedral pdb=" N SER B 418 " pdb=" C SER B 418 " pdb=" CA SER B 418 " pdb=" CB SER B 418 " ideal model delta harmonic sigma weight residual 122.80 146.72 -23.92 0 2.50e+00 1.60e-01 9.16e+01 ... (remaining 12752 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.170: 3066 0.170 - 0.340: 70 0.340 - 0.510: 8 0.510 - 0.680: 1 0.680 - 0.850: 1 Chirality restraints: 3146 Sorted by residual: chirality pdb=" CA SER B 418 " pdb=" N SER B 418 " pdb=" C SER B 418 " pdb=" CB SER B 418 " both_signs ideal model delta sigma weight residual False 2.51 1.66 0.85 2.00e-01 2.50e+01 1.81e+01 chirality pdb=" CA LYS C 169 " pdb=" N LYS C 169 " pdb=" C LYS C 169 " pdb=" CB LYS C 169 " both_signs ideal model delta sigma weight residual False 2.51 1.93 0.58 2.00e-01 2.50e+01 8.51e+00 chirality pdb=" CA THR B 412 " pdb=" N THR B 412 " pdb=" C THR B 412 " pdb=" CB THR B 412 " both_signs ideal model delta sigma weight residual False 2.53 2.04 0.48 2.00e-01 2.50e+01 5.80e+00 ... (remaining 3143 not shown) Planarity restraints: 3837 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO E 403 " -0.081 5.00e-02 4.00e+02 1.22e-01 2.38e+01 pdb=" N PRO E 404 " 0.211 5.00e-02 4.00e+02 pdb=" CA PRO E 404 " -0.065 5.00e-02 4.00e+02 pdb=" CD PRO E 404 " -0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS F 425 " -0.063 5.00e-02 4.00e+02 9.59e-02 1.47e+01 pdb=" N PRO F 426 " 0.166 5.00e-02 4.00e+02 pdb=" CA PRO F 426 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO F 426 " -0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D 216 " -0.061 5.00e-02 4.00e+02 9.16e-02 1.34e+01 pdb=" N PRO D 217 " 0.158 5.00e-02 4.00e+02 pdb=" CA PRO D 217 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO D 217 " -0.050 5.00e-02 4.00e+02 ... (remaining 3834 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.37: 115 2.37 - 3.00: 11184 3.00 - 3.64: 34263 3.64 - 4.27: 47258 4.27 - 4.90: 72669 Nonbonded interactions: 165489 Sorted by model distance: nonbonded pdb=" O VAL A 27 " pdb=" O SER A 375 " model vdw 1.738 3.040 nonbonded pdb=" O TYR A 26 " pdb=" CD1 ILE A 376 " model vdw 1.940 3.460 nonbonded pdb=" NE2 GLN B 419 " pdb=" N ILE B 421 " model vdw 1.941 3.200 nonbonded pdb=" O THR B 422 " pdb=" SG CYS B 423 " model vdw 1.990 3.400 nonbonded pdb=" CB ARG B 414 " pdb=" NE2 GLN B 424 " model vdw 1.998 3.520 ... (remaining 165484 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 26 through 468) selection = (chain 'B' and resid 26 through 468) selection = (chain 'C' and resid 26 through 468) selection = (chain 'D' and resid 26 through 468) selection = chain 'E' selection = (chain 'F' and resid 26 through 468) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 17.910 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.108 21458 Z= 0.363 Angle : 1.259 22.581 29192 Z= 0.718 Chirality : 0.072 0.850 3146 Planarity : 0.009 0.122 3837 Dihedral : 16.233 86.344 7844 Min Nonbonded Distance : 1.738 Molprobity Statistics. All-atom Clashscore : 16.72 Ramachandran Plot: Outliers : 0.34 % Allowed : 11.66 % Favored : 88.00 % Rotamer: Outliers : 2.27 % Allowed : 14.62 % Favored : 83.11 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 2.78 % Twisted General : 0.36 % 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 are not related in a simple way. whole: -4.45 (0.13), residues: 2658 helix: -4.27 (0.17), residues: 197 sheet: -2.23 (0.19), residues: 593 loop : -3.29 (0.12), residues: 1868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 106 TYR 0.031 0.003 TYR C 67 PHE 0.043 0.003 PHE A 369 TRP 0.028 0.003 TRP F 97 HIS 0.016 0.003 HIS A 35 Details of bonding type rmsd covalent geometry : bond 0.00699 (21457) covalent geometry : angle 1.25887 (29190) SS BOND : bond 0.00478 ( 1) SS BOND : angle 0.64104 ( 2) hydrogen bonds : bond 0.31864 ( 337) hydrogen bonds : angle 11.94436 ( 870) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 738 residues out of total 2333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 685 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.6633 (m110) cc_final: 0.5240 (m110) REVERT: A 195 ASP cc_start: 0.8012 (t70) cc_final: 0.7697 (t0) REVERT: A 210 GLN cc_start: 0.4474 (mt0) cc_final: 0.4205 (mt0) REVERT: A 250 GLN cc_start: 0.7435 (mm-40) cc_final: 0.7177 (mm-40) REVERT: A 255 HIS cc_start: 0.8514 (m90) cc_final: 0.8191 (m-70) REVERT: A 257 PHE cc_start: 0.9036 (t80) cc_final: 0.8458 (t80) REVERT: A 288 VAL cc_start: 0.8580 (m) cc_final: 0.8195 (m) REVERT: A 302 LEU cc_start: 0.9215 (mm) cc_final: 0.8775 (mm) REVERT: A 303 PHE cc_start: 0.8612 (m-10) cc_final: 0.8394 (m-80) REVERT: A 305 LYS cc_start: 0.9428 (mmtm) cc_final: 0.9178 (mppt) REVERT: A 364 GLU cc_start: 0.8481 (tt0) cc_final: 0.8262 (tt0) REVERT: A 371 PHE cc_start: 0.8703 (m-80) cc_final: 0.8267 (m-80) REVERT: A 389 MET cc_start: 0.9060 (ttt) cc_final: 0.8462 (tmm) REVERT: A 450 PHE cc_start: 0.8819 (m-10) cc_final: 0.8533 (m-10) REVERT: B 26 TYR cc_start: 0.8140 (m-80) cc_final: 0.7625 (m-80) REVERT: B 61 LYS cc_start: 0.8176 (tttt) cc_final: 0.7806 (ttpt) REVERT: B 74 LEU cc_start: 0.9126 (tp) cc_final: 0.8749 (tp) REVERT: B 151 GLN cc_start: 0.9176 (mt0) cc_final: 0.8920 (mt0) REVERT: B 206 PHE cc_start: 0.9301 (m-80) cc_final: 0.9085 (m-80) REVERT: B 210 GLN cc_start: 0.9519 (mp10) cc_final: 0.9035 (mp10) REVERT: B 211 THR cc_start: 0.8888 (p) cc_final: 0.8501 (p) REVERT: B 236 ASP cc_start: 0.8964 (t0) cc_final: 0.8748 (t70) REVERT: B 262 GLU cc_start: 0.7917 (mt-10) cc_final: 0.7128 (mt-10) REVERT: B 273 ILE cc_start: 0.9328 (mm) cc_final: 0.9100 (mm) REVERT: B 301 GLN cc_start: 0.9144 (mp-120) cc_final: 0.8715 (mp10) REVERT: B 302 LEU cc_start: 0.8896 (pp) cc_final: 0.8589 (pp) REVERT: B 305 LYS cc_start: 0.9351 (mtpt) cc_final: 0.8990 (mtpt) REVERT: B 338 MET cc_start: 0.8437 (mpp) cc_final: 0.8193 (mpp) REVERT: B 355 TYR cc_start: 0.7177 (m-80) cc_final: 0.6793 (m-10) REVERT: B 359 MET cc_start: 0.8261 (mmm) cc_final: 0.7802 (mmm) REVERT: B 389 MET cc_start: 0.8764 (ppp) cc_final: 0.8555 (ppp) REVERT: B 449 LYS cc_start: 0.8844 (mmtp) cc_final: 0.8484 (mtpt) REVERT: B 461 ARG cc_start: 0.9298 (ttp-170) cc_final: 0.8631 (mtm-85) REVERT: B 462 LYS cc_start: 0.9187 (mtpt) cc_final: 0.8895 (mmtt) REVERT: C 53 ARG cc_start: 0.7013 (mmt-90) cc_final: 0.6732 (tpt-90) REVERT: C 108 GLN cc_start: 0.8824 (mm-40) cc_final: 0.8356 (mm-40) REVERT: C 171 CYS cc_start: 0.4719 (OUTLIER) cc_final: 0.4389 (t) REVERT: C 201 PHE cc_start: 0.8438 (m-10) cc_final: 0.7813 (m-80) REVERT: C 232 GLN cc_start: 0.8666 (mt0) cc_final: 0.8351 (mm-40) REVERT: C 302 LEU cc_start: 0.9527 (mm) cc_final: 0.9325 (mm) REVERT: C 305 LYS cc_start: 0.8950 (mppt) cc_final: 0.8622 (mppt) REVERT: C 310 GLN cc_start: 0.8998 (tm-30) cc_final: 0.8638 (tm-30) REVERT: C 395 GLU cc_start: 0.9140 (tm-30) cc_final: 0.8874 (tm-30) REVERT: C 415 TYR cc_start: -0.0971 (OUTLIER) cc_final: -0.1259 (t80) REVERT: D 69 VAL cc_start: 0.8504 (t) cc_final: 0.8294 (t) REVERT: D 117 HIS cc_start: 0.8596 (t-90) cc_final: 0.7960 (t-90) REVERT: D 120 LEU cc_start: 0.8500 (mt) cc_final: 0.8091 (mt) REVERT: D 121 ASN cc_start: 0.7466 (t0) cc_final: 0.7049 (t0) REVERT: D 147 TYR cc_start: 0.8507 (m-80) cc_final: 0.8244 (m-80) REVERT: D 165 TRP cc_start: 0.8466 (m-90) cc_final: 0.7885 (m100) REVERT: D 187 ILE cc_start: 0.9410 (mt) cc_final: 0.9015 (mt) REVERT: D 193 ASP cc_start: 0.7590 (t0) cc_final: 0.7091 (t0) REVERT: D 206 PHE cc_start: 0.8267 (m-80) cc_final: 0.7939 (m-80) REVERT: D 219 ASP cc_start: 0.9263 (p0) cc_final: 0.9045 (p0) REVERT: D 226 LYS cc_start: 0.8092 (mtpt) cc_final: 0.7769 (mtpp) REVERT: D 233 MET cc_start: 0.8808 (mmp) cc_final: 0.8590 (mmm) REVERT: D 355 TYR cc_start: 0.7904 (m-80) cc_final: 0.7689 (m-80) REVERT: D 361 HIS cc_start: 0.7015 (t-90) cc_final: 0.6588 (t70) REVERT: D 364 GLU cc_start: 0.8770 (tm-30) cc_final: 0.8565 (tm-30) REVERT: D 397 TRP cc_start: 0.8843 (m-90) cc_final: 0.8614 (m100) REVERT: D 449 LYS cc_start: 0.7830 (mmtp) cc_final: 0.7499 (mmmt) REVERT: E 41 LEU cc_start: 0.8249 (tt) cc_final: 0.7835 (tt) REVERT: E 120 LEU cc_start: 0.8984 (mt) cc_final: 0.8341 (mt) REVERT: E 184 LEU cc_start: 0.9132 (tp) cc_final: 0.8767 (tp) REVERT: E 226 LYS cc_start: 0.8580 (mmtt) cc_final: 0.8256 (mmtm) REVERT: E 232 GLN cc_start: 0.8461 (mt0) cc_final: 0.7735 (tp-100) REVERT: E 233 MET cc_start: 0.9576 (mtm) cc_final: 0.9003 (mtt) REVERT: E 256 PHE cc_start: 0.9186 (m-80) cc_final: 0.8874 (m-10) REVERT: E 257 PHE cc_start: 0.8583 (m-80) cc_final: 0.8290 (m-80) REVERT: E 265 GLU cc_start: 0.8422 (mt-10) cc_final: 0.8198 (mt-10) REVERT: E 324 GLN cc_start: 0.8839 (mt0) cc_final: 0.8594 (mt0) REVERT: E 352 ASN cc_start: 0.9379 (p0) cc_final: 0.9171 (p0) REVERT: E 374 CYS cc_start: 0.9331 (m) cc_final: 0.8902 (p) REVERT: E 397 TRP cc_start: 0.6823 (m100) cc_final: 0.6118 (m100) REVERT: F 65 TYR cc_start: 0.9121 (m-80) cc_final: 0.8782 (m-10) REVERT: F 103 GLU cc_start: 0.8068 (tp30) cc_final: 0.7576 (tp30) REVERT: F 106 ARG cc_start: 0.8392 (mmm160) cc_final: 0.8163 (tpp80) REVERT: F 125 ASP cc_start: 0.9035 (p0) cc_final: 0.8661 (p0) REVERT: F 149 GLN cc_start: 0.8145 (pt0) cc_final: 0.7573 (pm20) REVERT: F 150 THR cc_start: 0.9453 (m) cc_final: 0.8326 (m) REVERT: F 165 TRP cc_start: 0.8931 (m100) cc_final: 0.8331 (m100) REVERT: F 170 GLN cc_start: 0.8345 (OUTLIER) cc_final: 0.7795 (tm-30) REVERT: F 184 LEU cc_start: 0.8144 (tp) cc_final: 0.7870 (tp) REVERT: F 186 LEU cc_start: 0.8813 (tp) cc_final: 0.8393 (tp) REVERT: F 196 MET cc_start: 0.7829 (mmm) cc_final: 0.7082 (mmm) REVERT: F 204 MET cc_start: 0.8533 (mpp) cc_final: 0.8329 (mpp) REVERT: F 210 GLN cc_start: 0.9423 (tp40) cc_final: 0.9122 (mm110) REVERT: F 219 ASP cc_start: 0.9286 (m-30) cc_final: 0.9018 (m-30) REVERT: F 249 GLU cc_start: 0.8747 (mp0) cc_final: 0.8522 (mp0) REVERT: F 251 MET cc_start: 0.8743 (tmm) cc_final: 0.8534 (tpp) REVERT: F 273 ILE cc_start: 0.8042 (mm) cc_final: 0.7593 (mm) REVERT: F 334 ARG cc_start: 0.9215 (mtt90) cc_final: 0.8551 (mtp85) REVERT: F 357 GLU cc_start: 0.8530 (tm-30) cc_final: 0.8218 (tm-30) REVERT: F 360 ARG cc_start: 0.7286 (mtt180) cc_final: 0.7058 (mtt180) REVERT: F 373 LEU cc_start: 0.9056 (mm) cc_final: 0.8774 (mm) REVERT: F 414 ARG cc_start: 0.7517 (mmp-170) cc_final: 0.6615 (mpt-90) REVERT: F 445 ASN cc_start: 0.8799 (t0) cc_final: 0.8578 (p0) outliers start: 53 outliers final: 19 residues processed: 729 average time/residue: 0.1362 time to fit residues: 153.0623 Evaluate side-chains 568 residues out of total 2333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 546 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 197 optimal weight: 20.0000 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 30.0000 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 0.0050 chunk 207 optimal weight: 30.0000 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 8.9990 chunk 111 optimal weight: 4.9990 overall best weight: 4.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 258 ASN A 289 ASN ** A 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 372 GLN ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 55 ASN ** B 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 192 GLN B 212 ASN B 255 HIS B 419 GLN C 78 ASN C 139 ASN C 142 ASN ** C 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 212 ASN ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 HIS ** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 139 ASN ** D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 258 ASN ** D 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 78 ASN ** E 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 212 ASN E 337 ASN ** F 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 139 ASN F 149 GLN ** F 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 289 ASN F 301 GLN F 316 ASN F 337 ASN F 361 HIS F 387 HIS Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.132721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.106302 restraints weight = 63605.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.109955 restraints weight = 37278.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.112516 restraints weight = 25385.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.114351 restraints weight = 19054.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.115647 restraints weight = 15340.017| |-----------------------------------------------------------------------------| r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 21458 Z= 0.176 Angle : 0.787 12.838 29192 Z= 0.408 Chirality : 0.050 0.285 3146 Planarity : 0.007 0.110 3837 Dihedral : 7.294 44.929 2886 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 16.14 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.27 % Favored : 89.62 % Rotamer: Outliers : 0.21 % Allowed : 6.43 % Favored : 93.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 2.22 % Twisted General : 0.20 % 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 are not related in a simple way. whole: -3.87 (0.14), residues: 2658 helix: -2.99 (0.25), residues: 234 sheet: -1.99 (0.19), residues: 630 loop : -2.91 (0.13), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 40 TYR 0.022 0.002 TYR E 230 PHE 0.032 0.002 PHE A 88 TRP 0.022 0.002 TRP D 165 HIS 0.009 0.002 HIS B 35 Details of bonding type rmsd covalent geometry : bond 0.00378 (21457) covalent geometry : angle 0.78685 (29190) SS BOND : bond 0.00197 ( 1) SS BOND : angle 0.40289 ( 2) hydrogen bonds : bond 0.05330 ( 337) hydrogen bonds : angle 8.56989 ( 870) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 683 residues out of total 2333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 678 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 55 ASN cc_start: 0.9137 (m110) cc_final: 0.8877 (m110) REVERT: A 223 THR cc_start: 0.8549 (t) cc_final: 0.8265 (t) REVERT: A 371 PHE cc_start: 0.8595 (m-80) cc_final: 0.8000 (m-80) REVERT: A 389 MET cc_start: 0.8958 (ttt) cc_final: 0.8137 (tmm) REVERT: A 449 LYS cc_start: 0.9127 (mmtm) cc_final: 0.8735 (mmtm) REVERT: A 450 PHE cc_start: 0.8786 (m-10) cc_final: 0.8528 (m-10) REVERT: B 26 TYR cc_start: 0.8245 (m-80) cc_final: 0.7927 (m-80) REVERT: B 74 LEU cc_start: 0.9122 (tp) cc_final: 0.8737 (tp) REVERT: B 151 GLN cc_start: 0.9073 (mt0) cc_final: 0.8859 (mt0) REVERT: B 210 GLN cc_start: 0.9311 (mp10) cc_final: 0.8978 (mp10) REVERT: B 219 ASP cc_start: 0.9099 (p0) cc_final: 0.8898 (p0) REVERT: B 220 ILE cc_start: 0.9678 (pt) cc_final: 0.9464 (pt) REVERT: B 246 LEU cc_start: 0.9355 (mt) cc_final: 0.9081 (mt) REVERT: B 247 ARG cc_start: 0.8381 (mpp-170) cc_final: 0.8152 (mtp-110) REVERT: B 273 ILE cc_start: 0.9462 (mm) cc_final: 0.9252 (mm) REVERT: B 301 GLN cc_start: 0.9172 (mp-120) cc_final: 0.8748 (mp10) REVERT: B 302 LEU cc_start: 0.8983 (pp) cc_final: 0.8639 (pp) REVERT: B 305 LYS cc_start: 0.9459 (mtpt) cc_final: 0.9097 (mtpt) REVERT: B 307 TYR cc_start: 0.8262 (m-80) cc_final: 0.7822 (m-10) REVERT: B 357 GLU cc_start: 0.8906 (mm-30) cc_final: 0.8644 (mp0) REVERT: B 421 ILE cc_start: 0.7906 (mp) cc_final: 0.6958 (mp) REVERT: B 461 ARG cc_start: 0.9136 (ttp-110) cc_final: 0.8441 (mtm110) REVERT: C 49 PHE cc_start: 0.8569 (t80) cc_final: 0.7944 (t80) REVERT: C 51 ILE cc_start: 0.8324 (tt) cc_final: 0.8040 (tt) REVERT: C 53 ARG cc_start: 0.6960 (mmt-90) cc_final: 0.6703 (ttt-90) REVERT: C 108 GLN cc_start: 0.8517 (mm-40) cc_final: 0.7914 (mm-40) REVERT: C 201 PHE cc_start: 0.8576 (m-10) cc_final: 0.7890 (m-80) REVERT: C 232 GLN cc_start: 0.8631 (mt0) cc_final: 0.8395 (mm-40) REVERT: C 310 GLN cc_start: 0.8781 (tm-30) cc_final: 0.8410 (tm-30) REVERT: C 359 MET cc_start: 0.8288 (mmm) cc_final: 0.7863 (mmt) REVERT: C 395 GLU cc_start: 0.9080 (tm-30) cc_final: 0.8803 (tm-30) REVERT: C 457 TYR cc_start: 0.9305 (m-80) cc_final: 0.8950 (m-80) REVERT: D 69 VAL cc_start: 0.8361 (t) cc_final: 0.8134 (t) REVERT: D 120 LEU cc_start: 0.8431 (mt) cc_final: 0.8087 (mt) REVERT: D 125 ASP cc_start: 0.8375 (t70) cc_final: 0.8112 (m-30) REVERT: D 147 TYR cc_start: 0.8057 (m-80) cc_final: 0.7807 (m-80) REVERT: D 197 VAL cc_start: 0.8378 (t) cc_final: 0.8114 (m) REVERT: D 206 PHE cc_start: 0.8184 (m-80) cc_final: 0.7776 (m-80) REVERT: D 257 PHE cc_start: 0.8010 (m-10) cc_final: 0.7757 (m-10) REVERT: D 339 THR cc_start: 0.7629 (p) cc_final: 0.7307 (p) REVERT: D 355 TYR cc_start: 0.7967 (m-80) cc_final: 0.7702 (m-80) REVERT: D 361 HIS cc_start: 0.6397 (t-90) cc_final: 0.6167 (t70) REVERT: D 397 TRP cc_start: 0.8794 (m-90) cc_final: 0.8518 (m100) REVERT: D 445 ASN cc_start: 0.9157 (t0) cc_final: 0.8912 (t0) REVERT: D 449 LYS cc_start: 0.7904 (mmtp) cc_final: 0.7535 (mmmt) REVERT: E 41 LEU cc_start: 0.8176 (tt) cc_final: 0.7436 (tt) REVERT: E 66 GLN cc_start: 0.6981 (mt0) cc_final: 0.6422 (mt0) REVERT: E 120 LEU cc_start: 0.8583 (mt) cc_final: 0.8095 (mt) REVERT: E 146 ASP cc_start: 0.8862 (p0) cc_final: 0.8643 (p0) REVERT: E 196 MET cc_start: 0.8888 (mpp) cc_final: 0.8582 (mpp) REVERT: E 232 GLN cc_start: 0.8270 (mt0) cc_final: 0.7679 (tp-100) REVERT: E 233 MET cc_start: 0.9220 (mtm) cc_final: 0.8870 (mtm) REVERT: E 326 PHE cc_start: 0.8959 (m-80) cc_final: 0.8287 (m-80) REVERT: E 371 PHE cc_start: 0.9523 (m-80) cc_final: 0.9301 (m-80) REVERT: E 411 ASP cc_start: 0.8002 (t0) cc_final: 0.7713 (t70) REVERT: E 450 PHE cc_start: 0.8307 (m-80) cc_final: 0.8061 (m-80) REVERT: E 461 ARG cc_start: 0.9018 (ptp90) cc_final: 0.8769 (ptp90) REVERT: F 103 GLU cc_start: 0.7681 (tp30) cc_final: 0.7290 (tp30) REVERT: F 125 ASP cc_start: 0.9243 (p0) cc_final: 0.8873 (p0) REVERT: F 148 LYS cc_start: 0.9039 (ptmm) cc_final: 0.8751 (ptmm) REVERT: F 165 TRP cc_start: 0.8830 (m100) cc_final: 0.8049 (m100) REVERT: F 196 MET cc_start: 0.7619 (mmm) cc_final: 0.6649 (mmm) REVERT: F 204 MET cc_start: 0.8303 (mpp) cc_final: 0.7723 (mpp) REVERT: F 230 TYR cc_start: 0.8771 (m-80) cc_final: 0.8436 (m-80) REVERT: F 273 ILE cc_start: 0.8257 (mm) cc_final: 0.7817 (mm) REVERT: F 315 HIS cc_start: 0.7753 (m90) cc_final: 0.7131 (m90) REVERT: F 334 ARG cc_start: 0.8996 (mtt90) cc_final: 0.8763 (mtt-85) REVERT: F 357 GLU cc_start: 0.7988 (tm-30) cc_final: 0.7697 (tm-30) REVERT: F 359 MET cc_start: 0.8345 (tpp) cc_final: 0.7880 (tpp) REVERT: F 373 LEU cc_start: 0.8909 (mm) cc_final: 0.8658 (mm) REVERT: F 450 PHE cc_start: 0.8847 (m-80) cc_final: 0.8383 (m-80) REVERT: F 461 ARG cc_start: 0.8784 (mtt180) cc_final: 0.8511 (mtt180) outliers start: 5 outliers final: 1 residues processed: 682 average time/residue: 0.1380 time to fit residues: 143.7897 Evaluate side-chains 540 residues out of total 2333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 539 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 15 optimal weight: 0.0770 chunk 32 optimal weight: 0.0010 chunk 121 optimal weight: 30.0000 chunk 19 optimal weight: 0.3980 chunk 92 optimal weight: 30.0000 chunk 232 optimal weight: 20.0000 chunk 202 optimal weight: 20.0000 chunk 4 optimal weight: 20.0000 chunk 41 optimal weight: 10.0000 chunk 95 optimal weight: 1.9990 chunk 112 optimal weight: 0.0060 overall best weight: 0.4962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 HIS A 139 ASN ** A 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 210 GLN A 255 HIS A 323 ASN A 337 ASN A 361 HIS A 445 ASN B 78 ASN B 212 ASN ** C 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 323 ASN D 108 GLN D 151 GLN D 255 HIS D 352 ASN E 139 ASN E 212 ASN E 316 ASN F 149 GLN F 301 GLN F 315 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.140011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.114201 restraints weight = 57616.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.118291 restraints weight = 32830.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.121142 restraints weight = 21714.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.123187 restraints weight = 15838.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.124642 restraints weight = 12405.664| |-----------------------------------------------------------------------------| r_work (final): 0.3857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7010 moved from start: 0.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 21458 Z= 0.137 Angle : 0.727 10.746 29192 Z= 0.368 Chirality : 0.049 0.322 3146 Planarity : 0.006 0.104 3837 Dihedral : 6.443 43.023 2886 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.84 % Favored : 91.12 % Rotamer: Outliers : 0.04 % Allowed : 5.40 % Favored : 94.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 2.22 % Twisted General : 0.08 % 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 are not related in a simple way. whole: -3.48 (0.15), residues: 2658 helix: -2.56 (0.28), residues: 235 sheet: -1.67 (0.20), residues: 615 loop : -2.68 (0.13), residues: 1808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 254 TYR 0.024 0.002 TYR E 230 PHE 0.021 0.002 PHE D 369 TRP 0.019 0.001 TRP F 308 HIS 0.014 0.001 HIS B 255 Details of bonding type rmsd covalent geometry : bond 0.00298 (21457) covalent geometry : angle 0.72718 (29190) SS BOND : bond 0.00037 ( 1) SS BOND : angle 0.31175 ( 2) hydrogen bonds : bond 0.04052 ( 337) hydrogen bonds : angle 7.67758 ( 870) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 717 residues out of total 2333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 716 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 TYR cc_start: 0.8577 (m-80) cc_final: 0.8178 (m-80) REVERT: A 148 LYS cc_start: 0.8316 (ptpt) cc_final: 0.8072 (ptpt) REVERT: A 223 THR cc_start: 0.8403 (t) cc_final: 0.8014 (t) REVERT: A 233 MET cc_start: 0.8770 (mmt) cc_final: 0.7775 (mmm) REVERT: A 246 LEU cc_start: 0.9380 (mt) cc_final: 0.9167 (mt) REVERT: A 247 ARG cc_start: 0.8278 (ptt180) cc_final: 0.7658 (ptp-170) REVERT: A 257 PHE cc_start: 0.8661 (t80) cc_final: 0.8133 (t80) REVERT: A 288 VAL cc_start: 0.9025 (m) cc_final: 0.8664 (m) REVERT: A 366 ASP cc_start: 0.7689 (t0) cc_final: 0.7095 (t0) REVERT: A 369 PHE cc_start: 0.8953 (m-80) cc_final: 0.8625 (m-80) REVERT: A 371 PHE cc_start: 0.8362 (m-80) cc_final: 0.7595 (m-80) REVERT: A 381 GLU cc_start: 0.9091 (mp0) cc_final: 0.8841 (mp0) REVERT: A 389 MET cc_start: 0.8717 (ttt) cc_final: 0.8265 (ppp) REVERT: B 26 TYR cc_start: 0.8311 (m-80) cc_final: 0.7927 (m-80) REVERT: B 32 ILE cc_start: 0.9298 (mp) cc_final: 0.9075 (mp) REVERT: B 74 LEU cc_start: 0.9119 (tp) cc_final: 0.8747 (tp) REVERT: B 151 GLN cc_start: 0.9005 (mt0) cc_final: 0.8723 (mt0) REVERT: B 187 ILE cc_start: 0.8826 (mp) cc_final: 0.7213 (mp) REVERT: B 210 GLN cc_start: 0.9129 (mp10) cc_final: 0.8811 (mp10) REVERT: B 220 ILE cc_start: 0.9682 (pt) cc_final: 0.9419 (pt) REVERT: B 236 ASP cc_start: 0.8401 (t70) cc_final: 0.7954 (t70) REVERT: B 246 LEU cc_start: 0.9426 (mt) cc_final: 0.9027 (mt) REVERT: B 273 ILE cc_start: 0.9377 (mm) cc_final: 0.9157 (mm) REVERT: B 301 GLN cc_start: 0.9101 (mp-120) cc_final: 0.8591 (mp10) REVERT: B 302 LEU cc_start: 0.8988 (pp) cc_final: 0.8559 (pp) REVERT: B 305 LYS cc_start: 0.9523 (mtpt) cc_final: 0.9137 (mtmt) REVERT: B 307 TYR cc_start: 0.8252 (m-80) cc_final: 0.7731 (m-10) REVERT: B 308 TRP cc_start: 0.9256 (m100) cc_final: 0.8985 (m100) REVERT: B 328 THR cc_start: 0.9243 (m) cc_final: 0.8375 (p) REVERT: B 355 TYR cc_start: 0.7373 (m-80) cc_final: 0.6971 (m-80) REVERT: B 364 GLU cc_start: 0.8846 (pp20) cc_final: 0.8477 (tp30) REVERT: B 373 LEU cc_start: 0.8970 (mm) cc_final: 0.8647 (mm) REVERT: B 461 ARG cc_start: 0.9061 (ttp-110) cc_final: 0.8636 (ptp-110) REVERT: C 53 ARG cc_start: 0.6928 (mmt-90) cc_final: 0.6723 (ttt-90) REVERT: C 108 GLN cc_start: 0.8626 (tp-100) cc_final: 0.8147 (mm-40) REVERT: C 154 MET cc_start: 0.8839 (mmp) cc_final: 0.8526 (mmm) REVERT: C 232 GLN cc_start: 0.8625 (mt0) cc_final: 0.8337 (mm-40) REVERT: C 246 LEU cc_start: 0.9295 (mp) cc_final: 0.9085 (mp) REVERT: C 310 GLN cc_start: 0.8809 (tm-30) cc_final: 0.8436 (tm-30) REVERT: C 394 LEU cc_start: 0.9460 (mt) cc_final: 0.9213 (mp) REVERT: C 395 GLU cc_start: 0.9123 (tm-30) cc_final: 0.8861 (tm-30) REVERT: C 456 GLN cc_start: 0.9194 (tm-30) cc_final: 0.8788 (tp40) REVERT: D 32 ILE cc_start: 0.9506 (mp) cc_final: 0.9282 (mp) REVERT: D 63 SER cc_start: 0.9401 (t) cc_final: 0.8837 (p) REVERT: D 94 ARG cc_start: 0.4994 (mpp-170) cc_final: 0.3573 (mtm180) REVERT: D 117 HIS cc_start: 0.8603 (t-90) cc_final: 0.7677 (t-170) REVERT: D 120 LEU cc_start: 0.8595 (mt) cc_final: 0.8104 (mt) REVERT: D 145 MET cc_start: 0.9168 (ppp) cc_final: 0.8765 (ppp) REVERT: D 149 GLN cc_start: 0.8342 (tm-30) cc_final: 0.8032 (tm-30) REVERT: D 165 TRP cc_start: 0.8949 (m100) cc_final: 0.8612 (m100) REVERT: D 197 VAL cc_start: 0.8328 (t) cc_final: 0.7948 (m) REVERT: D 206 PHE cc_start: 0.8328 (m-80) cc_final: 0.7927 (m-80) REVERT: D 303 PHE cc_start: 0.8483 (m-80) cc_final: 0.8186 (m-80) REVERT: D 339 THR cc_start: 0.7344 (p) cc_final: 0.6968 (p) REVERT: D 355 TYR cc_start: 0.8032 (m-80) cc_final: 0.7635 (m-80) REVERT: D 397 TRP cc_start: 0.8705 (m-90) cc_final: 0.8440 (m100) REVERT: D 449 LYS cc_start: 0.7654 (mmtp) cc_final: 0.7285 (mmmt) REVERT: E 41 LEU cc_start: 0.8139 (tt) cc_final: 0.7444 (tt) REVERT: E 66 GLN cc_start: 0.6717 (mt0) cc_final: 0.5472 (mt0) REVERT: E 120 LEU cc_start: 0.8717 (mt) cc_final: 0.8233 (mt) REVERT: E 196 MET cc_start: 0.8733 (mpp) cc_final: 0.8274 (mmt) REVERT: E 233 MET cc_start: 0.9432 (mtm) cc_final: 0.8799 (mtp) REVERT: E 257 PHE cc_start: 0.8635 (m-10) cc_final: 0.8308 (m-80) REVERT: E 326 PHE cc_start: 0.8998 (m-80) cc_final: 0.8658 (m-80) REVERT: E 352 ASN cc_start: 0.9044 (p0) cc_final: 0.8731 (p0) REVERT: E 359 MET cc_start: 0.8448 (mmm) cc_final: 0.8054 (mmm) REVERT: E 374 CYS cc_start: 0.8975 (m) cc_final: 0.8537 (p) REVERT: E 389 MET cc_start: 0.9058 (mmp) cc_final: 0.8844 (mmm) REVERT: E 411 ASP cc_start: 0.7848 (t0) cc_final: 0.7566 (t70) REVERT: E 450 PHE cc_start: 0.8465 (m-80) cc_final: 0.8048 (m-80) REVERT: E 457 TYR cc_start: 0.8600 (m-80) cc_final: 0.8297 (m-80) REVERT: E 461 ARG cc_start: 0.9065 (ptp90) cc_final: 0.8725 (ptp90) REVERT: F 65 TYR cc_start: 0.9223 (m-80) cc_final: 0.8839 (m-10) REVERT: F 103 GLU cc_start: 0.7400 (tp30) cc_final: 0.6803 (tp30) REVERT: F 125 ASP cc_start: 0.9024 (p0) cc_final: 0.8711 (p0) REVERT: F 145 MET cc_start: 0.8887 (tmm) cc_final: 0.8564 (tmm) REVERT: F 148 LYS cc_start: 0.9098 (ptmm) cc_final: 0.8437 (ptmm) REVERT: F 149 GLN cc_start: 0.8314 (pt0) cc_final: 0.7982 (pt0) REVERT: F 150 THR cc_start: 0.9458 (m) cc_final: 0.8111 (m) REVERT: F 151 GLN cc_start: 0.8289 (tt0) cc_final: 0.7308 (tt0) REVERT: F 164 HIS cc_start: 0.8146 (p90) cc_final: 0.7830 (p-80) REVERT: F 165 TRP cc_start: 0.8947 (m100) cc_final: 0.8010 (m100) REVERT: F 185 GLU cc_start: 0.7978 (tp30) cc_final: 0.7626 (mt-10) REVERT: F 196 MET cc_start: 0.7466 (mmm) cc_final: 0.6835 (mmm) REVERT: F 204 MET cc_start: 0.8446 (mpp) cc_final: 0.7985 (mpp) REVERT: F 215 ASP cc_start: 0.8382 (m-30) cc_final: 0.7910 (m-30) REVERT: F 216 VAL cc_start: 0.6966 (m) cc_final: 0.6747 (m) REVERT: F 249 GLU cc_start: 0.8494 (mp0) cc_final: 0.8011 (mp0) REVERT: F 273 ILE cc_start: 0.8203 (mm) cc_final: 0.7766 (mm) REVERT: F 302 LEU cc_start: 0.9013 (mt) cc_final: 0.8100 (mt) REVERT: F 315 HIS cc_start: 0.8102 (m-70) cc_final: 0.7454 (m90) REVERT: F 334 ARG cc_start: 0.9135 (mtt90) cc_final: 0.8583 (mtt-85) REVERT: F 355 TYR cc_start: 0.8714 (m-80) cc_final: 0.8204 (m-80) REVERT: F 356 LYS cc_start: 0.9212 (mmpt) cc_final: 0.8974 (mmtt) REVERT: F 359 MET cc_start: 0.8307 (tpp) cc_final: 0.7842 (tpp) REVERT: F 368 GLN cc_start: 0.9113 (mp-120) cc_final: 0.8371 (mp-120) outliers start: 1 outliers final: 0 residues processed: 716 average time/residue: 0.1420 time to fit residues: 157.0639 Evaluate side-chains 568 residues out of total 2333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 568 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 189 optimal weight: 20.0000 chunk 52 optimal weight: 20.0000 chunk 225 optimal weight: 3.9990 chunk 79 optimal weight: 9.9990 chunk 161 optimal weight: 40.0000 chunk 99 optimal weight: 20.0000 chunk 164 optimal weight: 50.0000 chunk 98 optimal weight: 0.0970 chunk 191 optimal weight: 7.9990 chunk 72 optimal weight: 0.6980 chunk 200 optimal weight: 0.9990 overall best weight: 2.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 192 GLN ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 149 GLN ** C 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 HIS D 301 GLN E 212 ASN ** E 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 372 GLN ** F 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 301 GLN F 317 ASN F 337 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.137724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.111786 restraints weight = 59764.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.115683 restraints weight = 34943.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.118443 restraints weight = 23543.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.120399 restraints weight = 17388.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.121821 restraints weight = 13776.385| |-----------------------------------------------------------------------------| r_work (final): 0.3857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.3755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21458 Z= 0.133 Angle : 0.707 11.810 29192 Z= 0.357 Chirality : 0.048 0.335 3146 Planarity : 0.006 0.103 3837 Dihedral : 6.143 39.573 2886 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.52 % Favored : 90.44 % Rotamer: Outliers : 0.09 % Allowed : 3.73 % Favored : 96.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 1.11 % Twisted General : 0.08 % 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 are not related in a simple way. whole: -3.26 (0.15), residues: 2658 helix: -2.26 (0.30), residues: 228 sheet: -1.59 (0.20), residues: 604 loop : -2.52 (0.13), residues: 1826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 254 TYR 0.028 0.002 TYR C 365 PHE 0.031 0.002 PHE A 88 TRP 0.018 0.001 TRP A 308 HIS 0.011 0.001 HIS D 361 Details of bonding type rmsd covalent geometry : bond 0.00296 (21457) covalent geometry : angle 0.70747 (29190) SS BOND : bond 0.00098 ( 1) SS BOND : angle 0.22917 ( 2) hydrogen bonds : bond 0.03562 ( 337) hydrogen bonds : angle 7.30561 ( 870) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 685 residues out of total 2333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 683 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 TYR cc_start: 0.8567 (m-80) cc_final: 0.8271 (m-80) REVERT: A 74 LEU cc_start: 0.8794 (tp) cc_final: 0.8545 (tp) REVERT: A 97 TRP cc_start: 0.8104 (m100) cc_final: 0.7874 (m100) REVERT: A 165 TRP cc_start: 0.8938 (m100) cc_final: 0.8458 (m100) REVERT: A 195 ASP cc_start: 0.8148 (t70) cc_final: 0.7180 (t0) REVERT: A 196 MET cc_start: 0.7902 (mtp) cc_final: 0.7433 (mtm) REVERT: A 247 ARG cc_start: 0.8352 (ptt180) cc_final: 0.7702 (ptp-170) REVERT: A 250 GLN cc_start: 0.8564 (mp-120) cc_final: 0.8216 (mp-120) REVERT: A 257 PHE cc_start: 0.8731 (t80) cc_final: 0.8198 (t80) REVERT: A 288 VAL cc_start: 0.9086 (m) cc_final: 0.8755 (m) REVERT: A 369 PHE cc_start: 0.8928 (m-80) cc_final: 0.8574 (m-80) REVERT: A 371 PHE cc_start: 0.8174 (m-80) cc_final: 0.7440 (m-80) REVERT: A 381 GLU cc_start: 0.9098 (mp0) cc_final: 0.8857 (mp0) REVERT: A 389 MET cc_start: 0.8715 (ttt) cc_final: 0.8278 (tmm) REVERT: A 412 THR cc_start: 0.9373 (t) cc_final: 0.9040 (t) REVERT: B 26 TYR cc_start: 0.8262 (m-80) cc_final: 0.7914 (m-80) REVERT: B 74 LEU cc_start: 0.9045 (tp) cc_final: 0.8726 (tp) REVERT: B 151 GLN cc_start: 0.8934 (mt0) cc_final: 0.8679 (mt0) REVERT: B 210 GLN cc_start: 0.9215 (mp10) cc_final: 0.8750 (mp10) REVERT: B 220 ILE cc_start: 0.9757 (pt) cc_final: 0.9496 (pt) REVERT: B 236 ASP cc_start: 0.8408 (t70) cc_final: 0.8070 (t70) REVERT: B 246 LEU cc_start: 0.9284 (mt) cc_final: 0.8993 (mt) REVERT: B 273 ILE cc_start: 0.9375 (mm) cc_final: 0.9149 (mm) REVERT: B 289 ASN cc_start: 0.9402 (t0) cc_final: 0.8953 (t0) REVERT: B 301 GLN cc_start: 0.9113 (mp-120) cc_final: 0.8505 (mp10) REVERT: B 302 LEU cc_start: 0.9015 (pp) cc_final: 0.8643 (pp) REVERT: B 305 LYS cc_start: 0.9528 (mtpt) cc_final: 0.9149 (mtmt) REVERT: B 307 TYR cc_start: 0.8350 (m-80) cc_final: 0.8061 (m-10) REVERT: B 328 THR cc_start: 0.9224 (m) cc_final: 0.8391 (p) REVERT: B 355 TYR cc_start: 0.7550 (m-80) cc_final: 0.6917 (m-80) REVERT: B 359 MET cc_start: 0.7662 (mmp) cc_final: 0.7229 (mmp) REVERT: B 364 GLU cc_start: 0.8818 (pp20) cc_final: 0.8534 (tp30) REVERT: B 461 ARG cc_start: 0.9047 (ttp-110) cc_final: 0.8572 (mtm110) REVERT: C 51 ILE cc_start: 0.8258 (tt) cc_final: 0.7995 (tt) REVERT: C 53 ARG cc_start: 0.6968 (mmt-90) cc_final: 0.6720 (ttt-90) REVERT: C 108 GLN cc_start: 0.8619 (tp-100) cc_final: 0.8203 (mm-40) REVERT: C 154 MET cc_start: 0.8817 (mmp) cc_final: 0.8565 (mmm) REVERT: C 204 MET cc_start: 0.7566 (pmm) cc_final: 0.6593 (pmm) REVERT: C 232 GLN cc_start: 0.8728 (mt0) cc_final: 0.8474 (mm-40) REVERT: C 310 GLN cc_start: 0.8873 (tm-30) cc_final: 0.8514 (tm-30) REVERT: C 319 ILE cc_start: 0.8937 (mp) cc_final: 0.8725 (mp) REVERT: C 359 MET cc_start: 0.8359 (mmt) cc_final: 0.8121 (mmt) REVERT: C 395 GLU cc_start: 0.9149 (tm-30) cc_final: 0.8889 (tm-30) REVERT: C 456 GLN cc_start: 0.9319 (tm-30) cc_final: 0.9115 (tm-30) REVERT: D 48 TYR cc_start: 0.7732 (m-80) cc_final: 0.7255 (m-80) REVERT: D 63 SER cc_start: 0.9323 (t) cc_final: 0.9009 (p) REVERT: D 117 HIS cc_start: 0.8431 (t-90) cc_final: 0.7779 (t-170) REVERT: D 120 LEU cc_start: 0.8665 (mt) cc_final: 0.8152 (mt) REVERT: D 145 MET cc_start: 0.9187 (ppp) cc_final: 0.8804 (ppp) REVERT: D 149 GLN cc_start: 0.8393 (tm-30) cc_final: 0.8129 (tm-30) REVERT: D 197 VAL cc_start: 0.8296 (t) cc_final: 0.7927 (m) REVERT: D 206 PHE cc_start: 0.8327 (m-80) cc_final: 0.7834 (m-80) REVERT: D 233 MET cc_start: 0.8895 (mmp) cc_final: 0.8667 (mmm) REVERT: D 303 PHE cc_start: 0.8544 (m-80) cc_final: 0.8237 (m-80) REVERT: D 355 TYR cc_start: 0.7981 (m-80) cc_final: 0.7629 (m-80) REVERT: D 397 TRP cc_start: 0.8709 (m-90) cc_final: 0.8444 (m100) REVERT: D 449 LYS cc_start: 0.7684 (mmtp) cc_final: 0.7368 (mmmt) REVERT: D 459 LEU cc_start: 0.8558 (pp) cc_final: 0.8357 (pp) REVERT: E 41 LEU cc_start: 0.7055 (tt) cc_final: 0.6450 (tt) REVERT: E 120 LEU cc_start: 0.8797 (mt) cc_final: 0.8347 (mt) REVERT: E 196 MET cc_start: 0.8859 (mpp) cc_final: 0.8597 (mpp) REVERT: E 233 MET cc_start: 0.9422 (mtm) cc_final: 0.8785 (mtt) REVERT: E 249 GLU cc_start: 0.8993 (mp0) cc_final: 0.8718 (mp0) REVERT: E 250 GLN cc_start: 0.8269 (mm-40) cc_final: 0.7776 (tm-30) REVERT: E 254 ARG cc_start: 0.9169 (ttm-80) cc_final: 0.8481 (ttm110) REVERT: E 257 PHE cc_start: 0.8548 (m-10) cc_final: 0.8272 (m-80) REVERT: E 326 PHE cc_start: 0.8988 (m-80) cc_final: 0.8670 (m-80) REVERT: E 338 MET cc_start: 0.9131 (mpp) cc_final: 0.8532 (mpp) REVERT: E 352 ASN cc_start: 0.9096 (p0) cc_final: 0.8844 (p0) REVERT: E 359 MET cc_start: 0.8079 (mmm) cc_final: 0.7523 (mmm) REVERT: E 363 GLU cc_start: 0.8917 (mm-30) cc_final: 0.8455 (mm-30) REVERT: E 364 GLU cc_start: 0.7664 (mm-30) cc_final: 0.6806 (mm-30) REVERT: E 372 GLN cc_start: 0.7718 (OUTLIER) cc_final: 0.7469 (tm-30) REVERT: E 411 ASP cc_start: 0.7955 (t0) cc_final: 0.7679 (t70) REVERT: E 450 PHE cc_start: 0.8372 (m-80) cc_final: 0.8096 (m-80) REVERT: E 457 TYR cc_start: 0.8679 (m-80) cc_final: 0.8154 (m-80) REVERT: E 461 ARG cc_start: 0.9091 (ptp90) cc_final: 0.8692 (ptp90) REVERT: F 65 TYR cc_start: 0.9253 (m-80) cc_final: 0.9023 (m-10) REVERT: F 103 GLU cc_start: 0.7405 (tp30) cc_final: 0.6933 (tp30) REVERT: F 125 ASP cc_start: 0.9028 (p0) cc_final: 0.8743 (p0) REVERT: F 148 LYS cc_start: 0.9144 (ptmm) cc_final: 0.8531 (ptmm) REVERT: F 149 GLN cc_start: 0.8842 (pt0) cc_final: 0.8471 (pt0) REVERT: F 150 THR cc_start: 0.9440 (m) cc_final: 0.8063 (m) REVERT: F 151 GLN cc_start: 0.8270 (tt0) cc_final: 0.7266 (tt0) REVERT: F 165 TRP cc_start: 0.8889 (m100) cc_final: 0.8056 (m100) REVERT: F 185 GLU cc_start: 0.7990 (tp30) cc_final: 0.7679 (mt-10) REVERT: F 196 MET cc_start: 0.7474 (mmm) cc_final: 0.6756 (mmm) REVERT: F 204 MET cc_start: 0.8539 (mpp) cc_final: 0.8009 (mpp) REVERT: F 244 PHE cc_start: 0.8539 (t80) cc_final: 0.8272 (t80) REVERT: F 249 GLU cc_start: 0.8475 (mp0) cc_final: 0.8108 (mp0) REVERT: F 273 ILE cc_start: 0.8235 (mm) cc_final: 0.7828 (mm) REVERT: F 302 LEU cc_start: 0.8909 (mt) cc_final: 0.7990 (mt) REVERT: F 315 HIS cc_start: 0.8030 (m-70) cc_final: 0.7483 (m90) REVERT: F 324 GLN cc_start: 0.9109 (mt0) cc_final: 0.8879 (mm-40) REVERT: F 334 ARG cc_start: 0.9015 (mtt90) cc_final: 0.8641 (mtt-85) REVERT: F 355 TYR cc_start: 0.8445 (m-80) cc_final: 0.8104 (m-80) REVERT: F 356 LYS cc_start: 0.9130 (mmpt) cc_final: 0.8874 (mmtt) REVERT: F 360 ARG cc_start: 0.7051 (mtt180) cc_final: 0.6188 (mtt180) REVERT: F 363 GLU cc_start: 0.8483 (mp0) cc_final: 0.7927 (mp0) REVERT: F 368 GLN cc_start: 0.9183 (mp-120) cc_final: 0.8584 (mp-120) outliers start: 2 outliers final: 1 residues processed: 684 average time/residue: 0.1368 time to fit residues: 144.6613 Evaluate side-chains 554 residues out of total 2333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 552 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 188 optimal weight: 5.9990 chunk 195 optimal weight: 0.9980 chunk 189 optimal weight: 7.9990 chunk 236 optimal weight: 30.0000 chunk 221 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 234 optimal weight: 7.9990 chunk 224 optimal weight: 8.9990 chunk 76 optimal weight: 50.0000 chunk 227 optimal weight: 9.9990 chunk 134 optimal weight: 7.9990 overall best weight: 6.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 66 GLN A 192 GLN ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 HIS A 466 GLN ** B 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 387 HIS ** C 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 212 ASN ** E 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 313 GLN E 337 ASN ** F 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 301 GLN F 337 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.133650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.106975 restraints weight = 62135.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.110670 restraints weight = 36973.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.113331 restraints weight = 25370.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.115229 restraints weight = 19039.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.116574 restraints weight = 15310.278| |-----------------------------------------------------------------------------| r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.3923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 21458 Z= 0.174 Angle : 0.721 11.550 29192 Z= 0.367 Chirality : 0.048 0.321 3146 Planarity : 0.006 0.105 3837 Dihedral : 6.214 37.469 2886 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 17.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.65 % Favored : 89.35 % Rotamer: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 1.67 % Twisted General : 0.08 % 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 are not related in a simple way. whole: -3.26 (0.15), residues: 2658 helix: -2.21 (0.29), residues: 247 sheet: -1.56 (0.20), residues: 596 loop : -2.53 (0.13), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 259 TYR 0.030 0.002 TYR C 365 PHE 0.032 0.002 PHE D 33 TRP 0.019 0.001 TRP A 308 HIS 0.013 0.002 HIS B 255 Details of bonding type rmsd covalent geometry : bond 0.00380 (21457) covalent geometry : angle 0.72132 (29190) SS BOND : bond 0.00228 ( 1) SS BOND : angle 0.10653 ( 2) hydrogen bonds : bond 0.03575 ( 337) hydrogen bonds : angle 7.17220 ( 870) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 661 residues out of total 2333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 661 time to evaluate : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 GLN cc_start: 0.8567 (mp10) cc_final: 0.8292 (mp10) REVERT: A 97 TRP cc_start: 0.8114 (m100) cc_final: 0.7881 (m100) REVERT: A 204 MET cc_start: 0.5045 (pmm) cc_final: 0.3084 (ttt) REVERT: A 246 LEU cc_start: 0.9381 (mt) cc_final: 0.9167 (mt) REVERT: A 247 ARG cc_start: 0.8211 (ptt180) cc_final: 0.7569 (ptt180) REVERT: A 250 GLN cc_start: 0.8348 (mp-120) cc_final: 0.8076 (mp-120) REVERT: A 257 PHE cc_start: 0.8836 (t80) cc_final: 0.8499 (t80) REVERT: A 288 VAL cc_start: 0.9107 (m) cc_final: 0.8858 (m) REVERT: A 369 PHE cc_start: 0.8937 (m-80) cc_final: 0.8634 (m-80) REVERT: A 371 PHE cc_start: 0.8287 (m-80) cc_final: 0.7560 (m-80) REVERT: A 381 GLU cc_start: 0.9090 (mp0) cc_final: 0.8816 (mp0) REVERT: A 389 MET cc_start: 0.8929 (ttt) cc_final: 0.8290 (tmm) REVERT: B 26 TYR cc_start: 0.8281 (m-80) cc_final: 0.7944 (m-80) REVERT: B 32 ILE cc_start: 0.9231 (mp) cc_final: 0.9016 (mp) REVERT: B 46 HIS cc_start: 0.9154 (t70) cc_final: 0.8681 (t-170) REVERT: B 61 LYS cc_start: 0.8289 (tttt) cc_final: 0.7874 (ttpt) REVERT: B 151 GLN cc_start: 0.8705 (mt0) cc_final: 0.8505 (mt0) REVERT: B 206 PHE cc_start: 0.8932 (m-10) cc_final: 0.8687 (m-10) REVERT: B 210 GLN cc_start: 0.9220 (mp10) cc_final: 0.8634 (mp10) REVERT: B 220 ILE cc_start: 0.9704 (pt) cc_final: 0.9476 (pt) REVERT: B 223 THR cc_start: 0.9275 (t) cc_final: 0.9064 (t) REVERT: B 233 MET cc_start: 0.8782 (mmt) cc_final: 0.8125 (mmt) REVERT: B 236 ASP cc_start: 0.8504 (t70) cc_final: 0.8176 (t70) REVERT: B 246 LEU cc_start: 0.9238 (mt) cc_final: 0.8972 (mt) REVERT: B 273 ILE cc_start: 0.9427 (mm) cc_final: 0.9226 (mm) REVERT: B 298 SER cc_start: 0.9127 (p) cc_final: 0.8688 (p) REVERT: B 301 GLN cc_start: 0.9057 (mp-120) cc_final: 0.8217 (mp10) REVERT: B 302 LEU cc_start: 0.8942 (pp) cc_final: 0.8528 (pp) REVERT: B 305 LYS cc_start: 0.9509 (mtpt) cc_final: 0.9150 (mtmt) REVERT: B 307 TYR cc_start: 0.8322 (m-80) cc_final: 0.8077 (m-10) REVERT: B 359 MET cc_start: 0.7886 (mmp) cc_final: 0.7182 (mmp) REVERT: B 364 GLU cc_start: 0.8720 (pp20) cc_final: 0.8199 (tp30) REVERT: B 373 LEU cc_start: 0.8839 (mm) cc_final: 0.8591 (mm) REVERT: C 53 ARG cc_start: 0.6954 (mmt-90) cc_final: 0.6732 (ttt-90) REVERT: C 74 LEU cc_start: 0.8962 (tp) cc_final: 0.8650 (tp) REVERT: C 108 GLN cc_start: 0.8593 (tp-100) cc_final: 0.8160 (mm-40) REVERT: C 146 ASP cc_start: 0.8497 (m-30) cc_final: 0.8287 (m-30) REVERT: C 154 MET cc_start: 0.8786 (mmp) cc_final: 0.8554 (mmm) REVERT: C 201 PHE cc_start: 0.8154 (m-10) cc_final: 0.7702 (m-80) REVERT: C 204 MET cc_start: 0.7584 (pmm) cc_final: 0.6396 (pmm) REVERT: C 232 GLN cc_start: 0.8792 (mt0) cc_final: 0.8480 (mm-40) REVERT: C 310 GLN cc_start: 0.8815 (tm-30) cc_final: 0.8457 (tm-30) REVERT: C 333 THR cc_start: 0.9514 (p) cc_final: 0.9044 (p) REVERT: C 359 MET cc_start: 0.8137 (mmt) cc_final: 0.7855 (mmt) REVERT: C 395 GLU cc_start: 0.9186 (tm-30) cc_final: 0.8856 (tm-30) REVERT: C 438 ASN cc_start: 0.9161 (m110) cc_final: 0.8884 (m-40) REVERT: D 63 SER cc_start: 0.9492 (t) cc_final: 0.9068 (p) REVERT: D 117 HIS cc_start: 0.8306 (t-90) cc_final: 0.7548 (t-170) REVERT: D 120 LEU cc_start: 0.8534 (mt) cc_final: 0.7960 (mt) REVERT: D 184 LEU cc_start: 0.8168 (tp) cc_final: 0.7967 (tp) REVERT: D 206 PHE cc_start: 0.8181 (m-80) cc_final: 0.7730 (m-80) REVERT: D 209 LEU cc_start: 0.9290 (mt) cc_final: 0.8759 (mt) REVERT: D 233 MET cc_start: 0.8844 (mmp) cc_final: 0.8614 (mmm) REVERT: D 355 TYR cc_start: 0.8049 (m-80) cc_final: 0.7664 (m-80) REVERT: D 359 MET cc_start: 0.8026 (tpp) cc_final: 0.7803 (mmm) REVERT: D 397 TRP cc_start: 0.8729 (m-90) cc_final: 0.8318 (m100) REVERT: D 445 ASN cc_start: 0.9131 (t0) cc_final: 0.8931 (t0) REVERT: D 449 LYS cc_start: 0.7871 (mmtp) cc_final: 0.7489 (mmmt) REVERT: E 41 LEU cc_start: 0.7203 (tt) cc_final: 0.6608 (tt) REVERT: E 66 GLN cc_start: 0.7364 (mt0) cc_final: 0.6112 (mt0) REVERT: E 120 LEU cc_start: 0.8549 (mt) cc_final: 0.7899 (mt) REVERT: E 146 ASP cc_start: 0.8794 (p0) cc_final: 0.8541 (p0) REVERT: E 196 MET cc_start: 0.8935 (mpp) cc_final: 0.8436 (mmt) REVERT: E 232 GLN cc_start: 0.8417 (mt0) cc_final: 0.7782 (tp-100) REVERT: E 254 ARG cc_start: 0.9169 (ttm-80) cc_final: 0.8649 (ttm110) REVERT: E 257 PHE cc_start: 0.8365 (m-10) cc_final: 0.8156 (m-80) REVERT: E 326 PHE cc_start: 0.8969 (m-80) cc_final: 0.8686 (m-80) REVERT: E 338 MET cc_start: 0.9047 (mpp) cc_final: 0.8623 (mpp) REVERT: E 359 MET cc_start: 0.8013 (mmm) cc_final: 0.7776 (mmm) REVERT: E 364 GLU cc_start: 0.7686 (mm-30) cc_final: 0.6849 (mm-30) REVERT: E 389 MET cc_start: 0.9033 (mmp) cc_final: 0.8821 (mmm) REVERT: E 397 TRP cc_start: 0.7656 (m100) cc_final: 0.7301 (m100) REVERT: E 411 ASP cc_start: 0.8011 (t0) cc_final: 0.7746 (t70) REVERT: E 450 PHE cc_start: 0.8268 (m-80) cc_final: 0.7724 (m-80) REVERT: E 461 ARG cc_start: 0.9005 (ptp90) cc_final: 0.8613 (ptp90) REVERT: F 40 ARG cc_start: 0.7397 (ttm110) cc_final: 0.7000 (ttm110) REVERT: F 65 TYR cc_start: 0.9217 (m-80) cc_final: 0.8959 (m-80) REVERT: F 71 LYS cc_start: 0.8121 (tmtt) cc_final: 0.7904 (tptp) REVERT: F 103 GLU cc_start: 0.7552 (tp30) cc_final: 0.7224 (tp30) REVERT: F 125 ASP cc_start: 0.9064 (p0) cc_final: 0.8721 (p0) REVERT: F 148 LYS cc_start: 0.9011 (ptmm) cc_final: 0.8721 (ptmm) REVERT: F 149 GLN cc_start: 0.8785 (pt0) cc_final: 0.8214 (pt0) REVERT: F 150 THR cc_start: 0.9330 (m) cc_final: 0.8033 (m) REVERT: F 165 TRP cc_start: 0.8856 (m100) cc_final: 0.8138 (m100) REVERT: F 192 GLN cc_start: 0.9019 (mt0) cc_final: 0.8643 (mm-40) REVERT: F 196 MET cc_start: 0.7521 (mmm) cc_final: 0.6912 (mmm) REVERT: F 204 MET cc_start: 0.8545 (mpp) cc_final: 0.8283 (mpp) REVERT: F 210 GLN cc_start: 0.8999 (mm110) cc_final: 0.8750 (mm-40) REVERT: F 249 GLU cc_start: 0.8518 (mp0) cc_final: 0.8201 (mp0) REVERT: F 273 ILE cc_start: 0.8400 (mm) cc_final: 0.8009 (mm) REVERT: F 315 HIS cc_start: 0.7915 (m-70) cc_final: 0.7466 (m90) REVERT: F 356 LYS cc_start: 0.9291 (mmpt) cc_final: 0.8987 (mmtt) REVERT: F 360 ARG cc_start: 0.6800 (mtt180) cc_final: 0.6111 (mtt180) REVERT: F 363 GLU cc_start: 0.8473 (mp0) cc_final: 0.7961 (mp0) outliers start: 0 outliers final: 0 residues processed: 661 average time/residue: 0.1301 time to fit residues: 133.6113 Evaluate side-chains 552 residues out of total 2333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 552 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 234 optimal weight: 10.0000 chunk 198 optimal weight: 6.9990 chunk 148 optimal weight: 30.0000 chunk 104 optimal weight: 0.5980 chunk 74 optimal weight: 20.0000 chunk 120 optimal weight: 0.9980 chunk 261 optimal weight: 5.9990 chunk 213 optimal weight: 7.9990 chunk 12 optimal weight: 8.9990 chunk 207 optimal weight: 40.0000 chunk 188 optimal weight: 10.0000 overall best weight: 4.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 192 GLN ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 372 GLN ** B 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 255 HIS ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 HIS ** C 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 164 HIS ** D 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 212 ASN ** E 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 301 GLN F 337 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.134987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.108169 restraints weight = 62232.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.111838 restraints weight = 37461.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.114446 restraints weight = 25904.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.116329 restraints weight = 19562.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.117677 restraints weight = 15796.236| |-----------------------------------------------------------------------------| r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.4199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 21458 Z= 0.145 Angle : 0.713 13.375 29192 Z= 0.356 Chirality : 0.048 0.263 3146 Planarity : 0.006 0.103 3837 Dihedral : 6.017 35.942 2886 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 16.84 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.71 % Favored : 90.26 % Rotamer: Outliers : 0.09 % Allowed : 2.83 % Favored : 97.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 1.11 % Twisted General : 0.08 % 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 are not related in a simple way. whole: -3.15 (0.15), residues: 2658 helix: -2.06 (0.29), residues: 247 sheet: -1.39 (0.20), residues: 588 loop : -2.49 (0.14), residues: 1823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 461 TYR 0.022 0.002 TYR E 307 PHE 0.050 0.002 PHE D 257 TRP 0.021 0.001 TRP F 397 HIS 0.009 0.002 HIS B 255 Details of bonding type rmsd covalent geometry : bond 0.00323 (21457) covalent geometry : angle 0.71261 (29190) SS BOND : bond 0.00162 ( 1) SS BOND : angle 0.16685 ( 2) hydrogen bonds : bond 0.03164 ( 337) hydrogen bonds : angle 6.93507 ( 870) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 660 residues out of total 2333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 658 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 TYR cc_start: 0.8305 (m-80) cc_final: 0.8061 (m-80) REVERT: A 97 TRP cc_start: 0.8134 (m100) cc_final: 0.7804 (m100) REVERT: A 165 TRP cc_start: 0.8776 (m100) cc_final: 0.8370 (m100) REVERT: A 246 LEU cc_start: 0.9401 (mt) cc_final: 0.9198 (mt) REVERT: A 250 GLN cc_start: 0.8304 (mp-120) cc_final: 0.8091 (mp-120) REVERT: A 257 PHE cc_start: 0.8811 (t80) cc_final: 0.8442 (t80) REVERT: A 288 VAL cc_start: 0.9001 (m) cc_final: 0.8676 (m) REVERT: A 369 PHE cc_start: 0.8898 (m-80) cc_final: 0.8593 (m-80) REVERT: A 371 PHE cc_start: 0.8162 (m-80) cc_final: 0.7482 (m-80) REVERT: A 381 GLU cc_start: 0.9080 (mp0) cc_final: 0.8803 (mp0) REVERT: A 389 MET cc_start: 0.8882 (ttt) cc_final: 0.8283 (tmm) REVERT: A 412 THR cc_start: 0.9300 (t) cc_final: 0.8872 (t) REVERT: B 26 TYR cc_start: 0.8294 (m-80) cc_final: 0.7990 (m-80) REVERT: B 46 HIS cc_start: 0.9072 (t70) cc_final: 0.8665 (t-170) REVERT: B 61 LYS cc_start: 0.8253 (tttt) cc_final: 0.7839 (ttpt) REVERT: B 67 TYR cc_start: 0.8141 (m-80) cc_final: 0.7561 (m-80) REVERT: B 74 LEU cc_start: 0.8966 (tp) cc_final: 0.8569 (tp) REVERT: B 151 GLN cc_start: 0.8646 (mt0) cc_final: 0.8240 (mt0) REVERT: B 206 PHE cc_start: 0.9209 (m-10) cc_final: 0.8869 (m-10) REVERT: B 210 GLN cc_start: 0.9270 (mp10) cc_final: 0.8824 (mp10) REVERT: B 211 THR cc_start: 0.8944 (p) cc_final: 0.8699 (p) REVERT: B 220 ILE cc_start: 0.9721 (pt) cc_final: 0.9469 (pt) REVERT: B 233 MET cc_start: 0.8771 (mmt) cc_final: 0.8129 (mmt) REVERT: B 236 ASP cc_start: 0.8444 (t70) cc_final: 0.8224 (t70) REVERT: B 251 MET cc_start: 0.8798 (tpt) cc_final: 0.8447 (tpt) REVERT: B 298 SER cc_start: 0.9034 (p) cc_final: 0.8665 (p) REVERT: B 301 GLN cc_start: 0.9039 (mp-120) cc_final: 0.8234 (mp10) REVERT: B 302 LEU cc_start: 0.9000 (pp) cc_final: 0.8600 (pp) REVERT: B 305 LYS cc_start: 0.9532 (mtpt) cc_final: 0.9146 (mtmt) REVERT: B 307 TYR cc_start: 0.8323 (m-80) cc_final: 0.7989 (m-10) REVERT: B 359 MET cc_start: 0.8108 (mmp) cc_final: 0.7325 (mmp) REVERT: B 395 GLU cc_start: 0.9205 (OUTLIER) cc_final: 0.8991 (pm20) REVERT: B 461 ARG cc_start: 0.8946 (ttp-110) cc_final: 0.8501 (mtm110) REVERT: C 68 ARG cc_start: 0.8808 (mmt-90) cc_final: 0.8537 (mmt-90) REVERT: C 108 GLN cc_start: 0.8613 (tp-100) cc_final: 0.8152 (mm-40) REVERT: C 163 GLU cc_start: 0.8569 (pm20) cc_final: 0.8309 (pm20) REVERT: C 201 PHE cc_start: 0.8192 (m-10) cc_final: 0.7788 (m-80) REVERT: C 204 MET cc_start: 0.7578 (pmm) cc_final: 0.6306 (pmm) REVERT: C 220 ILE cc_start: 0.9591 (mp) cc_final: 0.9385 (mp) REVERT: C 232 GLN cc_start: 0.8782 (mt0) cc_final: 0.8493 (mm-40) REVERT: C 310 GLN cc_start: 0.8785 (tm-30) cc_final: 0.8459 (tm-30) REVERT: C 395 GLU cc_start: 0.9182 (tm-30) cc_final: 0.8876 (tm-30) REVERT: C 438 ASN cc_start: 0.9152 (m110) cc_final: 0.8885 (m110) REVERT: D 48 TYR cc_start: 0.8041 (m-80) cc_final: 0.7563 (m-80) REVERT: D 63 SER cc_start: 0.9383 (t) cc_final: 0.8993 (p) REVERT: D 106 ARG cc_start: 0.8014 (mmm-85) cc_final: 0.7569 (mmm-85) REVERT: D 117 HIS cc_start: 0.8307 (t-90) cc_final: 0.7503 (t-170) REVERT: D 120 LEU cc_start: 0.8546 (mt) cc_final: 0.8026 (mt) REVERT: D 145 MET cc_start: 0.8914 (ppp) cc_final: 0.8707 (ppp) REVERT: D 184 LEU cc_start: 0.8238 (tp) cc_final: 0.7991 (tp) REVERT: D 206 PHE cc_start: 0.8143 (m-80) cc_final: 0.7623 (m-80) REVERT: D 233 MET cc_start: 0.8815 (mmp) cc_final: 0.8597 (mmm) REVERT: D 355 TYR cc_start: 0.7994 (m-80) cc_final: 0.7623 (m-80) REVERT: D 361 HIS cc_start: 0.6111 (t70) cc_final: 0.5824 (t70) REVERT: D 364 GLU cc_start: 0.8623 (tm-30) cc_final: 0.8213 (tm-30) REVERT: D 397 TRP cc_start: 0.8696 (m-90) cc_final: 0.8246 (m100) REVERT: D 449 LYS cc_start: 0.7911 (mmtp) cc_final: 0.7510 (mmmt) REVERT: E 41 LEU cc_start: 0.7294 (tt) cc_final: 0.6707 (tt) REVERT: E 120 LEU cc_start: 0.8689 (mt) cc_final: 0.8050 (mt) REVERT: E 146 ASP cc_start: 0.8757 (p0) cc_final: 0.8437 (p0) REVERT: E 196 MET cc_start: 0.9020 (mpp) cc_final: 0.8751 (mpp) REVERT: E 254 ARG cc_start: 0.9232 (ttm-80) cc_final: 0.8661 (ttm110) REVERT: E 326 PHE cc_start: 0.8990 (m-80) cc_final: 0.8716 (m-80) REVERT: E 338 MET cc_start: 0.8999 (mpp) cc_final: 0.8797 (mpp) REVERT: E 352 ASN cc_start: 0.9155 (p0) cc_final: 0.8913 (p0) REVERT: E 363 GLU cc_start: 0.8610 (mm-30) cc_final: 0.8246 (mm-30) REVERT: E 364 GLU cc_start: 0.7669 (mm-30) cc_final: 0.6554 (mm-30) REVERT: E 389 MET cc_start: 0.9052 (mmp) cc_final: 0.8851 (mmm) REVERT: E 397 TRP cc_start: 0.7701 (m100) cc_final: 0.7384 (m100) REVERT: E 411 ASP cc_start: 0.8036 (t0) cc_final: 0.7816 (t70) REVERT: E 450 PHE cc_start: 0.8233 (m-80) cc_final: 0.7775 (m-80) REVERT: E 452 SER cc_start: 0.9121 (m) cc_final: 0.8860 (t) REVERT: E 461 ARG cc_start: 0.8956 (ptp90) cc_final: 0.8546 (ptp90) REVERT: F 40 ARG cc_start: 0.7516 (ttm110) cc_final: 0.7082 (ttm110) REVERT: F 65 TYR cc_start: 0.9250 (m-80) cc_final: 0.8944 (m-80) REVERT: F 103 GLU cc_start: 0.7614 (tp30) cc_final: 0.7293 (tp30) REVERT: F 125 ASP cc_start: 0.9057 (p0) cc_final: 0.8786 (p0) REVERT: F 148 LYS cc_start: 0.8969 (ptmm) cc_final: 0.8529 (ptmm) REVERT: F 149 GLN cc_start: 0.8826 (pt0) cc_final: 0.8313 (pt0) REVERT: F 150 THR cc_start: 0.9347 (m) cc_final: 0.7770 (m) REVERT: F 151 GLN cc_start: 0.8190 (tt0) cc_final: 0.6849 (tt0) REVERT: F 165 TRP cc_start: 0.8871 (m100) cc_final: 0.7973 (m100) REVERT: F 186 LEU cc_start: 0.8766 (tp) cc_final: 0.8543 (tp) REVERT: F 192 GLN cc_start: 0.8947 (mt0) cc_final: 0.8593 (mt0) REVERT: F 196 MET cc_start: 0.7573 (mmm) cc_final: 0.6922 (mmm) REVERT: F 204 MET cc_start: 0.8485 (mpp) cc_final: 0.7980 (mpp) REVERT: F 237 PRO cc_start: 0.9234 (Cg_endo) cc_final: 0.8791 (Cg_exo) REVERT: F 248 LYS cc_start: 0.9125 (mttt) cc_final: 0.8912 (mttt) REVERT: F 249 GLU cc_start: 0.8462 (mp0) cc_final: 0.8032 (mp0) REVERT: F 273 ILE cc_start: 0.8411 (mm) cc_final: 0.8044 (mm) REVERT: F 302 LEU cc_start: 0.8835 (mt) cc_final: 0.7981 (mt) REVERT: F 315 HIS cc_start: 0.7846 (m-70) cc_final: 0.7449 (m90) REVERT: F 355 TYR cc_start: 0.8379 (m-80) cc_final: 0.8045 (m-80) REVERT: F 357 GLU cc_start: 0.8161 (tm-30) cc_final: 0.7857 (tm-30) REVERT: F 360 ARG cc_start: 0.6830 (mtt180) cc_final: 0.5969 (mpt180) REVERT: F 363 GLU cc_start: 0.8440 (mp0) cc_final: 0.7855 (mp0) REVERT: F 444 VAL cc_start: 0.9588 (m) cc_final: 0.9371 (m) outliers start: 2 outliers final: 1 residues processed: 659 average time/residue: 0.1331 time to fit residues: 136.1327 Evaluate side-chains 554 residues out of total 2333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 552 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 177 optimal weight: 30.0000 chunk 100 optimal weight: 9.9990 chunk 19 optimal weight: 6.9990 chunk 228 optimal weight: 20.0000 chunk 216 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 69 optimal weight: 30.0000 chunk 37 optimal weight: 7.9990 chunk 18 optimal weight: 10.0000 chunk 17 optimal weight: 5.9990 chunk 108 optimal weight: 8.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 212 ASN ** E 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 108 GLN ** F 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 255 HIS F 301 GLN F 337 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.131221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.104709 restraints weight = 63457.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.108245 restraints weight = 38465.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.110780 restraints weight = 26640.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.112596 restraints weight = 20168.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.113921 restraints weight = 16324.821| |-----------------------------------------------------------------------------| r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.4419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 21458 Z= 0.208 Angle : 0.769 11.305 29192 Z= 0.392 Chirality : 0.049 0.227 3146 Planarity : 0.006 0.105 3837 Dihedral : 6.285 35.502 2886 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 21.44 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.47 % Favored : 88.49 % Rotamer: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.56 % Twisted General : 0.08 % 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 are not related in a simple way. whole: -3.29 (0.15), residues: 2658 helix: -2.29 (0.28), residues: 241 sheet: -1.55 (0.20), residues: 576 loop : -2.55 (0.13), residues: 1841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 254 TYR 0.021 0.002 TYR E 457 PHE 0.029 0.002 PHE C 33 TRP 0.052 0.002 TRP C 308 HIS 0.013 0.002 HIS F 35 Details of bonding type rmsd covalent geometry : bond 0.00450 (21457) covalent geometry : angle 0.76900 (29190) SS BOND : bond 0.00277 ( 1) SS BOND : angle 0.19788 ( 2) hydrogen bonds : bond 0.03677 ( 337) hydrogen bonds : angle 7.26354 ( 870) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 631 residues out of total 2333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 631 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 TYR cc_start: 0.8354 (m-80) cc_final: 0.8060 (m-80) REVERT: A 97 TRP cc_start: 0.8108 (m100) cc_final: 0.7737 (m100) REVERT: A 103 GLU cc_start: 0.8076 (tp30) cc_final: 0.7556 (tp30) REVERT: A 257 PHE cc_start: 0.8896 (t80) cc_final: 0.8639 (t80) REVERT: A 288 VAL cc_start: 0.8970 (m) cc_final: 0.8702 (m) REVERT: A 371 PHE cc_start: 0.8307 (m-80) cc_final: 0.7659 (m-80) REVERT: A 381 GLU cc_start: 0.9141 (mp0) cc_final: 0.8868 (mp0) REVERT: A 389 MET cc_start: 0.8920 (ttt) cc_final: 0.8319 (tmm) REVERT: A 412 THR cc_start: 0.9305 (t) cc_final: 0.8893 (t) REVERT: A 450 PHE cc_start: 0.8732 (m-10) cc_final: 0.8511 (m-10) REVERT: B 26 TYR cc_start: 0.8364 (m-80) cc_final: 0.7990 (m-80) REVERT: B 32 ILE cc_start: 0.9116 (mp) cc_final: 0.8851 (mp) REVERT: B 46 HIS cc_start: 0.9220 (t70) cc_final: 0.8917 (t-170) REVERT: B 67 TYR cc_start: 0.8263 (m-80) cc_final: 0.7709 (m-80) REVERT: B 74 LEU cc_start: 0.9019 (tp) cc_final: 0.8795 (tp) REVERT: B 151 GLN cc_start: 0.8812 (mt0) cc_final: 0.8422 (mt0) REVERT: B 186 LEU cc_start: 0.8412 (pp) cc_final: 0.7414 (pp) REVERT: B 210 GLN cc_start: 0.9303 (mp10) cc_final: 0.9026 (mp10) REVERT: B 220 ILE cc_start: 0.9742 (pt) cc_final: 0.9512 (pt) REVERT: B 223 THR cc_start: 0.9063 (t) cc_final: 0.8849 (t) REVERT: B 233 MET cc_start: 0.8824 (mmt) cc_final: 0.8177 (mmt) REVERT: B 236 ASP cc_start: 0.8533 (t70) cc_final: 0.8329 (t70) REVERT: B 251 MET cc_start: 0.8716 (tpt) cc_final: 0.8206 (tpt) REVERT: B 298 SER cc_start: 0.9108 (p) cc_final: 0.8632 (p) REVERT: B 301 GLN cc_start: 0.9083 (mp-120) cc_final: 0.8316 (mp10) REVERT: B 302 LEU cc_start: 0.9065 (pp) cc_final: 0.8650 (pp) REVERT: B 305 LYS cc_start: 0.9464 (mtpt) cc_final: 0.9095 (mtpt) REVERT: B 307 TYR cc_start: 0.8342 (m-80) cc_final: 0.7777 (m-10) REVERT: B 355 TYR cc_start: 0.7397 (m-80) cc_final: 0.6982 (m-80) REVERT: B 359 MET cc_start: 0.8201 (mmp) cc_final: 0.7511 (mmm) REVERT: C 74 LEU cc_start: 0.9017 (tp) cc_final: 0.8575 (tp) REVERT: C 108 GLN cc_start: 0.8554 (tp-100) cc_final: 0.8270 (mm-40) REVERT: C 154 MET cc_start: 0.8901 (mmp) cc_final: 0.8695 (mmm) REVERT: C 201 PHE cc_start: 0.8288 (m-10) cc_final: 0.7841 (m-10) REVERT: C 204 MET cc_start: 0.7768 (pmm) cc_final: 0.6986 (pmm) REVERT: C 232 GLN cc_start: 0.8739 (mt0) cc_final: 0.8446 (mm-40) REVERT: C 310 GLN cc_start: 0.8704 (tm-30) cc_final: 0.8365 (tm-30) REVERT: C 323 ASN cc_start: 0.6576 (m110) cc_final: 0.6207 (m110) REVERT: C 324 GLN cc_start: 0.8626 (mt0) cc_final: 0.8230 (mm-40) REVERT: C 340 LEU cc_start: 0.8783 (tp) cc_final: 0.8475 (mm) REVERT: C 359 MET cc_start: 0.7867 (mmt) cc_final: 0.7511 (mmt) REVERT: C 372 GLN cc_start: 0.8073 (tt0) cc_final: 0.7612 (pp30) REVERT: C 383 MET cc_start: 0.8689 (mmt) cc_final: 0.8193 (mmt) REVERT: C 386 ILE cc_start: 0.9515 (pt) cc_final: 0.9267 (pt) REVERT: C 395 GLU cc_start: 0.9201 (tm-30) cc_final: 0.8851 (tm-30) REVERT: C 438 ASN cc_start: 0.9177 (m110) cc_final: 0.8916 (m-40) REVERT: D 63 SER cc_start: 0.9418 (t) cc_final: 0.9059 (p) REVERT: D 106 ARG cc_start: 0.7852 (mmm-85) cc_final: 0.7590 (mmm-85) REVERT: D 117 HIS cc_start: 0.8343 (t-90) cc_final: 0.7668 (t-170) REVERT: D 120 LEU cc_start: 0.8475 (mt) cc_final: 0.7885 (pp) REVERT: D 184 LEU cc_start: 0.8088 (tp) cc_final: 0.7806 (tp) REVERT: D 206 PHE cc_start: 0.8120 (m-80) cc_final: 0.7772 (m-80) REVERT: D 233 MET cc_start: 0.8827 (mmp) cc_final: 0.8617 (mmm) REVERT: D 355 TYR cc_start: 0.8123 (m-80) cc_final: 0.7666 (m-80) REVERT: D 361 HIS cc_start: 0.6270 (t70) cc_final: 0.5921 (t70) REVERT: D 364 GLU cc_start: 0.8856 (tm-30) cc_final: 0.8337 (tm-30) REVERT: D 449 LYS cc_start: 0.7916 (mmtp) cc_final: 0.7500 (mmmt) REVERT: E 65 TYR cc_start: 0.7920 (m-10) cc_final: 0.7711 (m-10) REVERT: E 66 GLN cc_start: 0.7340 (mt0) cc_final: 0.6072 (mt0) REVERT: E 120 LEU cc_start: 0.8748 (mt) cc_final: 0.8075 (mt) REVERT: E 146 ASP cc_start: 0.8872 (p0) cc_final: 0.8512 (p0) REVERT: E 150 THR cc_start: 0.9072 (m) cc_final: 0.8861 (m) REVERT: E 196 MET cc_start: 0.8980 (mpp) cc_final: 0.8402 (mmt) REVERT: E 204 MET cc_start: 0.8046 (mmp) cc_final: 0.7666 (mmp) REVERT: E 225 CYS cc_start: 0.8613 (m) cc_final: 0.8383 (m) REVERT: E 254 ARG cc_start: 0.9188 (ttm-80) cc_final: 0.8650 (ttm110) REVERT: E 257 PHE cc_start: 0.8333 (m-80) cc_final: 0.8112 (m-80) REVERT: E 397 TRP cc_start: 0.7757 (m100) cc_final: 0.7422 (m100) REVERT: E 411 ASP cc_start: 0.8098 (t0) cc_final: 0.7877 (t70) REVERT: E 452 SER cc_start: 0.9096 (m) cc_final: 0.8822 (t) REVERT: E 461 ARG cc_start: 0.8953 (ptp90) cc_final: 0.8564 (ptp90) REVERT: F 65 TYR cc_start: 0.9206 (m-80) cc_final: 0.8947 (m-80) REVERT: F 103 GLU cc_start: 0.7603 (tp30) cc_final: 0.7225 (tp30) REVERT: F 148 LYS cc_start: 0.9012 (ptmm) cc_final: 0.8707 (ptmm) REVERT: F 149 GLN cc_start: 0.8848 (pt0) cc_final: 0.8392 (pt0) REVERT: F 151 GLN cc_start: 0.8232 (tt0) cc_final: 0.6797 (tt0) REVERT: F 165 TRP cc_start: 0.8924 (m100) cc_final: 0.8127 (m100) REVERT: F 196 MET cc_start: 0.7585 (mmm) cc_final: 0.7059 (mmm) REVERT: F 204 MET cc_start: 0.8562 (mpp) cc_final: 0.8281 (mpp) REVERT: F 237 PRO cc_start: 0.9224 (Cg_endo) cc_final: 0.8840 (Cg_exo) REVERT: F 248 LYS cc_start: 0.9189 (mttt) cc_final: 0.8936 (mttt) REVERT: F 249 GLU cc_start: 0.8422 (mp0) cc_final: 0.8002 (mp0) REVERT: F 254 ARG cc_start: 0.9144 (tpt-90) cc_final: 0.8881 (tpp-160) REVERT: F 273 ILE cc_start: 0.8456 (mm) cc_final: 0.8091 (mm) REVERT: F 302 LEU cc_start: 0.8821 (mt) cc_final: 0.8160 (mt) REVERT: F 315 HIS cc_start: 0.7847 (m-70) cc_final: 0.7387 (m90) REVERT: F 334 ARG cc_start: 0.9017 (mtt180) cc_final: 0.8617 (mtt180) REVERT: F 357 GLU cc_start: 0.8207 (tm-30) cc_final: 0.7968 (tm-30) REVERT: F 397 TRP cc_start: 0.7567 (m-10) cc_final: 0.7254 (m-10) outliers start: 0 outliers final: 0 residues processed: 631 average time/residue: 0.1261 time to fit residues: 125.0514 Evaluate side-chains 523 residues out of total 2333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 523 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 62 optimal weight: 9.9990 chunk 127 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 chunk 204 optimal weight: 10.0000 chunk 224 optimal weight: 9.9990 chunk 122 optimal weight: 9.9990 chunk 179 optimal weight: 30.0000 chunk 252 optimal weight: 30.0000 chunk 131 optimal weight: 6.9990 chunk 198 optimal weight: 5.9990 chunk 247 optimal weight: 6.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 142 ASN A 192 GLN ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 GLN ** C 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 HIS ** C 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 212 ASN ** E 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 151 GLN F 210 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.132540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.105810 restraints weight = 63042.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.109361 restraints weight = 38093.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.111889 restraints weight = 26390.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.113708 restraints weight = 20041.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.115012 restraints weight = 16254.176| |-----------------------------------------------------------------------------| r_work (final): 0.3793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.4606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 21458 Z= 0.169 Angle : 0.738 11.792 29192 Z= 0.373 Chirality : 0.048 0.268 3146 Planarity : 0.006 0.103 3837 Dihedral : 6.125 35.532 2886 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 19.35 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.53 % Favored : 89.43 % Rotamer: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.56 % Twisted General : 0.08 % 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 are not related in a simple way. whole: -3.21 (0.15), residues: 2658 helix: -2.10 (0.28), residues: 240 sheet: -1.55 (0.20), residues: 600 loop : -2.50 (0.14), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 94 TYR 0.023 0.002 TYR F 457 PHE 0.035 0.002 PHE D 257 TRP 0.032 0.002 TRP C 308 HIS 0.008 0.002 HIS A 35 Details of bonding type rmsd covalent geometry : bond 0.00373 (21457) covalent geometry : angle 0.73759 (29190) SS BOND : bond 0.00199 ( 1) SS BOND : angle 0.18142 ( 2) hydrogen bonds : bond 0.03244 ( 337) hydrogen bonds : angle 7.10902 ( 870) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 639 residues out of total 2333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 639 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 TYR cc_start: 0.8277 (m-80) cc_final: 0.8005 (m-80) REVERT: A 97 TRP cc_start: 0.8084 (m100) cc_final: 0.7692 (m100) REVERT: A 165 TRP cc_start: 0.8778 (m100) cc_final: 0.8391 (m100) REVERT: A 247 ARG cc_start: 0.8534 (ptt180) cc_final: 0.7917 (ptp-170) REVERT: A 257 PHE cc_start: 0.8883 (t80) cc_final: 0.8615 (t80) REVERT: A 288 VAL cc_start: 0.9077 (m) cc_final: 0.8866 (m) REVERT: A 364 GLU cc_start: 0.8439 (pt0) cc_final: 0.7940 (pp20) REVERT: A 369 PHE cc_start: 0.8928 (m-80) cc_final: 0.8588 (m-80) REVERT: A 371 PHE cc_start: 0.8292 (m-80) cc_final: 0.7539 (m-80) REVERT: A 381 GLU cc_start: 0.9149 (mp0) cc_final: 0.8872 (mp0) REVERT: A 389 MET cc_start: 0.8906 (ttt) cc_final: 0.8361 (tmm) REVERT: A 412 THR cc_start: 0.9235 (t) cc_final: 0.8883 (t) REVERT: B 26 TYR cc_start: 0.8325 (m-80) cc_final: 0.7995 (m-80) REVERT: B 32 ILE cc_start: 0.9246 (mp) cc_final: 0.9023 (mp) REVERT: B 67 TYR cc_start: 0.8225 (m-80) cc_final: 0.7765 (m-80) REVERT: B 74 LEU cc_start: 0.8939 (tp) cc_final: 0.8534 (tp) REVERT: B 161 LEU cc_start: 0.8738 (tp) cc_final: 0.8256 (tp) REVERT: B 186 LEU cc_start: 0.8233 (pp) cc_final: 0.7235 (pp) REVERT: B 204 MET cc_start: 0.8970 (mpp) cc_final: 0.8755 (mpp) REVERT: B 206 PHE cc_start: 0.9162 (m-10) cc_final: 0.8933 (m-10) REVERT: B 210 GLN cc_start: 0.9309 (mp10) cc_final: 0.8942 (mp10) REVERT: B 220 ILE cc_start: 0.9708 (pt) cc_final: 0.9460 (pt) REVERT: B 223 THR cc_start: 0.9101 (t) cc_final: 0.8760 (p) REVERT: B 233 MET cc_start: 0.8785 (mmt) cc_final: 0.8143 (mmt) REVERT: B 251 MET cc_start: 0.8667 (tpt) cc_final: 0.8165 (tpt) REVERT: B 298 SER cc_start: 0.9110 (p) cc_final: 0.8851 (p) REVERT: B 301 GLN cc_start: 0.9045 (mp-120) cc_final: 0.8470 (mp10) REVERT: B 359 MET cc_start: 0.8405 (mmp) cc_final: 0.7798 (mmp) REVERT: C 33 PHE cc_start: 0.8123 (m-80) cc_final: 0.7794 (m-80) REVERT: C 74 LEU cc_start: 0.9027 (tp) cc_final: 0.8577 (tp) REVERT: C 108 GLN cc_start: 0.8508 (tp-100) cc_final: 0.8143 (mm-40) REVERT: C 154 MET cc_start: 0.8872 (mmp) cc_final: 0.8642 (mmm) REVERT: C 201 PHE cc_start: 0.8356 (m-10) cc_final: 0.7922 (m-10) REVERT: C 204 MET cc_start: 0.7906 (pmm) cc_final: 0.7301 (pmm) REVERT: C 232 GLN cc_start: 0.8716 (mt0) cc_final: 0.8423 (mm-40) REVERT: C 310 GLN cc_start: 0.8703 (tm-30) cc_final: 0.8401 (tm-30) REVERT: C 323 ASN cc_start: 0.6779 (m110) cc_final: 0.6357 (m110) REVERT: C 359 MET cc_start: 0.7728 (mmt) cc_final: 0.7297 (mmt) REVERT: C 372 GLN cc_start: 0.8100 (tt0) cc_final: 0.7644 (pp30) REVERT: C 383 MET cc_start: 0.8709 (mmt) cc_final: 0.8267 (mmm) REVERT: C 386 ILE cc_start: 0.9505 (pt) cc_final: 0.9299 (pt) REVERT: C 395 GLU cc_start: 0.9180 (tm-30) cc_final: 0.8826 (tm-30) REVERT: C 438 ASN cc_start: 0.9146 (m110) cc_final: 0.8888 (m110) REVERT: D 48 TYR cc_start: 0.8023 (m-80) cc_final: 0.7758 (m-80) REVERT: D 63 SER cc_start: 0.9402 (t) cc_final: 0.9059 (p) REVERT: D 117 HIS cc_start: 0.8239 (t-90) cc_final: 0.7531 (t-170) REVERT: D 120 LEU cc_start: 0.8358 (mt) cc_final: 0.7782 (mt) REVERT: D 184 LEU cc_start: 0.8216 (tp) cc_final: 0.7924 (tp) REVERT: D 204 MET cc_start: 0.7901 (mpp) cc_final: 0.7623 (mpp) REVERT: D 233 MET cc_start: 0.8779 (mmp) cc_final: 0.8570 (mmm) REVERT: D 355 TYR cc_start: 0.8004 (m-80) cc_final: 0.7595 (m-80) REVERT: D 361 HIS cc_start: 0.6194 (t70) cc_final: 0.5966 (t70) REVERT: D 364 GLU cc_start: 0.8807 (tm-30) cc_final: 0.8455 (tm-30) REVERT: D 449 LYS cc_start: 0.7918 (mmtp) cc_final: 0.7488 (mmmt) REVERT: E 66 GLN cc_start: 0.7251 (mt0) cc_final: 0.5914 (mt0) REVERT: E 120 LEU cc_start: 0.8672 (mt) cc_final: 0.7993 (mt) REVERT: E 150 THR cc_start: 0.9079 (m) cc_final: 0.8737 (m) REVERT: E 196 MET cc_start: 0.9047 (mpp) cc_final: 0.8460 (mmt) REVERT: E 225 CYS cc_start: 0.8577 (m) cc_final: 0.8349 (m) REVERT: E 232 GLN cc_start: 0.8463 (mt0) cc_final: 0.7946 (tp-100) REVERT: E 249 GLU cc_start: 0.8668 (mp0) cc_final: 0.8270 (mp0) REVERT: E 254 ARG cc_start: 0.9221 (ttm-80) cc_final: 0.8695 (ttm110) REVERT: E 290 THR cc_start: 0.8112 (m) cc_final: 0.7548 (m) REVERT: E 303 PHE cc_start: 0.9171 (m-10) cc_final: 0.8704 (m-80) REVERT: E 397 TRP cc_start: 0.7528 (m100) cc_final: 0.7089 (m100) REVERT: E 411 ASP cc_start: 0.8052 (t0) cc_final: 0.7819 (t70) REVERT: E 452 SER cc_start: 0.9159 (m) cc_final: 0.8810 (t) REVERT: E 461 ARG cc_start: 0.8914 (ptp90) cc_final: 0.8556 (ptp90) REVERT: F 65 TYR cc_start: 0.9194 (m-80) cc_final: 0.8897 (m-10) REVERT: F 71 LYS cc_start: 0.7875 (tptp) cc_final: 0.7149 (tptp) REVERT: F 103 GLU cc_start: 0.7417 (tp30) cc_final: 0.7133 (tp30) REVERT: F 125 ASP cc_start: 0.8921 (p0) cc_final: 0.8472 (p0) REVERT: F 149 GLN cc_start: 0.8833 (pt0) cc_final: 0.8527 (pt0) REVERT: F 150 THR cc_start: 0.9329 (m) cc_final: 0.8183 (m) REVERT: F 151 GLN cc_start: 0.8835 (tt0) cc_final: 0.7930 (tt0) REVERT: F 165 TRP cc_start: 0.8857 (m100) cc_final: 0.7971 (m100) REVERT: F 192 GLN cc_start: 0.8932 (mt0) cc_final: 0.8631 (mt0) REVERT: F 196 MET cc_start: 0.7525 (mmm) cc_final: 0.6965 (mmm) REVERT: F 204 MET cc_start: 0.8437 (mpp) cc_final: 0.7978 (mpp) REVERT: F 237 PRO cc_start: 0.9212 (Cg_endo) cc_final: 0.8821 (Cg_exo) REVERT: F 249 GLU cc_start: 0.8438 (mp0) cc_final: 0.8004 (mp0) REVERT: F 254 ARG cc_start: 0.9217 (tpt-90) cc_final: 0.8702 (tpp-160) REVERT: F 273 ILE cc_start: 0.8454 (mm) cc_final: 0.8093 (mm) REVERT: F 302 LEU cc_start: 0.8815 (mt) cc_final: 0.8450 (mt) REVERT: F 315 HIS cc_start: 0.7813 (m-70) cc_final: 0.7377 (m90) REVERT: F 334 ARG cc_start: 0.9107 (mtt180) cc_final: 0.8679 (mtt180) REVERT: F 397 TRP cc_start: 0.7715 (m-10) cc_final: 0.7365 (m-10) outliers start: 0 outliers final: 0 residues processed: 639 average time/residue: 0.1326 time to fit residues: 132.0494 Evaluate side-chains 532 residues out of total 2333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 532 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 29 optimal weight: 20.0000 chunk 56 optimal weight: 7.9990 chunk 74 optimal weight: 20.0000 chunk 247 optimal weight: 8.9990 chunk 136 optimal weight: 9.9990 chunk 192 optimal weight: 30.0000 chunk 236 optimal weight: 10.0000 chunk 83 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 66 optimal weight: 9.9990 chunk 229 optimal weight: 0.4980 overall best weight: 4.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 192 GLN ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 372 GLN ** B 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 HIS ** C 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 164 HIS E 212 ASN ** E 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 210 GLN F 337 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.135269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.109324 restraints weight = 60641.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.113007 restraints weight = 35882.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.115649 restraints weight = 24477.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.117529 restraints weight = 18313.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.118881 restraints weight = 14699.404| |-----------------------------------------------------------------------------| r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.4769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 21458 Z= 0.144 Angle : 0.725 12.245 29192 Z= 0.364 Chirality : 0.048 0.240 3146 Planarity : 0.006 0.103 3837 Dihedral : 5.927 35.274 2886 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 18.06 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.84 % Favored : 89.13 % Rotamer: Outliers : 0.04 % Allowed : 0.94 % Favored : 99.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.56 % Twisted General : 0.08 % 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 are not related in a simple way. whole: -3.10 (0.15), residues: 2658 helix: -2.00 (0.29), residues: 237 sheet: -1.51 (0.20), residues: 620 loop : -2.42 (0.14), residues: 1801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 254 TYR 0.031 0.002 TYR D 227 PHE 0.032 0.002 PHE D 257 TRP 0.025 0.001 TRP C 308 HIS 0.010 0.002 HIS A 164 Details of bonding type rmsd covalent geometry : bond 0.00325 (21457) covalent geometry : angle 0.72536 (29190) SS BOND : bond 0.00090 ( 1) SS BOND : angle 0.36779 ( 2) hydrogen bonds : bond 0.03102 ( 337) hydrogen bonds : angle 6.98404 ( 870) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 630 residues out of total 2333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 629 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 TYR cc_start: 0.8469 (m-80) cc_final: 0.8228 (m-80) REVERT: A 48 TYR cc_start: 0.7312 (m-80) cc_final: 0.6728 (m-80) REVERT: A 97 TRP cc_start: 0.8141 (m100) cc_final: 0.7713 (m100) REVERT: A 165 TRP cc_start: 0.8857 (m100) cc_final: 0.8468 (m100) REVERT: A 233 MET cc_start: 0.8589 (mmt) cc_final: 0.7749 (mmm) REVERT: A 257 PHE cc_start: 0.8848 (t80) cc_final: 0.8594 (t80) REVERT: A 288 VAL cc_start: 0.9077 (m) cc_final: 0.8875 (m) REVERT: A 364 GLU cc_start: 0.8514 (pt0) cc_final: 0.7956 (pp20) REVERT: A 369 PHE cc_start: 0.8991 (m-80) cc_final: 0.8640 (m-80) REVERT: A 371 PHE cc_start: 0.8242 (m-80) cc_final: 0.7698 (m-80) REVERT: A 381 GLU cc_start: 0.9135 (mp0) cc_final: 0.8860 (mp0) REVERT: A 389 MET cc_start: 0.8790 (ttt) cc_final: 0.8313 (tmm) REVERT: A 412 THR cc_start: 0.9241 (t) cc_final: 0.8956 (t) REVERT: B 26 TYR cc_start: 0.8302 (m-80) cc_final: 0.8070 (m-80) REVERT: B 46 HIS cc_start: 0.9105 (t70) cc_final: 0.8689 (t-170) REVERT: B 67 TYR cc_start: 0.8337 (m-80) cc_final: 0.7835 (m-80) REVERT: B 74 LEU cc_start: 0.9070 (tp) cc_final: 0.8645 (tp) REVERT: B 164 HIS cc_start: 0.9194 (p90) cc_final: 0.8752 (p90) REVERT: B 204 MET cc_start: 0.9015 (mpp) cc_final: 0.8692 (mpp) REVERT: B 206 PHE cc_start: 0.9211 (m-10) cc_final: 0.8998 (m-80) REVERT: B 210 GLN cc_start: 0.9333 (mp10) cc_final: 0.8960 (mp10) REVERT: B 220 ILE cc_start: 0.9731 (pt) cc_final: 0.9462 (pt) REVERT: B 223 THR cc_start: 0.9066 (t) cc_final: 0.8725 (p) REVERT: B 233 MET cc_start: 0.8809 (mmt) cc_final: 0.8192 (mmt) REVERT: B 236 ASP cc_start: 0.8537 (t70) cc_final: 0.8262 (t70) REVERT: B 246 LEU cc_start: 0.9334 (mt) cc_final: 0.9020 (mt) REVERT: B 251 MET cc_start: 0.8673 (tpt) cc_final: 0.8117 (tpt) REVERT: B 298 SER cc_start: 0.9001 (p) cc_final: 0.8749 (p) REVERT: B 301 GLN cc_start: 0.9184 (mp-120) cc_final: 0.8538 (mp10) REVERT: B 302 LEU cc_start: 0.9171 (pp) cc_final: 0.8842 (pp) REVERT: B 305 LYS cc_start: 0.9525 (mtmt) cc_final: 0.9169 (mtpt) REVERT: B 359 MET cc_start: 0.8255 (mmp) cc_final: 0.7442 (mmp) REVERT: B 461 ARG cc_start: 0.9084 (ttp-110) cc_final: 0.8525 (mtm110) REVERT: C 74 LEU cc_start: 0.9013 (tp) cc_final: 0.8542 (tp) REVERT: C 108 GLN cc_start: 0.8479 (tp-100) cc_final: 0.8025 (mm-40) REVERT: C 154 MET cc_start: 0.8883 (mmp) cc_final: 0.8620 (mmm) REVERT: C 201 PHE cc_start: 0.8293 (m-10) cc_final: 0.7870 (m-10) REVERT: C 204 MET cc_start: 0.7890 (pmm) cc_final: 0.7383 (pmm) REVERT: C 232 GLN cc_start: 0.8705 (mt0) cc_final: 0.8396 (mm-40) REVERT: C 310 GLN cc_start: 0.8717 (tm-30) cc_final: 0.8410 (tm-30) REVERT: C 323 ASN cc_start: 0.6831 (m110) cc_final: 0.6141 (m110) REVERT: C 324 GLN cc_start: 0.8694 (mt0) cc_final: 0.8461 (mt0) REVERT: C 359 MET cc_start: 0.7793 (mmt) cc_final: 0.7398 (mmt) REVERT: C 383 MET cc_start: 0.8725 (mmt) cc_final: 0.8283 (mmm) REVERT: C 395 GLU cc_start: 0.9152 (tm-30) cc_final: 0.8836 (tm-30) REVERT: C 438 ASN cc_start: 0.9164 (m110) cc_final: 0.8901 (m110) REVERT: D 48 TYR cc_start: 0.8133 (m-80) cc_final: 0.7698 (m-80) REVERT: D 63 SER cc_start: 0.9366 (t) cc_final: 0.9004 (p) REVERT: D 117 HIS cc_start: 0.8285 (t-90) cc_final: 0.7589 (t-170) REVERT: D 120 LEU cc_start: 0.8367 (mt) cc_final: 0.7811 (mt) REVERT: D 145 MET cc_start: 0.8943 (ppp) cc_final: 0.8728 (ppp) REVERT: D 184 LEU cc_start: 0.8225 (tp) cc_final: 0.7998 (tp) REVERT: D 204 MET cc_start: 0.7884 (mpp) cc_final: 0.7655 (mpp) REVERT: D 355 TYR cc_start: 0.7937 (m-80) cc_final: 0.7548 (m-80) REVERT: D 397 TRP cc_start: 0.8709 (m-90) cc_final: 0.8329 (m100) REVERT: D 449 LYS cc_start: 0.7927 (mmtp) cc_final: 0.7585 (mmmt) REVERT: E 41 LEU cc_start: 0.7373 (tt) cc_final: 0.6862 (tt) REVERT: E 66 GLN cc_start: 0.7114 (mt0) cc_final: 0.5843 (mt0) REVERT: E 120 LEU cc_start: 0.8790 (mt) cc_final: 0.8029 (mt) REVERT: E 148 LYS cc_start: 0.8135 (ptmm) cc_final: 0.7832 (ptmm) REVERT: E 150 THR cc_start: 0.9107 (m) cc_final: 0.8605 (m) REVERT: E 161 LEU cc_start: 0.9166 (mm) cc_final: 0.8856 (tt) REVERT: E 196 MET cc_start: 0.9014 (mpp) cc_final: 0.8485 (mmt) REVERT: E 225 CYS cc_start: 0.8636 (m) cc_final: 0.8393 (m) REVERT: E 233 MET cc_start: 0.9401 (mtt) cc_final: 0.9026 (mtt) REVERT: E 249 GLU cc_start: 0.8684 (mp0) cc_final: 0.8458 (mp0) REVERT: E 257 PHE cc_start: 0.8056 (m-80) cc_final: 0.7809 (m-80) REVERT: E 352 ASN cc_start: 0.9244 (p0) cc_final: 0.9015 (p0) REVERT: E 364 GLU cc_start: 0.7624 (mm-30) cc_final: 0.7034 (mm-30) REVERT: E 397 TRP cc_start: 0.7539 (m100) cc_final: 0.7090 (m100) REVERT: E 411 ASP cc_start: 0.8020 (t0) cc_final: 0.7819 (t70) REVERT: E 461 ARG cc_start: 0.8944 (ptp90) cc_final: 0.8588 (ptp90) REVERT: F 65 TYR cc_start: 0.9207 (m-80) cc_final: 0.8858 (m-10) REVERT: F 103 GLU cc_start: 0.7316 (tp30) cc_final: 0.7069 (tp30) REVERT: F 125 ASP cc_start: 0.8633 (p0) cc_final: 0.8296 (p0) REVERT: F 148 LYS cc_start: 0.8928 (ptmm) cc_final: 0.8553 (ptmm) REVERT: F 149 GLN cc_start: 0.8807 (pt0) cc_final: 0.8445 (pt0) REVERT: F 151 GLN cc_start: 0.8783 (tt0) cc_final: 0.8130 (tt0) REVERT: F 165 TRP cc_start: 0.8909 (m100) cc_final: 0.7958 (m100) REVERT: F 192 GLN cc_start: 0.8875 (mt0) cc_final: 0.8590 (mt0) REVERT: F 196 MET cc_start: 0.7531 (mmm) cc_final: 0.7028 (mmm) REVERT: F 204 MET cc_start: 0.8554 (mpp) cc_final: 0.8138 (mpp) REVERT: F 227 TYR cc_start: 0.9270 (t80) cc_final: 0.9041 (t80) REVERT: F 237 PRO cc_start: 0.9210 (Cg_endo) cc_final: 0.8832 (Cg_exo) REVERT: F 248 LYS cc_start: 0.9188 (mttt) cc_final: 0.8827 (mttt) REVERT: F 249 GLU cc_start: 0.8490 (mp0) cc_final: 0.7928 (mp0) REVERT: F 254 ARG cc_start: 0.9259 (tpt-90) cc_final: 0.8936 (tpp80) REVERT: F 273 ILE cc_start: 0.8482 (mm) cc_final: 0.8115 (mm) REVERT: F 315 HIS cc_start: 0.7842 (m-70) cc_final: 0.7377 (m90) REVERT: F 334 ARG cc_start: 0.9213 (mtt180) cc_final: 0.8748 (mtt180) REVERT: F 356 LYS cc_start: 0.9141 (mmmt) cc_final: 0.8627 (mmtt) REVERT: F 359 MET cc_start: 0.8200 (tpp) cc_final: 0.7645 (mmm) REVERT: F 397 TRP cc_start: 0.7715 (m-10) cc_final: 0.7503 (m-10) outliers start: 1 outliers final: 1 residues processed: 629 average time/residue: 0.1292 time to fit residues: 127.4706 Evaluate side-chains 536 residues out of total 2333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 535 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 103 optimal weight: 2.9990 chunk 201 optimal weight: 30.0000 chunk 107 optimal weight: 10.0000 chunk 80 optimal weight: 7.9990 chunk 122 optimal weight: 20.0000 chunk 132 optimal weight: 0.3980 chunk 163 optimal weight: 50.0000 chunk 58 optimal weight: 9.9990 chunk 210 optimal weight: 5.9990 chunk 232 optimal weight: 5.9990 chunk 246 optimal weight: 8.9990 overall best weight: 4.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 192 GLN A 210 GLN ** A 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 164 HIS D 210 GLN E 212 ASN E 255 HIS ** F 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 151 GLN F 210 GLN F 337 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.135717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.109854 restraints weight = 60847.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.113534 restraints weight = 35922.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.116134 restraints weight = 24563.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.117981 restraints weight = 18431.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.119325 restraints weight = 14830.775| |-----------------------------------------------------------------------------| r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.4948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 21458 Z= 0.149 Angle : 0.722 12.295 29192 Z= 0.363 Chirality : 0.048 0.247 3146 Planarity : 0.006 0.103 3837 Dihedral : 5.878 35.212 2886 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 17.79 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.53 % Favored : 89.43 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.56 % Twisted General : 0.08 % 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 are not related in a simple way. whole: -3.07 (0.15), residues: 2658 helix: -1.88 (0.30), residues: 231 sheet: -1.51 (0.20), residues: 594 loop : -2.40 (0.14), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 106 TYR 0.024 0.002 TYR A 147 PHE 0.064 0.002 PHE C 33 TRP 0.056 0.002 TRP C 308 HIS 0.009 0.002 HIS B 255 Details of bonding type rmsd covalent geometry : bond 0.00337 (21457) covalent geometry : angle 0.72179 (29190) SS BOND : bond 0.00189 ( 1) SS BOND : angle 0.19943 ( 2) hydrogen bonds : bond 0.03122 ( 337) hydrogen bonds : angle 6.91663 ( 870) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 635 residues out of total 2333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 635 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 TYR cc_start: 0.8542 (m-80) cc_final: 0.8294 (m-80) REVERT: A 48 TYR cc_start: 0.7385 (m-80) cc_final: 0.6848 (m-80) REVERT: A 97 TRP cc_start: 0.8026 (m100) cc_final: 0.7516 (m100) REVERT: A 103 GLU cc_start: 0.8139 (tp30) cc_final: 0.7860 (tp30) REVERT: A 165 TRP cc_start: 0.8879 (m100) cc_final: 0.8494 (m100) REVERT: A 233 MET cc_start: 0.8616 (mmt) cc_final: 0.7739 (mmm) REVERT: A 247 ARG cc_start: 0.8570 (ptt180) cc_final: 0.7738 (ptp-170) REVERT: A 257 PHE cc_start: 0.8916 (t80) cc_final: 0.8628 (t80) REVERT: A 288 VAL cc_start: 0.9092 (m) cc_final: 0.8880 (m) REVERT: A 364 GLU cc_start: 0.8555 (pt0) cc_final: 0.7981 (pp20) REVERT: A 369 PHE cc_start: 0.9035 (m-80) cc_final: 0.8730 (m-80) REVERT: A 371 PHE cc_start: 0.8254 (m-80) cc_final: 0.7658 (m-80) REVERT: A 381 GLU cc_start: 0.9147 (mp0) cc_final: 0.8874 (mp0) REVERT: A 389 MET cc_start: 0.8758 (ttt) cc_final: 0.8284 (tmm) REVERT: A 412 THR cc_start: 0.9235 (t) cc_final: 0.8931 (t) REVERT: B 26 TYR cc_start: 0.8309 (m-80) cc_final: 0.8102 (m-80) REVERT: B 32 ILE cc_start: 0.9220 (mp) cc_final: 0.8968 (mp) REVERT: B 46 HIS cc_start: 0.9170 (t70) cc_final: 0.8756 (t-170) REVERT: B 67 TYR cc_start: 0.8317 (m-80) cc_final: 0.7791 (m-80) REVERT: B 74 LEU cc_start: 0.9116 (tp) cc_final: 0.8915 (tp) REVERT: B 164 HIS cc_start: 0.9154 (p90) cc_final: 0.8716 (p90) REVERT: B 186 LEU cc_start: 0.8652 (pp) cc_final: 0.7864 (pp) REVERT: B 204 MET cc_start: 0.9054 (mpp) cc_final: 0.8677 (mpp) REVERT: B 210 GLN cc_start: 0.9364 (mp10) cc_final: 0.9031 (mp10) REVERT: B 220 ILE cc_start: 0.9720 (pt) cc_final: 0.9474 (pt) REVERT: B 223 THR cc_start: 0.9088 (t) cc_final: 0.8862 (t) REVERT: B 233 MET cc_start: 0.8803 (mmt) cc_final: 0.8185 (mmt) REVERT: B 236 ASP cc_start: 0.8491 (t70) cc_final: 0.8282 (t70) REVERT: B 246 LEU cc_start: 0.9293 (mt) cc_final: 0.8975 (mt) REVERT: B 251 MET cc_start: 0.8617 (tpt) cc_final: 0.8114 (tpt) REVERT: B 298 SER cc_start: 0.9033 (p) cc_final: 0.8765 (p) REVERT: B 301 GLN cc_start: 0.9095 (mp-120) cc_final: 0.8497 (mp10) REVERT: B 302 LEU cc_start: 0.9131 (pp) cc_final: 0.8807 (pp) REVERT: B 305 LYS cc_start: 0.9495 (mtmt) cc_final: 0.9155 (mtpt) REVERT: B 359 MET cc_start: 0.8323 (mmp) cc_final: 0.7478 (mmp) REVERT: B 461 ARG cc_start: 0.9091 (ttp-110) cc_final: 0.8557 (mtm110) REVERT: C 66 GLN cc_start: 0.8561 (mt0) cc_final: 0.7593 (mt0) REVERT: C 68 ARG cc_start: 0.8801 (mmt-90) cc_final: 0.8196 (mmt-90) REVERT: C 74 LEU cc_start: 0.8981 (tp) cc_final: 0.8525 (tp) REVERT: C 108 GLN cc_start: 0.8454 (tp-100) cc_final: 0.7997 (mm-40) REVERT: C 146 ASP cc_start: 0.8947 (m-30) cc_final: 0.8614 (m-30) REVERT: C 154 MET cc_start: 0.8819 (mmp) cc_final: 0.8530 (mmm) REVERT: C 201 PHE cc_start: 0.8371 (m-10) cc_final: 0.7942 (m-10) REVERT: C 204 MET cc_start: 0.7924 (pmm) cc_final: 0.7431 (pmm) REVERT: C 232 GLN cc_start: 0.8845 (mt0) cc_final: 0.8350 (mm-40) REVERT: C 310 GLN cc_start: 0.8664 (tm-30) cc_final: 0.8325 (tm-30) REVERT: C 323 ASN cc_start: 0.6767 (m110) cc_final: 0.6063 (m110) REVERT: C 324 GLN cc_start: 0.8680 (mt0) cc_final: 0.8444 (mt0) REVERT: C 359 MET cc_start: 0.7805 (mmt) cc_final: 0.7484 (mmt) REVERT: C 383 MET cc_start: 0.8735 (mmt) cc_final: 0.8295 (mmm) REVERT: C 438 ASN cc_start: 0.9166 (m110) cc_final: 0.8911 (m110) REVERT: D 40 ARG cc_start: 0.8338 (ptt180) cc_final: 0.8073 (ptp-170) REVERT: D 46 HIS cc_start: 0.8935 (t-90) cc_final: 0.8601 (t70) REVERT: D 63 SER cc_start: 0.9309 (t) cc_final: 0.8943 (p) REVERT: D 117 HIS cc_start: 0.8301 (t-90) cc_final: 0.7655 (t-170) REVERT: D 120 LEU cc_start: 0.8426 (mt) cc_final: 0.7839 (mt) REVERT: D 184 LEU cc_start: 0.8165 (tp) cc_final: 0.7839 (tp) REVERT: D 204 MET cc_start: 0.7986 (mpp) cc_final: 0.7630 (mpp) REVERT: D 233 MET cc_start: 0.8847 (mmp) cc_final: 0.8592 (mmm) REVERT: D 355 TYR cc_start: 0.7991 (m-80) cc_final: 0.7459 (m-80) REVERT: D 359 MET cc_start: 0.7827 (tpp) cc_final: 0.7538 (mmm) REVERT: D 361 HIS cc_start: 0.6168 (t70) cc_final: 0.5952 (t70) REVERT: D 397 TRP cc_start: 0.8711 (m-90) cc_final: 0.8333 (m100) REVERT: D 449 LYS cc_start: 0.7911 (mmtp) cc_final: 0.7589 (mmmt) REVERT: E 41 LEU cc_start: 0.7446 (tt) cc_final: 0.6958 (tt) REVERT: E 66 GLN cc_start: 0.6962 (mt0) cc_final: 0.6565 (mt0) REVERT: E 120 LEU cc_start: 0.8677 (mt) cc_final: 0.8035 (mt) REVERT: E 148 LYS cc_start: 0.8108 (ptmm) cc_final: 0.7751 (ptmm) REVERT: E 150 THR cc_start: 0.9156 (m) cc_final: 0.8845 (m) REVERT: E 161 LEU cc_start: 0.9173 (mm) cc_final: 0.8724 (tp) REVERT: E 196 MET cc_start: 0.9015 (mpp) cc_final: 0.8476 (mmt) REVERT: E 225 CYS cc_start: 0.8629 (m) cc_final: 0.8371 (m) REVERT: E 233 MET cc_start: 0.9372 (mtt) cc_final: 0.9120 (mtt) REVERT: E 248 LYS cc_start: 0.8232 (mmtp) cc_final: 0.7986 (mmtp) REVERT: E 249 GLU cc_start: 0.8733 (mp0) cc_final: 0.8490 (mp0) REVERT: E 257 PHE cc_start: 0.8029 (m-80) cc_final: 0.7762 (m-80) REVERT: E 352 ASN cc_start: 0.9255 (p0) cc_final: 0.9029 (p0) REVERT: E 364 GLU cc_start: 0.7666 (mm-30) cc_final: 0.7049 (mm-30) REVERT: E 397 TRP cc_start: 0.7519 (m100) cc_final: 0.7067 (m100) REVERT: E 457 TYR cc_start: 0.8567 (m-80) cc_final: 0.8078 (m-80) REVERT: E 461 ARG cc_start: 0.8969 (ptp90) cc_final: 0.8610 (ptp90) REVERT: F 65 TYR cc_start: 0.9244 (m-80) cc_final: 0.8865 (m-10) REVERT: F 103 GLU cc_start: 0.7303 (tp30) cc_final: 0.7065 (tp30) REVERT: F 148 LYS cc_start: 0.8897 (ptmm) cc_final: 0.8517 (ptmm) REVERT: F 149 GLN cc_start: 0.8761 (pt0) cc_final: 0.8353 (pt0) REVERT: F 151 GLN cc_start: 0.8858 (tt0) cc_final: 0.8219 (tt0) REVERT: F 165 TRP cc_start: 0.8932 (m100) cc_final: 0.8004 (m100) REVERT: F 192 GLN cc_start: 0.8878 (mt0) cc_final: 0.8569 (mt0) REVERT: F 196 MET cc_start: 0.7683 (mmm) cc_final: 0.7107 (mmm) REVERT: F 204 MET cc_start: 0.8576 (mpp) cc_final: 0.8118 (mpp) REVERT: F 237 PRO cc_start: 0.9021 (Cg_endo) cc_final: 0.8615 (Cg_exo) REVERT: F 248 LYS cc_start: 0.9161 (mttt) cc_final: 0.8831 (mttt) REVERT: F 249 GLU cc_start: 0.8471 (mp0) cc_final: 0.7896 (mp0) REVERT: F 254 ARG cc_start: 0.9231 (tpt-90) cc_final: 0.8791 (tpp-160) REVERT: F 273 ILE cc_start: 0.8508 (mm) cc_final: 0.8123 (mm) REVERT: F 315 HIS cc_start: 0.7893 (m-70) cc_final: 0.7460 (m90) REVERT: F 334 ARG cc_start: 0.9225 (mtt180) cc_final: 0.8854 (mtt180) REVERT: F 359 MET cc_start: 0.8222 (tpp) cc_final: 0.7716 (mmm) outliers start: 0 outliers final: 0 residues processed: 635 average time/residue: 0.1301 time to fit residues: 129.7807 Evaluate side-chains 533 residues out of total 2333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 533 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 170 optimal weight: 4.9990 chunk 94 optimal weight: 0.0980 chunk 150 optimal weight: 30.0000 chunk 86 optimal weight: 10.0000 chunk 140 optimal weight: 20.0000 chunk 72 optimal weight: 0.0070 chunk 245 optimal weight: 20.0000 chunk 240 optimal weight: 20.0000 chunk 225 optimal weight: 6.9990 chunk 141 optimal weight: 8.9990 chunk 128 optimal weight: 4.9990 overall best weight: 3.4204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 250 GLN ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 HIS ** C 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 164 HIS D 315 HIS E 212 ASN ** F 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 210 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.136861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.110872 restraints weight = 58937.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.114615 restraints weight = 34571.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.117280 restraints weight = 23537.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.119201 restraints weight = 17555.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.120553 restraints weight = 14013.023| |-----------------------------------------------------------------------------| r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.5089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21458 Z= 0.132 Angle : 0.716 12.414 29192 Z= 0.357 Chirality : 0.048 0.233 3146 Planarity : 0.005 0.102 3837 Dihedral : 5.744 34.984 2886 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 16.70 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.16 % Favored : 89.80 % Rotamer: Outliers : 0.13 % Allowed : 0.51 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.56 % Twisted General : 0.04 % 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 are not related in a simple way. whole: -3.00 (0.15), residues: 2658 helix: -1.79 (0.30), residues: 240 sheet: -1.45 (0.20), residues: 579 loop : -2.36 (0.14), residues: 1839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 254 TYR 0.020 0.002 TYR A 147 PHE 0.033 0.002 PHE D 257 TRP 0.031 0.001 TRP C 308 HIS 0.010 0.002 HIS A 164 Details of bonding type rmsd covalent geometry : bond 0.00300 (21457) covalent geometry : angle 0.71588 (29190) SS BOND : bond 0.00155 ( 1) SS BOND : angle 0.17598 ( 2) hydrogen bonds : bond 0.03005 ( 337) hydrogen bonds : angle 6.84135 ( 870) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3910.77 seconds wall clock time: 68 minutes 32.57 seconds (4112.57 seconds total)