Starting phenix.real_space_refine on Sun May 3 14:19:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xul_67270/05_2026/9xul_67270.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xul_67270/05_2026/9xul_67270.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9xul_67270/05_2026/9xul_67270.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xul_67270/05_2026/9xul_67270.map" model { file = "/net/cci-nas-00/data/ceres_data/9xul_67270/05_2026/9xul_67270.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xul_67270/05_2026/9xul_67270.cif" } resolution = 2.81 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= -0.000 sd= 0.025 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: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 50 5.16 5 C 8502 2.51 5 N 2284 2.21 5 O 2582 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 58 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13424 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3370 Classifications: {'peptide': 435} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 17, 'TRANS': 414} Chain breaks: 1 Chain: "B" Number of atoms: 3327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 3327 Classifications: {'peptide': 425} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 408} Chain breaks: 2 Chain: "C" Number of atoms: 3370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3370 Classifications: {'peptide': 435} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 17, 'TRANS': 414} Chain breaks: 1 Chain: "D" Number of atoms: 3327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 3327 Classifications: {'peptide': 425} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 408} Chain breaks: 2 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 10 Unusual residues: {'PO4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 10 Unusual residues: {'PO4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.38, per 1000 atoms: 0.25 Number of scatterers: 13424 At special positions: 0 Unit cell: (109.976, 102.52, 112.772, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 50 16.00 P 6 15.00 O 2582 8.00 N 2284 7.00 C 8502 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 81 " - pdb=" SG CYS C 81 " distance=2.03 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: 1.11 Conformation dependent library (CDL) restraints added in 664.5 milliseconds 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3184 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 24 sheets defined 26.6% alpha, 15.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 85 through 89 Processing helix chain 'A' and resid 111 through 114 Processing helix chain 'A' and resid 124 through 134 Processing helix chain 'A' and resid 149 through 158 removed outlier: 4.908A pdb=" N SER A 155 " --> pdb=" O ASN A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 195 Processing helix chain 'A' and resid 196 through 201 Processing helix chain 'A' and resid 220 through 231 removed outlier: 3.661A pdb=" N PHE A 224 " --> pdb=" O ASP A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 293 removed outlier: 4.161A pdb=" N GLU A 292 " --> pdb=" O GLN A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 314 removed outlier: 3.770A pdb=" N LEU A 310 " --> pdb=" O ARG A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 333 removed outlier: 3.744A pdb=" N SER A 333 " --> pdb=" O PRO A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 362 Processing helix chain 'A' and resid 363 through 365 No H-bonds generated for 'chain 'A' and resid 363 through 365' Processing helix chain 'A' and resid 443 through 450 removed outlier: 3.793A pdb=" N LEU A 449 " --> pdb=" O THR A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 454 removed outlier: 3.881A pdb=" N GLY A 454 " --> pdb=" O SER A 451 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 451 through 454' Processing helix chain 'B' and resid 111 through 114 Processing helix chain 'B' and resid 124 through 135 Processing helix chain 'B' and resid 147 through 158 Processing helix chain 'B' and resid 189 through 197 removed outlier: 3.779A pdb=" N PHE B 197 " --> pdb=" O ALA B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 201 Processing helix chain 'B' and resid 203 through 207 Processing helix chain 'B' and resid 224 through 235 removed outlier: 3.697A pdb=" N PHE B 228 " --> pdb=" O ASP B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 280 removed outlier: 3.557A pdb=" N LYS B 278 " --> pdb=" O GLY B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 288 Processing helix chain 'B' and resid 290 through 297 removed outlier: 3.511A pdb=" N GLU B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LYS B 296 " --> pdb=" O GLU B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 319 Processing helix chain 'B' and resid 355 through 365 Processing helix chain 'B' and resid 366 through 368 No H-bonds generated for 'chain 'B' and resid 366 through 368' Processing helix chain 'B' and resid 445 through 456 Processing helix chain 'C' and resid 85 through 89 Processing helix chain 'C' and resid 111 through 114 Processing helix chain 'C' and resid 124 through 134 Processing helix chain 'C' and resid 149 through 158 removed outlier: 4.870A pdb=" N SER C 155 " --> pdb=" O ASN C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 196 removed outlier: 3.847A pdb=" N VAL C 193 " --> pdb=" O THR C 189 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N TYR C 196 " --> pdb=" O ALA C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 201 Processing helix chain 'C' and resid 220 through 231 removed outlier: 3.608A pdb=" N PHE C 224 " --> pdb=" O ASP C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 250 removed outlier: 3.901A pdb=" N THR C 248 " --> pdb=" O GLN C 245 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ALA C 249 " --> pdb=" O ARG C 246 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N PHE C 250 " --> pdb=" O ALA C 247 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 245 through 250' Processing helix chain 'C' and resid 279 through 283 Processing helix chain 'C' and resid 286 through 291 removed outlier: 3.592A pdb=" N LYS C 291 " --> pdb=" O ASP C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 315 removed outlier: 3.608A pdb=" N ARG C 314 " --> pdb=" O LEU C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 332 Processing helix chain 'C' and resid 352 through 362 Processing helix chain 'C' and resid 363 through 365 No H-bonds generated for 'chain 'C' and resid 363 through 365' Processing helix chain 'C' and resid 443 through 450 removed outlier: 3.511A pdb=" N LEU C 450 " --> pdb=" O GLU C 446 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 454 removed outlier: 3.932A pdb=" N GLY C 454 " --> pdb=" O SER C 451 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 451 through 454' Processing helix chain 'C' and resid 494 through 498 Processing helix chain 'D' and resid 111 through 114 Processing helix chain 'D' and resid 124 through 135 Processing helix chain 'D' and resid 147 through 158 Processing helix chain 'D' and resid 189 through 197 removed outlier: 3.772A pdb=" N PHE D 197 " --> pdb=" O ALA D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 201 Processing helix chain 'D' and resid 203 through 207 Processing helix chain 'D' and resid 224 through 235 removed outlier: 3.830A pdb=" N PHE D 228 " --> pdb=" O ASP D 224 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASP D 231 " --> pdb=" O ASP D 227 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N HIS D 232 " --> pdb=" O PHE D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 281 Processing helix chain 'D' and resid 283 through 288 removed outlier: 4.188A pdb=" N ILE D 286 " --> pdb=" O ASP D 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 297 removed outlier: 3.913A pdb=" N LYS D 296 " --> pdb=" O GLU D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 319 removed outlier: 3.567A pdb=" N LEU D 314 " --> pdb=" O LYS D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 336 removed outlier: 3.937A pdb=" N ALA D 336 " --> pdb=" O PRO D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 365 Processing helix chain 'D' and resid 366 through 368 No H-bonds generated for 'chain 'D' and resid 366 through 368' Processing helix chain 'D' and resid 445 through 455 removed outlier: 3.932A pdb=" N GLU D 455 " --> pdb=" O ALA D 451 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 90 through 95 removed outlier: 7.072A pdb=" N VAL A 90 " --> pdb=" O LYS A 138 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N TYR A 140 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N GLY A 92 " --> pdb=" O TYR A 140 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N LEU A 142 " --> pdb=" O GLY A 92 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ILE A 94 " --> pdb=" O LEU A 142 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 170 through 175 current: chain 'A' and resid 261 through 264 Processing sheet with id=AA2, first strand: chain 'A' and resid 116 through 117 Processing sheet with id=AA3, first strand: chain 'A' and resid 215 through 217 Processing sheet with id=AA4, first strand: chain 'A' and resid 390 through 395 removed outlier: 6.265A pdb=" N LYS A 391 " --> pdb=" O ILE A 408 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL A 407 " --> pdb=" O ILE A 424 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 423 through 424 current: chain 'B' and resid 413 through 416 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 413 through 416 current: chain 'B' and resid 430 through 437 removed outlier: 6.232A pdb=" N GLN B 431 " --> pdb=" O ILE B 468 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N GLU B 470 " --> pdb=" O GLN B 431 " (cutoff:3.500A) removed outlier: 8.728A pdb=" N LYS B 433 " --> pdb=" O GLU B 470 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N ILE B 472 " --> pdb=" O LYS B 433 " (cutoff:3.500A) removed outlier: 9.188A pdb=" N THR B 435 " --> pdb=" O ILE B 472 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N LYS B 467 " --> pdb=" O ILE B 485 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 484 through 485 current: chain 'B' and resid 508 through 510 No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 501 through 502 removed outlier: 6.080A pdb=" N VAL A 417 " --> pdb=" O LEU A 435 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N VAL A 401 " --> pdb=" O VAL A 418 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LYS B 393 " --> pdb=" O LEU B 410 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N PHE B 409 " --> pdb=" O VAL B 426 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 412 through 414 removed outlier: 6.517A pdb=" N ILE A 429 " --> pdb=" O ILE A 466 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N HIS A 465 " --> pdb=" O ILE A 483 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 459 through 460 removed outlier: 5.655A pdb=" N GLY A 459 " --> pdb=" O ILE A 477 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ARG A 476 " --> pdb=" O ILE A 514 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 169 through 174 removed outlier: 4.877A pdb=" N LYS B 138 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N SER B 242 " --> pdb=" O MET B 303 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N VAL B 305 " --> pdb=" O SER B 240 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N SER B 240 " --> pdb=" O VAL B 305 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ILE B 239 " --> pdb=" O ASN B 342 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N TYR B 344 " --> pdb=" O ILE B 239 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ILE B 241 " --> pdb=" O TYR B 344 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 116 through 117 Processing sheet with id=AB1, first strand: chain 'B' and resid 219 through 221 Processing sheet with id=AB2, first strand: chain 'B' and resid 256 through 260 removed outlier: 6.384A pdb=" N ASP B 260 " --> pdb=" O VAL B 265 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N VAL B 265 " --> pdb=" O ASP B 260 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 461 through 462 removed outlier: 5.808A pdb=" N GLY B 461 " --> pdb=" O VAL B 479 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ARG B 478 " --> pdb=" O ILE B 516 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 90 through 95 removed outlier: 4.780A pdb=" N LYS C 138 " --> pdb=" O VAL C 90 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 170 through 175 current: chain 'C' and resid 261 through 264 Processing sheet with id=AB5, first strand: chain 'C' and resid 116 through 117 Processing sheet with id=AB6, first strand: chain 'C' and resid 215 through 217 Processing sheet with id=AB7, first strand: chain 'C' and resid 390 through 395 removed outlier: 6.353A pdb=" N LYS C 391 " --> pdb=" O ILE C 408 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL C 407 " --> pdb=" O ILE C 424 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 423 through 424 current: chain 'D' and resid 413 through 416 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 413 through 416 current: chain 'D' and resid 430 through 437 removed outlier: 6.200A pdb=" N GLN D 431 " --> pdb=" O ILE D 468 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N GLU D 470 " --> pdb=" O GLN D 431 " (cutoff:3.500A) removed outlier: 8.637A pdb=" N LYS D 433 " --> pdb=" O GLU D 470 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N ILE D 472 " --> pdb=" O LYS D 433 " (cutoff:3.500A) removed outlier: 9.332A pdb=" N THR D 435 " --> pdb=" O ILE D 472 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N LYS D 467 " --> pdb=" O ILE D 485 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 484 through 485 current: chain 'D' and resid 501 through 503 Processing sheet with id=AB8, first strand: chain 'C' and resid 501 through 502 removed outlier: 6.116A pdb=" N VAL C 417 " --> pdb=" O LEU C 435 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL C 401 " --> pdb=" O VAL C 418 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N LYS D 393 " --> pdb=" O LEU D 410 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N PHE D 409 " --> pdb=" O VAL D 426 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 412 through 414 removed outlier: 6.288A pdb=" N ILE C 429 " --> pdb=" O ILE C 466 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N HIS C 465 " --> pdb=" O ILE C 483 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 459 through 460 removed outlier: 5.591A pdb=" N GLY C 459 " --> pdb=" O ILE C 477 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ARG C 476 " --> pdb=" O ILE C 514 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'D' and resid 169 through 172 removed outlier: 4.807A pdb=" N LYS D 138 " --> pdb=" O VAL D 90 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N GLY D 304 " --> pdb=" O SER D 216 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ALA D 301 " --> pdb=" O ILE D 246 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE D 246 " --> pdb=" O ALA D 301 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N MET D 303 " --> pdb=" O ILE D 244 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N ILE D 244 " --> pdb=" O MET D 303 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N VAL D 305 " --> pdb=" O SER D 242 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ILE D 239 " --> pdb=" O ASN D 342 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N TYR D 344 " --> pdb=" O ILE D 239 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILE D 241 " --> pdb=" O TYR D 344 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 116 through 117 Processing sheet with id=AC4, first strand: chain 'D' and resid 219 through 221 Processing sheet with id=AC5, first strand: chain 'D' and resid 257 through 259 removed outlier: 3.629A pdb=" N SER D 267 " --> pdb=" O LYS D 258 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 461 through 462 removed outlier: 5.875A pdb=" N GLY D 461 " --> pdb=" O VAL D 479 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ARG D 478 " --> pdb=" O ILE D 516 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 308 hydrogen bonds defined for protein. 825 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: 2.55 Time building geometry restraints manager: 1.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4432 1.34 - 1.46: 2322 1.46 - 1.57: 6836 1.57 - 1.69: 0 1.69 - 1.81: 82 Bond restraints: 13672 Sorted by residual: bond pdb=" CA THR C 80 " pdb=" C THR C 80 " ideal model delta sigma weight residual 1.523 1.482 0.040 1.23e-02 6.61e+03 1.08e+01 bond pdb=" N THR C 80 " pdb=" CA THR C 80 " ideal model delta sigma weight residual 1.458 1.427 0.031 1.22e-02 6.72e+03 6.25e+00 bond pdb=" C TYR A 386 " pdb=" N LEU A 387 " ideal model delta sigma weight residual 1.330 1.297 0.033 1.47e-02 4.63e+03 5.10e+00 bond pdb=" CA THR A 80 " pdb=" C THR A 80 " ideal model delta sigma weight residual 1.521 1.498 0.023 1.19e-02 7.06e+03 3.82e+00 bond pdb=" CG1 ILE A 261 " pdb=" CD1 ILE A 261 " ideal model delta sigma weight residual 1.513 1.449 0.064 3.90e-02 6.57e+02 2.68e+00 ... (remaining 13667 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 18097 1.98 - 3.96: 353 3.96 - 5.95: 46 5.95 - 7.93: 13 7.93 - 9.91: 3 Bond angle restraints: 18512 Sorted by residual: angle pdb=" CA GLU D 338 " pdb=" CB GLU D 338 " pdb=" CG GLU D 338 " ideal model delta sigma weight residual 114.10 120.68 -6.58 2.00e+00 2.50e-01 1.08e+01 angle pdb=" CB GLU D 311 " pdb=" CG GLU D 311 " pdb=" CD GLU D 311 " ideal model delta sigma weight residual 112.60 117.81 -5.21 1.70e+00 3.46e-01 9.38e+00 angle pdb=" CA GLU D 311 " pdb=" CB GLU D 311 " pdb=" CG GLU D 311 " ideal model delta sigma weight residual 114.10 120.14 -6.04 2.00e+00 2.50e-01 9.11e+00 angle pdb=" CG1 ILE A 483 " pdb=" CB ILE A 483 " pdb=" CG2 ILE A 483 " ideal model delta sigma weight residual 110.70 101.69 9.01 3.00e+00 1.11e-01 9.01e+00 angle pdb=" N TYR B 145 " pdb=" CA TYR B 145 " pdb=" C TYR B 145 " ideal model delta sigma weight residual 112.03 115.82 -3.79 1.31e+00 5.83e-01 8.36e+00 ... (remaining 18507 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 7326 17.69 - 35.37: 716 35.37 - 53.06: 169 53.06 - 70.75: 24 70.75 - 88.44: 10 Dihedral angle restraints: 8245 sinusoidal: 3279 harmonic: 4966 Sorted by residual: dihedral pdb=" CA ASN A 151 " pdb=" C ASN A 151 " pdb=" N ARG A 152 " pdb=" CA ARG A 152 " ideal model delta harmonic sigma weight residual 180.00 157.42 22.58 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" CA ASN C 151 " pdb=" C ASN C 151 " pdb=" N ARG C 152 " pdb=" CA ARG C 152 " ideal model delta harmonic sigma weight residual 180.00 158.84 21.16 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" CA PHE B 308 " pdb=" C PHE B 308 " pdb=" N LYS B 309 " pdb=" CA LYS B 309 " ideal model delta harmonic sigma weight residual 180.00 159.83 20.17 0 5.00e+00 4.00e-02 1.63e+01 ... (remaining 8242 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1091 0.036 - 0.072: 627 0.072 - 0.107: 262 0.107 - 0.143: 97 0.143 - 0.179: 3 Chirality restraints: 2080 Sorted by residual: chirality pdb=" CG LEU D 314 " pdb=" CB LEU D 314 " pdb=" CD1 LEU D 314 " pdb=" CD2 LEU D 314 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 7.99e-01 chirality pdb=" CB ILE A 301 " pdb=" CA ILE A 301 " pdb=" CG1 ILE A 301 " pdb=" CG2 ILE A 301 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 6.96e-01 chirality pdb=" CB ILE A 483 " pdb=" CA ILE A 483 " pdb=" CG1 ILE A 483 " pdb=" CG2 ILE A 483 " both_signs ideal model delta sigma weight residual False 2.64 2.81 -0.17 2.00e-01 2.50e+01 6.83e-01 ... (remaining 2077 not shown) Planarity restraints: 2398 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN D 146 " 0.013 2.00e-02 2.50e+03 2.54e-02 6.47e+00 pdb=" C ASN D 146 " -0.044 2.00e-02 2.50e+03 pdb=" O ASN D 146 " 0.017 2.00e-02 2.50e+03 pdb=" N SER D 147 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 219 " 0.020 2.00e-02 2.50e+03 1.48e-02 3.27e+00 pdb=" CG HIS B 219 " -0.020 2.00e-02 2.50e+03 pdb=" ND1 HIS B 219 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 HIS B 219 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 HIS B 219 " 0.013 2.00e-02 2.50e+03 pdb=" NE2 HIS B 219 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 412 " 0.008 2.00e-02 2.50e+03 1.65e-02 2.71e+00 pdb=" C ASN B 412 " -0.028 2.00e-02 2.50e+03 pdb=" O ASN B 412 " 0.011 2.00e-02 2.50e+03 pdb=" N CYS B 413 " 0.009 2.00e-02 2.50e+03 ... (remaining 2395 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 809 2.73 - 3.27: 13228 3.27 - 3.81: 21714 3.81 - 4.36: 28056 4.36 - 4.90: 48304 Nonbonded interactions: 112111 Sorted by model distance: nonbonded pdb=" O ASN D 146 " pdb=" ND2 ASN D 146 " model vdw 2.184 3.120 nonbonded pdb=" N ASP B 218 " pdb=" OD1 ASP B 218 " model vdw 2.468 3.120 nonbonded pdb=" N GLU D 311 " pdb=" OE1 GLU D 311 " model vdw 2.473 3.120 nonbonded pdb=" C THR A 80 " pdb=" OG1 THR A 80 " model vdw 2.502 2.616 nonbonded pdb=" O ASN B 412 " pdb=" OD1 ASN B 412 " model vdw 2.502 3.040 ... (remaining 112106 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.090 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: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.680 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.020 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:8.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 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 : 0.009 0.071 13673 Z= 0.364 Angle : 0.713 9.909 18514 Z= 0.375 Chirality : 0.052 0.179 2080 Planarity : 0.004 0.048 2398 Dihedral : 14.638 88.437 5058 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.24 % Favored : 93.71 % Rotamer: Outliers : 1.87 % Allowed : 16.62 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.20), residues: 1700 helix: -1.30 (0.27), residues: 348 sheet: -1.12 (0.25), residues: 414 loop : -0.80 (0.20), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 320 TYR 0.015 0.002 TYR D 145 PHE 0.018 0.002 PHE B 228 TRP 0.007 0.001 TRP A 185 HIS 0.006 0.001 HIS D 369 Details of bonding type rmsd covalent geometry : bond 0.00865 (13672) covalent geometry : angle 0.71309 (18512) SS BOND : bond 0.00526 ( 1) SS BOND : angle 1.04038 ( 2) hydrogen bonds : bond 0.23065 ( 308) hydrogen bonds : angle 8.23296 ( 825) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 255 time to evaluate : 0.502 Fit side-chains REVERT: A 135 ASN cc_start: 0.7993 (t0) cc_final: 0.7132 (m110) REVERT: A 144 GLN cc_start: 0.7719 (tp40) cc_final: 0.7353 (mm-40) REVERT: A 156 ARG cc_start: 0.7665 (tpt-90) cc_final: 0.7282 (ttp-170) REVERT: A 223 LYS cc_start: 0.7322 (mttt) cc_final: 0.6968 (mtmm) REVERT: A 234 ASP cc_start: 0.7812 (m-30) cc_final: 0.7149 (m-30) REVERT: A 252 LEU cc_start: 0.7927 (mm) cc_final: 0.7572 (mm) REVERT: A 276 MET cc_start: 0.6911 (mtp) cc_final: 0.6080 (mmt) REVERT: A 293 MET cc_start: 0.5687 (mtt) cc_final: 0.5328 (mtt) REVERT: A 314 ARG cc_start: 0.6491 (mtt90) cc_final: 0.5823 (mtt-85) REVERT: A 339 GLN cc_start: 0.7911 (tp40) cc_final: 0.7706 (mm-40) REVERT: A 348 GLU cc_start: 0.7724 (tp30) cc_final: 0.7217 (tp30) REVERT: A 354 GLU cc_start: 0.7858 (tt0) cc_final: 0.7378 (tp30) REVERT: A 431 GLU cc_start: 0.7737 (tt0) cc_final: 0.7337 (mt-10) REVERT: A 446 GLU cc_start: 0.6954 (mt-10) cc_final: 0.6743 (mt-10) REVERT: A 502 LYS cc_start: 0.7417 (ttpp) cc_final: 0.6930 (mtpt) REVERT: B 88 ARG cc_start: 0.7421 (mtp180) cc_final: 0.6858 (mmm-85) REVERT: B 137 ASN cc_start: 0.8421 (p0) cc_final: 0.8096 (p0) REVERT: B 144 GLN cc_start: 0.7655 (tp40) cc_final: 0.7432 (tp-100) REVERT: B 156 ARG cc_start: 0.7479 (mtm-85) cc_final: 0.7103 (mtm180) REVERT: B 169 TYR cc_start: 0.8380 (p90) cc_final: 0.7394 (p90) REVERT: B 192 ASP cc_start: 0.7654 (m-30) cc_final: 0.7363 (m-30) REVERT: B 247 ASP cc_start: 0.6909 (p0) cc_final: 0.6679 (p0) REVERT: B 256 LEU cc_start: 0.7652 (mt) cc_final: 0.7281 (mm) REVERT: B 315 ASN cc_start: 0.6210 (m-40) cc_final: 0.5944 (t0) REVERT: B 316 LEU cc_start: 0.8334 (mt) cc_final: 0.8038 (mt) REVERT: B 320 ARG cc_start: 0.6209 (mmm160) cc_final: 0.5757 (tpp-160) REVERT: B 416 GLU cc_start: 0.8222 (mt-10) cc_final: 0.7867 (mt-10) REVERT: B 425 ARG cc_start: 0.8039 (mmm160) cc_final: 0.7276 (mtt90) REVERT: B 433 LYS cc_start: 0.7602 (tttt) cc_final: 0.6714 (tptt) REVERT: B 470 GLU cc_start: 0.7881 (tt0) cc_final: 0.7515 (tt0) REVERT: B 517 LYS cc_start: 0.7353 (mptt) cc_final: 0.6245 (mppt) REVERT: C 109 LYS cc_start: 0.8344 (mtmt) cc_final: 0.8135 (ptpp) REVERT: C 135 ASN cc_start: 0.7811 (m110) cc_final: 0.7157 (t0) REVERT: C 156 ARG cc_start: 0.7704 (mtp85) cc_final: 0.7389 (mtm180) REVERT: C 191 ASP cc_start: 0.7293 (m-30) cc_final: 0.6480 (m-30) REVERT: C 242 MET cc_start: 0.7685 (OUTLIER) cc_final: 0.7442 (mtp) REVERT: C 250 PHE cc_start: 0.7743 (m-80) cc_final: 0.7538 (m-80) REVERT: C 263 GLU cc_start: 0.7568 (tp30) cc_final: 0.7195 (tp30) REVERT: C 307 ASP cc_start: 0.7653 (p0) cc_final: 0.7426 (p0) REVERT: C 309 MET cc_start: 0.8023 (tpt) cc_final: 0.7677 (tpp) REVERT: C 310 LEU cc_start: 0.7979 (mp) cc_final: 0.7279 (mt) REVERT: C 311 ASP cc_start: 0.6526 (t70) cc_final: 0.5943 (m-30) REVERT: C 336 LEU cc_start: 0.7928 (mt) cc_final: 0.7719 (mt) REVERT: C 337 ARG cc_start: 0.6755 (mtp85) cc_final: 0.5881 (tpp80) REVERT: C 399 ASP cc_start: 0.7909 (t0) cc_final: 0.7668 (t70) REVERT: C 425 SER cc_start: 0.8318 (m) cc_final: 0.7946 (t) REVERT: C 431 GLU cc_start: 0.7923 (tt0) cc_final: 0.7085 (mt-10) REVERT: C 436 MET cc_start: 0.8858 (mmm) cc_final: 0.8504 (mtt) REVERT: C 462 LYS cc_start: 0.7386 (mttm) cc_final: 0.7044 (mttp) REVERT: C 487 ASP cc_start: 0.7414 (m-30) cc_final: 0.6801 (t0) REVERT: C 491 GLU cc_start: 0.7943 (mp0) cc_final: 0.7707 (mm-30) REVERT: C 494 ARG cc_start: 0.6040 (mmm-85) cc_final: 0.5798 (mmm160) REVERT: C 503 SER cc_start: 0.8291 (m) cc_final: 0.8075 (t) REVERT: D 88 ARG cc_start: 0.7209 (mtp-110) cc_final: 0.6946 (mtm180) REVERT: D 102 ARG cc_start: 0.6431 (mtm180) cc_final: 0.6229 (mtp-110) REVERT: D 145 TYR cc_start: 0.7370 (p90) cc_final: 0.6858 (p90) REVERT: D 208 ASP cc_start: 0.7321 (m-30) cc_final: 0.6405 (p0) REVERT: D 227 ASP cc_start: 0.7496 (m-30) cc_final: 0.7013 (t0) REVERT: D 320 ARG cc_start: 0.6108 (mmm160) cc_final: 0.5807 (mtt-85) REVERT: D 361 GLU cc_start: 0.7466 (mm-30) cc_final: 0.7217 (mm-30) REVERT: D 386 ARG cc_start: 0.7254 (ttp-170) cc_final: 0.6632 (ttt90) REVERT: D 411 THR cc_start: 0.8116 (OUTLIER) cc_final: 0.7895 (p) REVERT: D 425 ARG cc_start: 0.7774 (mmm160) cc_final: 0.7289 (mtt90) REVERT: D 433 LYS cc_start: 0.7137 (tttt) cc_final: 0.6230 (tmtt) REVERT: D 441 ASP cc_start: 0.7850 (m-30) cc_final: 0.7642 (m-30) REVERT: D 446 GLU cc_start: 0.7489 (mm-30) cc_final: 0.6543 (mm-30) REVERT: D 448 GLU cc_start: 0.7057 (mt-10) cc_final: 0.6751 (mt-10) REVERT: D 467 LYS cc_start: 0.7309 (mttt) cc_final: 0.6548 (mtpm) REVERT: D 484 ILE cc_start: 0.7667 (mt) cc_final: 0.7309 (mp) outliers start: 27 outliers final: 7 residues processed: 270 average time/residue: 0.6699 time to fit residues: 195.6664 Evaluate side-chains 224 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 215 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 218 ASP Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain C residue 242 MET Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain D residue 385 SER Chi-restraints excluded: chain D residue 411 THR Chi-restraints excluded: chain D residue 514 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 146 ASN C 383 GLN D 146 ASN D 347 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.166567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.122392 restraints weight = 14293.979| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 2.12 r_work: 0.3171 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.1138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13673 Z= 0.123 Angle : 0.532 9.904 18514 Z= 0.271 Chirality : 0.048 0.206 2080 Planarity : 0.003 0.033 2398 Dihedral : 4.483 27.653 1888 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.47 % Favored : 95.47 % Rotamer: Outliers : 3.19 % Allowed : 15.03 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.20), residues: 1700 helix: -0.69 (0.27), residues: 356 sheet: -0.87 (0.25), residues: 390 loop : -0.68 (0.21), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 318 TYR 0.013 0.001 TYR B 158 PHE 0.017 0.001 PHE D 360 TRP 0.006 0.001 TRP A 185 HIS 0.003 0.001 HIS D 232 Details of bonding type rmsd covalent geometry : bond 0.00294 (13672) covalent geometry : angle 0.53172 (18512) SS BOND : bond 0.00080 ( 1) SS BOND : angle 0.14364 ( 2) hydrogen bonds : bond 0.03916 ( 308) hydrogen bonds : angle 5.63249 ( 825) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 220 time to evaluate : 0.499 Fit side-chains revert: symmetry clash REVERT: A 83 ASP cc_start: 0.7902 (t70) cc_final: 0.7567 (p0) REVERT: A 135 ASN cc_start: 0.8323 (t0) cc_final: 0.7696 (m110) REVERT: A 156 ARG cc_start: 0.8105 (OUTLIER) cc_final: 0.7858 (ttp-170) REVERT: A 234 ASP cc_start: 0.8342 (m-30) cc_final: 0.7842 (m-30) REVERT: A 252 LEU cc_start: 0.8429 (mm) cc_final: 0.8080 (mm) REVERT: A 263 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.6668 (tm-30) REVERT: A 276 MET cc_start: 0.7420 (mtp) cc_final: 0.6180 (mmt) REVERT: A 293 MET cc_start: 0.6439 (mtt) cc_final: 0.5883 (mtt) REVERT: A 306 ARG cc_start: 0.8104 (OUTLIER) cc_final: 0.7690 (ttt-90) REVERT: A 314 ARG cc_start: 0.6795 (mtt90) cc_final: 0.6297 (mtt-85) REVERT: A 348 GLU cc_start: 0.8367 (tp30) cc_final: 0.8107 (tp30) REVERT: A 354 GLU cc_start: 0.8398 (tt0) cc_final: 0.7428 (mp0) REVERT: A 365 LYS cc_start: 0.7968 (ttpp) cc_final: 0.7157 (mttp) REVERT: A 399 ASP cc_start: 0.8543 (OUTLIER) cc_final: 0.8308 (t0) REVERT: A 494 ARG cc_start: 0.6687 (OUTLIER) cc_final: 0.6086 (mtm110) REVERT: A 502 LYS cc_start: 0.7979 (OUTLIER) cc_final: 0.7610 (mtpt) REVERT: B 88 ARG cc_start: 0.7653 (mtp180) cc_final: 0.7330 (mtm-85) REVERT: B 137 ASN cc_start: 0.8663 (p0) cc_final: 0.8229 (p0) REVERT: B 156 ARG cc_start: 0.8092 (mtm-85) cc_final: 0.7778 (mtm180) REVERT: B 192 ASP cc_start: 0.8188 (m-30) cc_final: 0.7980 (m-30) REVERT: B 256 LEU cc_start: 0.7704 (mt) cc_final: 0.7404 (mm) REVERT: B 280 MET cc_start: 0.7447 (tpp) cc_final: 0.7208 (tpp) REVERT: B 315 ASN cc_start: 0.6596 (m-40) cc_final: 0.6362 (t0) REVERT: B 316 LEU cc_start: 0.8663 (mt) cc_final: 0.8354 (mt) REVERT: B 320 ARG cc_start: 0.6520 (mmm160) cc_final: 0.6165 (tpp-160) REVERT: B 433 LYS cc_start: 0.8448 (tttt) cc_final: 0.7960 (tttm) REVERT: B 470 GLU cc_start: 0.8333 (tt0) cc_final: 0.8100 (tt0) REVERT: B 517 LYS cc_start: 0.7922 (mptt) cc_final: 0.7295 (mmmt) REVERT: C 135 ASN cc_start: 0.8431 (m110) cc_final: 0.7956 (t0) REVERT: C 156 ARG cc_start: 0.8252 (mtp85) cc_final: 0.8031 (mtm180) REVERT: C 231 THR cc_start: 0.9166 (m) cc_final: 0.8828 (m) REVERT: C 258 GLU cc_start: 0.7103 (pt0) cc_final: 0.6709 (pm20) REVERT: C 263 GLU cc_start: 0.7822 (tp30) cc_final: 0.7430 (tp30) REVERT: C 295 PHE cc_start: 0.7521 (m-80) cc_final: 0.7273 (m-80) REVERT: C 309 MET cc_start: 0.8507 (OUTLIER) cc_final: 0.8136 (tpp) REVERT: C 337 ARG cc_start: 0.7203 (mtp85) cc_final: 0.6640 (tpp80) REVERT: C 354 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8357 (tt0) REVERT: C 410 ASN cc_start: 0.8189 (p0) cc_final: 0.7926 (p0) REVERT: C 425 SER cc_start: 0.8863 (OUTLIER) cc_final: 0.8557 (t) REVERT: C 436 MET cc_start: 0.9197 (mmm) cc_final: 0.8679 (mtt) REVERT: C 462 LYS cc_start: 0.8337 (mttm) cc_final: 0.8044 (mttp) REVERT: C 487 ASP cc_start: 0.7396 (m-30) cc_final: 0.7027 (t0) REVERT: C 503 SER cc_start: 0.8626 (m) cc_final: 0.8400 (t) REVERT: D 145 TYR cc_start: 0.7716 (p90) cc_final: 0.7376 (p90) REVERT: D 208 ASP cc_start: 0.7374 (m-30) cc_final: 0.6909 (p0) REVERT: D 226 MET cc_start: 0.7470 (OUTLIER) cc_final: 0.7235 (mmt) REVERT: D 227 ASP cc_start: 0.7901 (m-30) cc_final: 0.7454 (t0) REVERT: D 238 ASP cc_start: 0.7703 (m-30) cc_final: 0.7437 (m-30) REVERT: D 241 ILE cc_start: 0.7939 (mt) cc_final: 0.7614 (mt) REVERT: D 320 ARG cc_start: 0.6328 (mmm160) cc_final: 0.6053 (mtt-85) REVERT: D 386 ARG cc_start: 0.7638 (ttp-170) cc_final: 0.7289 (ttt90) REVERT: D 433 LYS cc_start: 0.8118 (tttt) cc_final: 0.7378 (tmtt) REVERT: D 467 LYS cc_start: 0.7857 (mttt) cc_final: 0.7294 (mtpm) REVERT: D 484 ILE cc_start: 0.8336 (mt) cc_final: 0.8075 (mp) REVERT: D 493 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7535 (mp0) outliers start: 46 outliers final: 15 residues processed: 246 average time/residue: 0.6371 time to fit residues: 170.0533 Evaluate side-chains 226 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 200 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 156 ARG Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 226 GLN Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 263 GLU Chi-restraints excluded: chain A residue 306 ARG Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 494 ARG Chi-restraints excluded: chain A residue 502 LYS Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain C residue 309 MET Chi-restraints excluded: chain C residue 354 GLU Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 425 SER Chi-restraints excluded: chain D residue 226 MET Chi-restraints excluded: chain D residue 242 SER Chi-restraints excluded: chain D residue 493 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 168 optimal weight: 0.4980 chunk 91 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 154 optimal weight: 0.6980 chunk 94 optimal weight: 5.9990 chunk 112 optimal weight: 3.9990 chunk 142 optimal weight: 10.0000 chunk 52 optimal weight: 4.9990 chunk 111 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 144 GLN C 146 ASN D 146 ASN D 347 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.165637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.120773 restraints weight = 14522.211| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.15 r_work: 0.3144 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13673 Z= 0.140 Angle : 0.523 11.302 18514 Z= 0.266 Chirality : 0.048 0.176 2080 Planarity : 0.003 0.033 2398 Dihedral : 4.214 24.371 1876 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.18 % Favored : 94.76 % Rotamer: Outliers : 3.25 % Allowed : 16.62 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.20), residues: 1700 helix: -0.40 (0.28), residues: 356 sheet: -1.13 (0.24), residues: 426 loop : -0.69 (0.21), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 425 TYR 0.012 0.001 TYR D 145 PHE 0.016 0.001 PHE D 360 TRP 0.004 0.001 TRP A 185 HIS 0.003 0.001 HIS A 153 Details of bonding type rmsd covalent geometry : bond 0.00340 (13672) covalent geometry : angle 0.52285 (18512) SS BOND : bond 0.00114 ( 1) SS BOND : angle 0.25094 ( 2) hydrogen bonds : bond 0.03477 ( 308) hydrogen bonds : angle 5.19489 ( 825) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 208 time to evaluate : 0.514 Fit side-chains revert: symmetry clash REVERT: A 135 ASN cc_start: 0.8224 (t0) cc_final: 0.7609 (m110) REVERT: A 156 ARG cc_start: 0.8091 (OUTLIER) cc_final: 0.7785 (ttp-170) REVERT: A 234 ASP cc_start: 0.8346 (m-30) cc_final: 0.7840 (m-30) REVERT: A 252 LEU cc_start: 0.8524 (mm) cc_final: 0.8184 (mm) REVERT: A 263 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.6632 (tm-30) REVERT: A 276 MET cc_start: 0.7402 (mtp) cc_final: 0.6052 (mmt) REVERT: A 293 MET cc_start: 0.6433 (mtt) cc_final: 0.5865 (mtt) REVERT: A 306 ARG cc_start: 0.8122 (OUTLIER) cc_final: 0.7704 (ttt-90) REVERT: A 314 ARG cc_start: 0.6795 (mtt90) cc_final: 0.6285 (mtt-85) REVERT: A 325 SER cc_start: 0.8562 (OUTLIER) cc_final: 0.8315 (p) REVERT: A 348 GLU cc_start: 0.8425 (tp30) cc_final: 0.8197 (tp30) REVERT: A 354 GLU cc_start: 0.8409 (tm-30) cc_final: 0.7457 (mp0) REVERT: A 365 LYS cc_start: 0.8051 (ttpp) cc_final: 0.7169 (mttp) REVERT: A 399 ASP cc_start: 0.8608 (OUTLIER) cc_final: 0.8341 (t0) REVERT: A 431 GLU cc_start: 0.8347 (mt-10) cc_final: 0.8132 (mt-10) REVERT: A 494 ARG cc_start: 0.6731 (OUTLIER) cc_final: 0.6248 (mtm110) REVERT: A 502 LYS cc_start: 0.7944 (OUTLIER) cc_final: 0.7557 (mtpt) REVERT: B 88 ARG cc_start: 0.7711 (mtp180) cc_final: 0.7409 (mtm-85) REVERT: B 137 ASN cc_start: 0.8724 (p0) cc_final: 0.8340 (p0) REVERT: B 192 ASP cc_start: 0.8155 (m-30) cc_final: 0.7927 (m-30) REVERT: B 203 ASP cc_start: 0.6618 (t70) cc_final: 0.6106 (p0) REVERT: B 243 CYS cc_start: 0.8894 (OUTLIER) cc_final: 0.8554 (m) REVERT: B 247 ASP cc_start: 0.7065 (p0) cc_final: 0.6822 (p0) REVERT: B 256 LEU cc_start: 0.7712 (mt) cc_final: 0.7469 (mm) REVERT: B 316 LEU cc_start: 0.8644 (mt) cc_final: 0.8351 (mt) REVERT: B 320 ARG cc_start: 0.6563 (mmm160) cc_final: 0.6202 (tpp-160) REVERT: B 398 LYS cc_start: 0.8700 (tptm) cc_final: 0.8320 (tmtm) REVERT: B 433 LYS cc_start: 0.8413 (tttt) cc_final: 0.7937 (tttm) REVERT: B 470 GLU cc_start: 0.8379 (tt0) cc_final: 0.8137 (tt0) REVERT: B 517 LYS cc_start: 0.7902 (mptt) cc_final: 0.7253 (mmmt) REVERT: C 135 ASN cc_start: 0.8369 (m110) cc_final: 0.7977 (t0) REVERT: C 156 ARG cc_start: 0.8182 (mtp85) cc_final: 0.7946 (mtm180) REVERT: C 231 THR cc_start: 0.9102 (m) cc_final: 0.8777 (m) REVERT: C 258 GLU cc_start: 0.7017 (pt0) cc_final: 0.6613 (pm20) REVERT: C 263 GLU cc_start: 0.7826 (tp30) cc_final: 0.7439 (tp30) REVERT: C 309 MET cc_start: 0.8515 (OUTLIER) cc_final: 0.8207 (tpp) REVERT: C 337 ARG cc_start: 0.7184 (mtp85) cc_final: 0.6565 (tpp80) REVERT: C 410 ASN cc_start: 0.8222 (p0) cc_final: 0.7937 (p0) REVERT: C 425 SER cc_start: 0.8841 (OUTLIER) cc_final: 0.8526 (t) REVERT: C 436 MET cc_start: 0.9181 (mmm) cc_final: 0.8647 (mtt) REVERT: C 462 LYS cc_start: 0.8332 (mttm) cc_final: 0.8027 (mttp) REVERT: C 487 ASP cc_start: 0.7295 (m-30) cc_final: 0.6848 (t0) REVERT: C 503 SER cc_start: 0.8599 (m) cc_final: 0.8358 (t) REVERT: D 145 TYR cc_start: 0.7628 (p90) cc_final: 0.7349 (p90) REVERT: D 208 ASP cc_start: 0.7476 (OUTLIER) cc_final: 0.6856 (p0) REVERT: D 227 ASP cc_start: 0.7871 (m-30) cc_final: 0.7462 (t0) REVERT: D 238 ASP cc_start: 0.7792 (m-30) cc_final: 0.7521 (m-30) REVERT: D 241 ILE cc_start: 0.7810 (mt) cc_final: 0.7475 (mt) REVERT: D 320 ARG cc_start: 0.6213 (mmm160) cc_final: 0.5807 (mtt-85) REVERT: D 386 ARG cc_start: 0.7555 (ttp-170) cc_final: 0.7232 (ttt90) REVERT: D 433 LYS cc_start: 0.8118 (tttt) cc_final: 0.7367 (tmtt) REVERT: D 467 LYS cc_start: 0.7827 (mttt) cc_final: 0.7318 (mtpm) REVERT: D 484 ILE cc_start: 0.8333 (mt) cc_final: 0.8088 (mp) REVERT: D 493 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7547 (mp0) outliers start: 47 outliers final: 13 residues processed: 237 average time/residue: 0.6402 time to fit residues: 164.7860 Evaluate side-chains 224 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 199 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 156 ARG Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 263 GLU Chi-restraints excluded: chain A residue 306 ARG Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 494 ARG Chi-restraints excluded: chain A residue 502 LYS Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 309 MET Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 399 ASP Chi-restraints excluded: chain C residue 425 SER Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 208 ASP Chi-restraints excluded: chain D residue 493 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 101 optimal weight: 10.0000 chunk 13 optimal weight: 0.9990 chunk 147 optimal weight: 7.9990 chunk 33 optimal weight: 6.9990 chunk 160 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 161 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 102 optimal weight: 0.0980 chunk 34 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 overall best weight: 1.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 144 GLN C 146 ASN C 360 ASN D 146 ASN D 347 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.162484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.116302 restraints weight = 14420.419| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.22 r_work: 0.3081 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13673 Z= 0.182 Angle : 0.557 11.548 18514 Z= 0.282 Chirality : 0.049 0.221 2080 Planarity : 0.003 0.041 2398 Dihedral : 4.377 26.010 1876 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.06 % Favored : 94.88 % Rotamer: Outliers : 3.46 % Allowed : 16.76 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.20), residues: 1700 helix: -0.42 (0.27), residues: 370 sheet: -1.17 (0.23), residues: 436 loop : -0.71 (0.21), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 376 TYR 0.017 0.001 TYR D 145 PHE 0.017 0.002 PHE B 228 TRP 0.004 0.001 TRP A 198 HIS 0.004 0.001 HIS B 232 Details of bonding type rmsd covalent geometry : bond 0.00446 (13672) covalent geometry : angle 0.55744 (18512) SS BOND : bond 0.00152 ( 1) SS BOND : angle 0.33057 ( 2) hydrogen bonds : bond 0.03467 ( 308) hydrogen bonds : angle 5.11555 ( 825) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 200 time to evaluate : 0.645 Fit side-chains REVERT: A 135 ASN cc_start: 0.8184 (t0) cc_final: 0.7573 (m-40) REVERT: A 144 GLN cc_start: 0.8112 (tp40) cc_final: 0.7890 (mm110) REVERT: A 156 ARG cc_start: 0.8058 (OUTLIER) cc_final: 0.7717 (ttp-170) REVERT: A 234 ASP cc_start: 0.8407 (m-30) cc_final: 0.7908 (m-30) REVERT: A 252 LEU cc_start: 0.8547 (mm) cc_final: 0.8308 (mm) REVERT: A 276 MET cc_start: 0.7500 (mtp) cc_final: 0.6734 (mmt) REVERT: A 293 MET cc_start: 0.6322 (mtt) cc_final: 0.5797 (mtt) REVERT: A 306 ARG cc_start: 0.8057 (OUTLIER) cc_final: 0.7625 (ttt-90) REVERT: A 314 ARG cc_start: 0.6726 (mtt90) cc_final: 0.6235 (mtt-85) REVERT: A 325 SER cc_start: 0.8523 (OUTLIER) cc_final: 0.8267 (p) REVERT: A 348 GLU cc_start: 0.8500 (tp30) cc_final: 0.8298 (tp30) REVERT: A 354 GLU cc_start: 0.8453 (tm-30) cc_final: 0.7442 (mp0) REVERT: A 399 ASP cc_start: 0.8694 (OUTLIER) cc_final: 0.8405 (t0) REVERT: A 494 ARG cc_start: 0.6678 (OUTLIER) cc_final: 0.6298 (mtm110) REVERT: A 502 LYS cc_start: 0.8006 (OUTLIER) cc_final: 0.7554 (mtpt) REVERT: B 88 ARG cc_start: 0.7705 (mtp180) cc_final: 0.7358 (mmm-85) REVERT: B 137 ASN cc_start: 0.8727 (p0) cc_final: 0.8321 (p0) REVERT: B 192 ASP cc_start: 0.8153 (m-30) cc_final: 0.7899 (m-30) REVERT: B 203 ASP cc_start: 0.6706 (t70) cc_final: 0.6093 (p0) REVERT: B 320 ARG cc_start: 0.6611 (mmm160) cc_final: 0.6123 (tpp-160) REVERT: B 398 LYS cc_start: 0.8660 (tptm) cc_final: 0.8214 (tmtm) REVERT: B 433 LYS cc_start: 0.8389 (tttt) cc_final: 0.7754 (tptt) REVERT: B 493 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7805 (mm-30) REVERT: B 517 LYS cc_start: 0.7956 (mptt) cc_final: 0.7276 (mmmt) REVERT: C 135 ASN cc_start: 0.8398 (m110) cc_final: 0.7970 (t0) REVERT: C 156 ARG cc_start: 0.8189 (mtp85) cc_final: 0.7908 (mtm180) REVERT: C 263 GLU cc_start: 0.7765 (tp30) cc_final: 0.7365 (tp30) REVERT: C 309 MET cc_start: 0.8436 (OUTLIER) cc_final: 0.8083 (tpp) REVERT: C 334 LEU cc_start: 0.7742 (OUTLIER) cc_final: 0.7280 (mp) REVERT: C 337 ARG cc_start: 0.7230 (mtp85) cc_final: 0.6524 (tpp80) REVERT: C 354 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.8295 (tt0) REVERT: C 410 ASN cc_start: 0.8268 (p0) cc_final: 0.7997 (p0) REVERT: C 425 SER cc_start: 0.8771 (OUTLIER) cc_final: 0.8423 (t) REVERT: C 436 MET cc_start: 0.9250 (mmm) cc_final: 0.8731 (mtt) REVERT: C 462 LYS cc_start: 0.8357 (mttm) cc_final: 0.8021 (mttp) REVERT: C 487 ASP cc_start: 0.7402 (m-30) cc_final: 0.6868 (t0) REVERT: C 503 SER cc_start: 0.8593 (m) cc_final: 0.8337 (t) REVERT: D 145 TYR cc_start: 0.7618 (p90) cc_final: 0.7333 (p90) REVERT: D 208 ASP cc_start: 0.7405 (OUTLIER) cc_final: 0.6725 (p0) REVERT: D 227 ASP cc_start: 0.7897 (m-30) cc_final: 0.7592 (t0) REVERT: D 238 ASP cc_start: 0.7836 (m-30) cc_final: 0.7617 (m-30) REVERT: D 241 ILE cc_start: 0.7634 (mt) cc_final: 0.7334 (mt) REVERT: D 320 ARG cc_start: 0.6109 (mmm160) cc_final: 0.5621 (mtt-85) REVERT: D 386 ARG cc_start: 0.7625 (ttp-170) cc_final: 0.7249 (ttt90) REVERT: D 433 LYS cc_start: 0.8150 (tttt) cc_final: 0.7366 (tmtt) REVERT: D 467 LYS cc_start: 0.7871 (mttt) cc_final: 0.7332 (mtpm) REVERT: D 484 ILE cc_start: 0.8300 (mt) cc_final: 0.8028 (mp) outliers start: 50 outliers final: 19 residues processed: 231 average time/residue: 0.6156 time to fit residues: 154.8133 Evaluate side-chains 221 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 190 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 156 ARG Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 306 ARG Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 494 ARG Chi-restraints excluded: chain A residue 502 LYS Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 493 GLU Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 309 MET Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 354 GLU Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 399 ASP Chi-restraints excluded: chain C residue 400 SER Chi-restraints excluded: chain C residue 425 SER Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 208 ASP Chi-restraints excluded: chain D residue 242 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 144 optimal weight: 7.9990 chunk 109 optimal weight: 8.9990 chunk 166 optimal weight: 6.9990 chunk 96 optimal weight: 1.9990 chunk 125 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 137 optimal weight: 3.9990 chunk 98 optimal weight: 0.7980 chunk 103 optimal weight: 20.0000 chunk 60 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 144 GLN C 146 ASN D 146 ASN D 347 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.162155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.113332 restraints weight = 14413.140| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 2.20 r_work: 0.3148 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13673 Z= 0.175 Angle : 0.543 11.863 18514 Z= 0.277 Chirality : 0.048 0.159 2080 Planarity : 0.003 0.049 2398 Dihedral : 4.398 26.821 1876 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.24 % Favored : 94.71 % Rotamer: Outliers : 3.53 % Allowed : 16.83 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.20), residues: 1700 helix: -0.38 (0.27), residues: 376 sheet: -1.16 (0.23), residues: 436 loop : -0.73 (0.21), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 376 TYR 0.014 0.001 TYR D 145 PHE 0.016 0.001 PHE D 360 TRP 0.004 0.001 TRP A 185 HIS 0.004 0.001 HIS B 232 Details of bonding type rmsd covalent geometry : bond 0.00432 (13672) covalent geometry : angle 0.54351 (18512) SS BOND : bond 0.00150 ( 1) SS BOND : angle 0.31283 ( 2) hydrogen bonds : bond 0.03342 ( 308) hydrogen bonds : angle 5.04692 ( 825) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 197 time to evaluate : 0.526 Fit side-chains REVERT: A 135 ASN cc_start: 0.8309 (t0) cc_final: 0.7745 (m-40) REVERT: A 156 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.7941 (ttp-170) REVERT: A 234 ASP cc_start: 0.8534 (m-30) cc_final: 0.8123 (m-30) REVERT: A 263 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7070 (tm-30) REVERT: A 276 MET cc_start: 0.7634 (mtp) cc_final: 0.6354 (mmt) REVERT: A 293 MET cc_start: 0.6531 (mtt) cc_final: 0.6005 (mtt) REVERT: A 306 ARG cc_start: 0.8152 (OUTLIER) cc_final: 0.7736 (ttt-90) REVERT: A 314 ARG cc_start: 0.6917 (mtt90) cc_final: 0.6422 (mtt-85) REVERT: A 354 GLU cc_start: 0.8553 (tm-30) cc_final: 0.7684 (mp0) REVERT: A 399 ASP cc_start: 0.8719 (OUTLIER) cc_final: 0.8472 (t0) REVERT: A 494 ARG cc_start: 0.6831 (OUTLIER) cc_final: 0.6464 (mtm110) REVERT: A 502 LYS cc_start: 0.8116 (OUTLIER) cc_final: 0.7710 (mtpt) REVERT: B 88 ARG cc_start: 0.7698 (mtp180) cc_final: 0.7449 (mmm-85) REVERT: B 137 ASN cc_start: 0.8808 (p0) cc_final: 0.8413 (p0) REVERT: B 192 ASP cc_start: 0.8243 (m-30) cc_final: 0.8042 (m-30) REVERT: B 203 ASP cc_start: 0.6801 (OUTLIER) cc_final: 0.6209 (p0) REVERT: B 256 LEU cc_start: 0.7934 (mt) cc_final: 0.7654 (mm) REVERT: B 280 MET cc_start: 0.7562 (tpp) cc_final: 0.7353 (tpp) REVERT: B 316 LEU cc_start: 0.8784 (mt) cc_final: 0.8574 (mp) REVERT: B 320 ARG cc_start: 0.6632 (mmm160) cc_final: 0.6280 (tpp-160) REVERT: B 398 LYS cc_start: 0.8756 (tptm) cc_final: 0.8373 (tmtm) REVERT: B 433 LYS cc_start: 0.8522 (tttt) cc_final: 0.8003 (tptt) REVERT: B 493 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7866 (mm-30) REVERT: B 517 LYS cc_start: 0.8064 (mptt) cc_final: 0.7472 (mmmt) REVERT: C 135 ASN cc_start: 0.8457 (m110) cc_final: 0.8110 (t0) REVERT: C 156 ARG cc_start: 0.8318 (mtp85) cc_final: 0.8091 (mtm180) REVERT: C 231 THR cc_start: 0.9211 (m) cc_final: 0.8819 (m) REVERT: C 232 ASP cc_start: 0.8438 (t70) cc_final: 0.7678 (t0) REVERT: C 263 GLU cc_start: 0.7788 (tp30) cc_final: 0.7405 (tp30) REVERT: C 309 MET cc_start: 0.8614 (OUTLIER) cc_final: 0.8254 (tpp) REVERT: C 337 ARG cc_start: 0.7362 (mtp85) cc_final: 0.6790 (tpp80) REVERT: C 410 ASN cc_start: 0.8439 (p0) cc_final: 0.8168 (p0) REVERT: C 425 SER cc_start: 0.8828 (OUTLIER) cc_final: 0.8512 (t) REVERT: C 436 MET cc_start: 0.9228 (mmm) cc_final: 0.8697 (mtt) REVERT: C 462 LYS cc_start: 0.8551 (mttm) cc_final: 0.8244 (mttp) REVERT: C 487 ASP cc_start: 0.7425 (m-30) cc_final: 0.6911 (t0) REVERT: D 145 TYR cc_start: 0.7725 (p90) cc_final: 0.7441 (p90) REVERT: D 208 ASP cc_start: 0.7448 (OUTLIER) cc_final: 0.6825 (p0) REVERT: D 227 ASP cc_start: 0.7991 (m-30) cc_final: 0.7741 (t0) REVERT: D 320 ARG cc_start: 0.6217 (mmm160) cc_final: 0.5763 (mtt-85) REVERT: D 386 ARG cc_start: 0.7643 (ttp-170) cc_final: 0.7400 (ttt90) REVERT: D 433 LYS cc_start: 0.8321 (tttt) cc_final: 0.7637 (tmtt) REVERT: D 467 LYS cc_start: 0.7949 (mttt) cc_final: 0.7492 (mtpm) REVERT: D 484 ILE cc_start: 0.8442 (mt) cc_final: 0.8218 (mp) REVERT: D 493 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7538 (mp0) outliers start: 51 outliers final: 22 residues processed: 228 average time/residue: 0.5990 time to fit residues: 149.0113 Evaluate side-chains 225 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 191 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 156 ARG Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 263 GLU Chi-restraints excluded: chain A residue 306 ARG Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 494 ARG Chi-restraints excluded: chain A residue 502 LYS Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 493 GLU Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 309 MET Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 399 ASP Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 425 SER Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 208 ASP Chi-restraints excluded: chain D residue 242 SER Chi-restraints excluded: chain D residue 493 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 7 optimal weight: 1.9990 chunk 154 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 chunk 43 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 156 optimal weight: 5.9990 chunk 108 optimal weight: 7.9990 chunk 115 optimal weight: 3.9990 chunk 152 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 GLN A 144 GLN B 144 GLN C 146 ASN ** C 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 ASN D 347 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.163483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.116704 restraints weight = 14332.359| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.31 r_work: 0.3130 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13673 Z= 0.128 Angle : 0.518 12.187 18514 Z= 0.262 Chirality : 0.047 0.220 2080 Planarity : 0.003 0.030 2398 Dihedral : 4.254 26.539 1876 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.76 % Favored : 95.18 % Rotamer: Outliers : 2.98 % Allowed : 17.59 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.20), residues: 1700 helix: -0.20 (0.28), residues: 374 sheet: -1.11 (0.24), residues: 436 loop : -0.66 (0.21), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 425 TYR 0.012 0.001 TYR A 357 PHE 0.015 0.001 PHE D 360 TRP 0.005 0.001 TRP A 185 HIS 0.003 0.001 HIS B 232 Details of bonding type rmsd covalent geometry : bond 0.00313 (13672) covalent geometry : angle 0.51793 (18512) SS BOND : bond 0.00062 ( 1) SS BOND : angle 0.21538 ( 2) hydrogen bonds : bond 0.03064 ( 308) hydrogen bonds : angle 4.89759 ( 825) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 192 time to evaluate : 0.544 Fit side-chains REVERT: A 135 ASN cc_start: 0.8213 (t0) cc_final: 0.7541 (m-40) REVERT: A 156 ARG cc_start: 0.7969 (OUTLIER) cc_final: 0.7645 (ttp-170) REVERT: A 234 ASP cc_start: 0.8380 (m-30) cc_final: 0.7884 (m-30) REVERT: A 263 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.6780 (tm-30) REVERT: A 276 MET cc_start: 0.7450 (mtp) cc_final: 0.5985 (mmt) REVERT: A 293 MET cc_start: 0.6212 (mtt) cc_final: 0.5716 (mtt) REVERT: A 306 ARG cc_start: 0.8002 (OUTLIER) cc_final: 0.7523 (ttt-90) REVERT: A 314 ARG cc_start: 0.6659 (mtt90) cc_final: 0.6171 (mtt-85) REVERT: A 354 GLU cc_start: 0.8405 (tm-30) cc_final: 0.7344 (mp0) REVERT: A 399 ASP cc_start: 0.8577 (OUTLIER) cc_final: 0.8289 (t0) REVERT: A 431 GLU cc_start: 0.8324 (mt-10) cc_final: 0.8052 (mt-10) REVERT: A 494 ARG cc_start: 0.6653 (OUTLIER) cc_final: 0.6184 (mtm110) REVERT: A 502 LYS cc_start: 0.7991 (OUTLIER) cc_final: 0.7559 (mtpt) REVERT: B 88 ARG cc_start: 0.7685 (mtp180) cc_final: 0.7351 (mmm-85) REVERT: B 137 ASN cc_start: 0.8702 (p0) cc_final: 0.8290 (p0) REVERT: B 192 ASP cc_start: 0.8104 (m-30) cc_final: 0.7857 (m-30) REVERT: B 203 ASP cc_start: 0.6750 (OUTLIER) cc_final: 0.6135 (p0) REVERT: B 280 MET cc_start: 0.7439 (tpp) cc_final: 0.7127 (tpp) REVERT: B 316 LEU cc_start: 0.8639 (mt) cc_final: 0.8430 (mp) REVERT: B 320 ARG cc_start: 0.6596 (mmm160) cc_final: 0.6201 (tpp-160) REVERT: B 398 LYS cc_start: 0.8601 (tptm) cc_final: 0.8154 (tmtm) REVERT: B 433 LYS cc_start: 0.8334 (tttt) cc_final: 0.7647 (tptp) REVERT: B 493 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7725 (mm-30) REVERT: B 517 LYS cc_start: 0.7940 (mptt) cc_final: 0.7262 (mmmt) REVERT: C 135 ASN cc_start: 0.8293 (m110) cc_final: 0.7908 (t0) REVERT: C 156 ARG cc_start: 0.8165 (mtp85) cc_final: 0.7807 (mtm180) REVERT: C 231 THR cc_start: 0.9097 (m) cc_final: 0.8724 (m) REVERT: C 232 ASP cc_start: 0.8306 (t70) cc_final: 0.7475 (t0) REVERT: C 263 GLU cc_start: 0.7658 (tp30) cc_final: 0.7230 (tp30) REVERT: C 309 MET cc_start: 0.8480 (OUTLIER) cc_final: 0.8089 (tpp) REVERT: C 337 ARG cc_start: 0.7229 (mtp85) cc_final: 0.6541 (tpp80) REVERT: C 425 SER cc_start: 0.8722 (OUTLIER) cc_final: 0.8367 (t) REVERT: C 436 MET cc_start: 0.9184 (mmm) cc_final: 0.8610 (mtt) REVERT: C 462 LYS cc_start: 0.8334 (mttm) cc_final: 0.7978 (mttp) REVERT: C 487 ASP cc_start: 0.7298 (m-30) cc_final: 0.6825 (t0) REVERT: C 491 GLU cc_start: 0.8384 (mp0) cc_final: 0.8050 (mm-30) REVERT: D 145 TYR cc_start: 0.7568 (p90) cc_final: 0.7250 (p90) REVERT: D 208 ASP cc_start: 0.7366 (OUTLIER) cc_final: 0.6597 (p0) REVERT: D 227 ASP cc_start: 0.7820 (m-30) cc_final: 0.7483 (t0) REVERT: D 320 ARG cc_start: 0.6086 (mmm160) cc_final: 0.5696 (mtt-85) REVERT: D 386 ARG cc_start: 0.7421 (ttp-170) cc_final: 0.7154 (ttt90) REVERT: D 433 LYS cc_start: 0.8047 (tttt) cc_final: 0.7252 (tmtt) REVERT: D 467 LYS cc_start: 0.7808 (mttt) cc_final: 0.7260 (mtpm) REVERT: D 484 ILE cc_start: 0.8290 (mt) cc_final: 0.8033 (mp) REVERT: D 493 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7373 (mp0) outliers start: 43 outliers final: 18 residues processed: 214 average time/residue: 0.6359 time to fit residues: 148.0431 Evaluate side-chains 218 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 188 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 156 ARG Chi-restraints excluded: chain A residue 263 GLU Chi-restraints excluded: chain A residue 306 ARG Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 494 ARG Chi-restraints excluded: chain A residue 502 LYS Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 493 GLU Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 309 MET Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 425 SER Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain D residue 208 ASP Chi-restraints excluded: chain D residue 242 SER Chi-restraints excluded: chain D residue 493 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 49 optimal weight: 3.9990 chunk 168 optimal weight: 0.0870 chunk 158 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 147 optimal weight: 8.9990 chunk 47 optimal weight: 0.8980 chunk 156 optimal weight: 5.9990 chunk 58 optimal weight: 0.0000 chunk 146 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 139 optimal weight: 0.8980 overall best weight: 0.7764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 GLN B 144 GLN D 146 ASN D 347 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.164489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.118124 restraints weight = 14237.601| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.31 r_work: 0.3142 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13673 Z= 0.109 Angle : 0.500 12.279 18514 Z= 0.253 Chirality : 0.047 0.147 2080 Planarity : 0.003 0.042 2398 Dihedral : 4.116 25.979 1876 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.76 % Favored : 95.18 % Rotamer: Outliers : 3.25 % Allowed : 17.80 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.21), residues: 1700 helix: -0.07 (0.28), residues: 376 sheet: -1.02 (0.24), residues: 432 loop : -0.60 (0.22), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 376 TYR 0.012 0.001 TYR A 357 PHE 0.014 0.001 PHE D 360 TRP 0.005 0.001 TRP A 185 HIS 0.003 0.001 HIS B 232 Details of bonding type rmsd covalent geometry : bond 0.00264 (13672) covalent geometry : angle 0.49979 (18512) SS BOND : bond 0.00081 ( 1) SS BOND : angle 0.26329 ( 2) hydrogen bonds : bond 0.02900 ( 308) hydrogen bonds : angle 4.75039 ( 825) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 192 time to evaluate : 0.541 Fit side-chains REVERT: A 83 ASP cc_start: 0.7900 (t0) cc_final: 0.7629 (p0) REVERT: A 135 ASN cc_start: 0.8332 (t0) cc_final: 0.7826 (m-40) REVERT: A 156 ARG cc_start: 0.8149 (OUTLIER) cc_final: 0.7922 (ttp-170) REVERT: A 230 GLU cc_start: 0.7685 (tm-30) cc_final: 0.7436 (tm-30) REVERT: A 234 ASP cc_start: 0.8482 (m-30) cc_final: 0.8098 (m-30) REVERT: A 263 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.6823 (tm-30) REVERT: A 276 MET cc_start: 0.7479 (mtp) cc_final: 0.6030 (mmt) REVERT: A 293 MET cc_start: 0.6497 (mtt) cc_final: 0.5913 (mtt) REVERT: A 306 ARG cc_start: 0.8100 (OUTLIER) cc_final: 0.7666 (ttt-90) REVERT: A 314 ARG cc_start: 0.6862 (mtt90) cc_final: 0.6399 (mtt-85) REVERT: A 337 ARG cc_start: 0.7643 (ttp80) cc_final: 0.7398 (tpp80) REVERT: A 354 GLU cc_start: 0.8523 (tm-30) cc_final: 0.7643 (mp0) REVERT: A 399 ASP cc_start: 0.8630 (OUTLIER) cc_final: 0.8407 (t0) REVERT: A 494 ARG cc_start: 0.6778 (OUTLIER) cc_final: 0.6226 (mtm110) REVERT: A 502 LYS cc_start: 0.8152 (OUTLIER) cc_final: 0.7780 (mtpt) REVERT: B 88 ARG cc_start: 0.7748 (mtp180) cc_final: 0.7484 (mmm-85) REVERT: B 137 ASN cc_start: 0.8799 (p0) cc_final: 0.8389 (p0) REVERT: B 192 ASP cc_start: 0.8236 (m-30) cc_final: 0.8030 (m-30) REVERT: B 203 ASP cc_start: 0.6872 (OUTLIER) cc_final: 0.6396 (p0) REVERT: B 320 ARG cc_start: 0.6658 (mmm160) cc_final: 0.6347 (tpp-160) REVERT: B 338 GLU cc_start: 0.6055 (tp30) cc_final: 0.5743 (mp0) REVERT: B 398 LYS cc_start: 0.8711 (tptm) cc_final: 0.8359 (tmtm) REVERT: B 433 LYS cc_start: 0.8493 (tttt) cc_final: 0.7969 (tptp) REVERT: B 493 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7820 (mm-30) REVERT: B 517 LYS cc_start: 0.8048 (mptt) cc_final: 0.7460 (mmmt) REVERT: C 135 ASN cc_start: 0.8437 (m110) cc_final: 0.8123 (t0) REVERT: C 156 ARG cc_start: 0.8350 (mtp85) cc_final: 0.8081 (mtm180) REVERT: C 231 THR cc_start: 0.9169 (m) cc_final: 0.8774 (m) REVERT: C 232 ASP cc_start: 0.8366 (t70) cc_final: 0.7648 (t70) REVERT: C 263 GLU cc_start: 0.7664 (tp30) cc_final: 0.7307 (tp30) REVERT: C 309 MET cc_start: 0.8576 (OUTLIER) cc_final: 0.8256 (tpp) REVERT: C 334 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7603 (mp) REVERT: C 337 ARG cc_start: 0.7409 (mtp85) cc_final: 0.6876 (tpp80) REVERT: C 410 ASN cc_start: 0.8406 (p0) cc_final: 0.8135 (p0) REVERT: C 425 SER cc_start: 0.8762 (OUTLIER) cc_final: 0.8449 (t) REVERT: C 436 MET cc_start: 0.9101 (OUTLIER) cc_final: 0.8597 (mtt) REVERT: C 462 LYS cc_start: 0.8568 (mttm) cc_final: 0.8263 (mttp) REVERT: C 487 ASP cc_start: 0.7311 (m-30) cc_final: 0.6806 (t0) REVERT: D 208 ASP cc_start: 0.7411 (OUTLIER) cc_final: 0.6723 (p0) REVERT: D 227 ASP cc_start: 0.7953 (m-30) cc_final: 0.7593 (t0) REVERT: D 320 ARG cc_start: 0.6158 (mmm160) cc_final: 0.5694 (mtt-85) REVERT: D 355 THR cc_start: 0.8018 (OUTLIER) cc_final: 0.7671 (p) REVERT: D 433 LYS cc_start: 0.8262 (tttt) cc_final: 0.7592 (tmtt) REVERT: D 467 LYS cc_start: 0.7923 (mttt) cc_final: 0.7426 (mtpm) REVERT: D 484 ILE cc_start: 0.8430 (mt) cc_final: 0.8228 (mp) REVERT: D 493 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7566 (mp0) outliers start: 47 outliers final: 19 residues processed: 214 average time/residue: 0.6274 time to fit residues: 145.9340 Evaluate side-chains 223 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 189 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 156 ARG Chi-restraints excluded: chain A residue 263 GLU Chi-restraints excluded: chain A residue 306 ARG Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 488 ASN Chi-restraints excluded: chain A residue 494 ARG Chi-restraints excluded: chain A residue 502 LYS Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 493 GLU Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 242 MET Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 309 MET Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 425 SER Chi-restraints excluded: chain C residue 436 MET Chi-restraints excluded: chain D residue 208 ASP Chi-restraints excluded: chain D residue 242 SER Chi-restraints excluded: chain D residue 355 THR Chi-restraints excluded: chain D residue 493 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 83 optimal weight: 0.0980 chunk 161 optimal weight: 0.0870 chunk 10 optimal weight: 6.9990 chunk 117 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 46 optimal weight: 0.6980 chunk 54 optimal weight: 4.9990 chunk 125 optimal weight: 7.9990 chunk 36 optimal weight: 0.0000 chunk 5 optimal weight: 0.8980 overall best weight: 0.3562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 GLN B 144 GLN D 347 ASN D 363 ASN D 388 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.167059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.119125 restraints weight = 14216.407| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.19 r_work: 0.3177 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13673 Z= 0.088 Angle : 0.485 11.946 18514 Z= 0.244 Chirality : 0.046 0.217 2080 Planarity : 0.003 0.029 2398 Dihedral : 3.915 25.201 1876 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.00 % Favored : 95.94 % Rotamer: Outliers : 2.98 % Allowed : 18.42 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.21), residues: 1700 helix: 0.15 (0.28), residues: 376 sheet: -0.94 (0.24), residues: 430 loop : -0.54 (0.22), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 318 TYR 0.012 0.001 TYR C 357 PHE 0.013 0.001 PHE D 359 TRP 0.005 0.000 TRP A 185 HIS 0.003 0.001 HIS D 232 Details of bonding type rmsd covalent geometry : bond 0.00205 (13672) covalent geometry : angle 0.48497 (18512) SS BOND : bond 0.00029 ( 1) SS BOND : angle 0.20951 ( 2) hydrogen bonds : bond 0.02714 ( 308) hydrogen bonds : angle 4.59491 ( 825) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 202 time to evaluate : 0.542 Fit side-chains REVERT: A 83 ASP cc_start: 0.7915 (t0) cc_final: 0.7687 (p0) REVERT: A 135 ASN cc_start: 0.8354 (t0) cc_final: 0.7809 (m110) REVERT: A 156 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.7925 (ttp-170) REVERT: A 230 GLU cc_start: 0.7663 (tm-30) cc_final: 0.7397 (tm-30) REVERT: A 234 ASP cc_start: 0.8394 (m-30) cc_final: 0.8049 (m-30) REVERT: A 263 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.6637 (tm-30) REVERT: A 276 MET cc_start: 0.7431 (mtp) cc_final: 0.5870 (mmt) REVERT: A 293 MET cc_start: 0.6476 (mtt) cc_final: 0.5916 (mtt) REVERT: A 306 ARG cc_start: 0.8084 (OUTLIER) cc_final: 0.7686 (ttt-90) REVERT: A 314 ARG cc_start: 0.6848 (mtt90) cc_final: 0.6387 (mtt-85) REVERT: A 337 ARG cc_start: 0.7626 (ttp80) cc_final: 0.7374 (tpp80) REVERT: A 354 GLU cc_start: 0.8517 (tm-30) cc_final: 0.7574 (mp0) REVERT: A 365 LYS cc_start: 0.8144 (ttpp) cc_final: 0.7358 (mttp) REVERT: A 399 ASP cc_start: 0.8559 (OUTLIER) cc_final: 0.8353 (t0) REVERT: A 449 LEU cc_start: 0.7544 (mp) cc_final: 0.6919 (tp) REVERT: A 494 ARG cc_start: 0.6534 (OUTLIER) cc_final: 0.5874 (mtm110) REVERT: A 502 LYS cc_start: 0.8058 (OUTLIER) cc_final: 0.7673 (mtpt) REVERT: B 88 ARG cc_start: 0.7751 (mtp180) cc_final: 0.7462 (mmm-85) REVERT: B 137 ASN cc_start: 0.8783 (p0) cc_final: 0.8363 (p0) REVERT: B 203 ASP cc_start: 0.6829 (t70) cc_final: 0.6602 (p0) REVERT: B 320 ARG cc_start: 0.6634 (mmm160) cc_final: 0.6301 (tpp-160) REVERT: B 338 GLU cc_start: 0.6170 (tp30) cc_final: 0.5964 (mp0) REVERT: B 398 LYS cc_start: 0.8678 (tptm) cc_final: 0.8472 (tmtm) REVERT: B 470 GLU cc_start: 0.8253 (tt0) cc_final: 0.7973 (tt0) REVERT: B 517 LYS cc_start: 0.7960 (mptt) cc_final: 0.7377 (mmmt) REVERT: C 135 ASN cc_start: 0.8411 (m110) cc_final: 0.8105 (t0) REVERT: C 156 ARG cc_start: 0.8284 (mtp85) cc_final: 0.8019 (mtm180) REVERT: C 231 THR cc_start: 0.9122 (m) cc_final: 0.8754 (m) REVERT: C 232 ASP cc_start: 0.8341 (t70) cc_final: 0.7664 (t70) REVERT: C 263 GLU cc_start: 0.7585 (tp30) cc_final: 0.7256 (tp30) REVERT: C 309 MET cc_start: 0.8592 (OUTLIER) cc_final: 0.8291 (tpp) REVERT: C 337 ARG cc_start: 0.7333 (mtp85) cc_final: 0.6853 (tpp80) REVERT: C 376 ARG cc_start: 0.8150 (ttp-110) cc_final: 0.7757 (ptp-110) REVERT: C 410 ASN cc_start: 0.8386 (p0) cc_final: 0.8140 (p0) REVERT: C 425 SER cc_start: 0.8747 (OUTLIER) cc_final: 0.8431 (t) REVERT: C 462 LYS cc_start: 0.8556 (mttm) cc_final: 0.8253 (mttp) REVERT: C 487 ASP cc_start: 0.7320 (m-30) cc_final: 0.6940 (t0) REVERT: C 491 GLU cc_start: 0.8428 (mp0) cc_final: 0.8086 (mm-30) REVERT: D 208 ASP cc_start: 0.7361 (OUTLIER) cc_final: 0.6693 (p0) REVERT: D 227 ASP cc_start: 0.8010 (m-30) cc_final: 0.7662 (t0) REVERT: D 320 ARG cc_start: 0.6155 (mmm160) cc_final: 0.5755 (mtt-85) REVERT: D 355 THR cc_start: 0.7982 (OUTLIER) cc_final: 0.7694 (p) REVERT: D 433 LYS cc_start: 0.8248 (tttt) cc_final: 0.7578 (tmtt) REVERT: D 467 LYS cc_start: 0.7924 (mttt) cc_final: 0.7429 (mtpm) outliers start: 43 outliers final: 14 residues processed: 216 average time/residue: 0.6363 time to fit residues: 149.4094 Evaluate side-chains 218 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 194 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ARG Chi-restraints excluded: chain A residue 263 GLU Chi-restraints excluded: chain A residue 306 ARG Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 488 ASN Chi-restraints excluded: chain A residue 494 ARG Chi-restraints excluded: chain A residue 502 LYS Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain C residue 242 MET Chi-restraints excluded: chain C residue 309 MET Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 425 SER Chi-restraints excluded: chain D residue 208 ASP Chi-restraints excluded: chain D residue 242 SER Chi-restraints excluded: chain D residue 280 MET Chi-restraints excluded: chain D residue 355 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 130 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 52 optimal weight: 0.7980 chunk 118 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 129 optimal weight: 4.9990 chunk 69 optimal weight: 0.0770 chunk 98 optimal weight: 0.8980 chunk 144 optimal weight: 4.9990 overall best weight: 0.8940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 GLN B 144 GLN D 347 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.165407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.118903 restraints weight = 14440.611| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.33 r_work: 0.3148 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13673 Z= 0.115 Angle : 0.509 12.101 18514 Z= 0.256 Chirality : 0.047 0.141 2080 Planarity : 0.003 0.030 2398 Dihedral : 3.989 25.490 1876 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.88 % Favored : 95.06 % Rotamer: Outliers : 2.35 % Allowed : 19.81 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.21), residues: 1700 helix: 0.07 (0.27), residues: 382 sheet: -0.91 (0.24), residues: 430 loop : -0.54 (0.22), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 318 TYR 0.011 0.001 TYR A 357 PHE 0.013 0.001 PHE B 308 TRP 0.004 0.001 TRP A 185 HIS 0.003 0.001 HIS B 232 Details of bonding type rmsd covalent geometry : bond 0.00278 (13672) covalent geometry : angle 0.50866 (18512) SS BOND : bond 0.00075 ( 1) SS BOND : angle 0.22580 ( 2) hydrogen bonds : bond 0.02913 ( 308) hydrogen bonds : angle 4.65195 ( 825) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 192 time to evaluate : 0.533 Fit side-chains REVERT: A 83 ASP cc_start: 0.7847 (t0) cc_final: 0.7563 (p0) REVERT: A 135 ASN cc_start: 0.8286 (t0) cc_final: 0.7625 (m110) REVERT: A 156 ARG cc_start: 0.7988 (OUTLIER) cc_final: 0.7649 (ttp-170) REVERT: A 230 GLU cc_start: 0.7487 (tm-30) cc_final: 0.7216 (tm-30) REVERT: A 234 ASP cc_start: 0.8309 (m-30) cc_final: 0.7836 (m-30) REVERT: A 263 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.6570 (tm-30) REVERT: A 276 MET cc_start: 0.7345 (mtp) cc_final: 0.5869 (mmt) REVERT: A 293 MET cc_start: 0.6153 (mtt) cc_final: 0.5684 (mtt) REVERT: A 306 ARG cc_start: 0.7982 (OUTLIER) cc_final: 0.7551 (ttt-90) REVERT: A 314 ARG cc_start: 0.6610 (mtt90) cc_final: 0.6134 (mtt-85) REVERT: A 337 ARG cc_start: 0.7421 (ttp80) cc_final: 0.7129 (tpp80) REVERT: A 354 GLU cc_start: 0.8391 (tm-30) cc_final: 0.7284 (mp0) REVERT: A 365 LYS cc_start: 0.7892 (ttpp) cc_final: 0.6987 (mttp) REVERT: A 399 ASP cc_start: 0.8523 (OUTLIER) cc_final: 0.8240 (t0) REVERT: A 494 ARG cc_start: 0.6501 (OUTLIER) cc_final: 0.5939 (mtm110) REVERT: A 502 LYS cc_start: 0.7901 (OUTLIER) cc_final: 0.7481 (mtpt) REVERT: B 88 ARG cc_start: 0.7723 (mtp180) cc_final: 0.7334 (mmm-85) REVERT: B 137 ASN cc_start: 0.8723 (p0) cc_final: 0.8310 (p0) REVERT: B 203 ASP cc_start: 0.6811 (t70) cc_final: 0.6547 (p0) REVERT: B 320 ARG cc_start: 0.6558 (mmm160) cc_final: 0.6157 (tpp-160) REVERT: B 338 GLU cc_start: 0.6074 (tp30) cc_final: 0.5866 (mp0) REVERT: B 398 LYS cc_start: 0.8545 (tptm) cc_final: 0.8265 (tmtm) REVERT: B 470 GLU cc_start: 0.8187 (tt0) cc_final: 0.7830 (tt0) REVERT: B 493 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7736 (mm-30) REVERT: B 517 LYS cc_start: 0.7810 (mptt) cc_final: 0.7124 (mmmt) REVERT: C 135 ASN cc_start: 0.8256 (m110) cc_final: 0.7883 (t0) REVERT: C 156 ARG cc_start: 0.8085 (mtp85) cc_final: 0.7719 (mtm180) REVERT: C 172 GLU cc_start: 0.8223 (mm-30) cc_final: 0.7790 (mt-10) REVERT: C 231 THR cc_start: 0.9086 (m) cc_final: 0.8748 (m) REVERT: C 232 ASP cc_start: 0.8267 (t70) cc_final: 0.7519 (t70) REVERT: C 257 GLU cc_start: 0.7361 (OUTLIER) cc_final: 0.7130 (pm20) REVERT: C 263 GLU cc_start: 0.7464 (tp30) cc_final: 0.7095 (tp30) REVERT: C 309 MET cc_start: 0.8434 (OUTLIER) cc_final: 0.8129 (tpp) REVERT: C 337 ARG cc_start: 0.7166 (mtp85) cc_final: 0.6577 (tpp80) REVERT: C 410 ASN cc_start: 0.8227 (p0) cc_final: 0.7972 (p0) REVERT: C 425 SER cc_start: 0.8675 (OUTLIER) cc_final: 0.8308 (t) REVERT: C 462 LYS cc_start: 0.8288 (mttm) cc_final: 0.7950 (mttp) REVERT: C 491 GLU cc_start: 0.8350 (mp0) cc_final: 0.8043 (mm-30) REVERT: D 208 ASP cc_start: 0.7328 (OUTLIER) cc_final: 0.6585 (p0) REVERT: D 227 ASP cc_start: 0.7838 (m-30) cc_final: 0.7474 (t0) REVERT: D 320 ARG cc_start: 0.5971 (mmm160) cc_final: 0.5488 (mtt-85) REVERT: D 355 THR cc_start: 0.7710 (OUTLIER) cc_final: 0.7356 (p) REVERT: D 433 LYS cc_start: 0.8011 (tttt) cc_final: 0.7222 (tmtt) REVERT: D 467 LYS cc_start: 0.7798 (mttt) cc_final: 0.7181 (mtpm) outliers start: 34 outliers final: 18 residues processed: 207 average time/residue: 0.6316 time to fit residues: 142.4348 Evaluate side-chains 218 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 188 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ARG Chi-restraints excluded: chain A residue 263 GLU Chi-restraints excluded: chain A residue 306 ARG Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 488 ASN Chi-restraints excluded: chain A residue 494 ARG Chi-restraints excluded: chain A residue 502 LYS Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 493 GLU Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 242 MET Chi-restraints excluded: chain C residue 257 GLU Chi-restraints excluded: chain C residue 309 MET Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 425 SER Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 208 ASP Chi-restraints excluded: chain D residue 242 SER Chi-restraints excluded: chain D residue 280 MET Chi-restraints excluded: chain D residue 355 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 3 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 136 optimal weight: 6.9990 chunk 9 optimal weight: 8.9990 chunk 88 optimal weight: 0.6980 chunk 44 optimal weight: 5.9990 chunk 60 optimal weight: 6.9990 chunk 33 optimal weight: 0.0670 overall best weight: 1.7524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 GLN B 144 GLN C 146 ASN D 347 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.163362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.117029 restraints weight = 14257.210| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.24 r_work: 0.3094 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13673 Z= 0.177 Angle : 0.565 12.608 18514 Z= 0.285 Chirality : 0.049 0.214 2080 Planarity : 0.003 0.031 2398 Dihedral : 4.310 26.916 1876 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.00 % Favored : 94.94 % Rotamer: Outliers : 2.49 % Allowed : 19.32 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.20), residues: 1700 helix: -0.16 (0.27), residues: 376 sheet: -1.00 (0.24), residues: 432 loop : -0.59 (0.22), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 318 TYR 0.013 0.001 TYR D 145 PHE 0.016 0.001 PHE B 308 TRP 0.004 0.001 TRP A 185 HIS 0.003 0.001 HIS D 232 Details of bonding type rmsd covalent geometry : bond 0.00438 (13672) covalent geometry : angle 0.56484 (18512) SS BOND : bond 0.00136 ( 1) SS BOND : angle 0.33461 ( 2) hydrogen bonds : bond 0.03312 ( 308) hydrogen bonds : angle 4.86654 ( 825) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 191 time to evaluate : 0.530 Fit side-chains revert: symmetry clash REVERT: A 135 ASN cc_start: 0.8250 (t0) cc_final: 0.7614 (m-40) REVERT: A 156 ARG cc_start: 0.8075 (OUTLIER) cc_final: 0.7773 (ttp-170) REVERT: A 223 LYS cc_start: 0.8158 (mttt) cc_final: 0.7829 (mtmm) REVERT: A 230 GLU cc_start: 0.7559 (tm-30) cc_final: 0.7345 (tm-30) REVERT: A 234 ASP cc_start: 0.8404 (m-30) cc_final: 0.7951 (m-30) REVERT: A 263 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.6594 (tm-30) REVERT: A 276 MET cc_start: 0.7497 (mtp) cc_final: 0.6008 (mmt) REVERT: A 293 MET cc_start: 0.6342 (mtt) cc_final: 0.5854 (mtt) REVERT: A 306 ARG cc_start: 0.8017 (OUTLIER) cc_final: 0.7550 (ttt-90) REVERT: A 314 ARG cc_start: 0.6709 (mtt90) cc_final: 0.6220 (mtt-85) REVERT: A 354 GLU cc_start: 0.8499 (tm-30) cc_final: 0.7413 (mp0) REVERT: A 399 ASP cc_start: 0.8704 (OUTLIER) cc_final: 0.8408 (t0) REVERT: A 431 GLU cc_start: 0.8430 (mt-10) cc_final: 0.8203 (mt-10) REVERT: A 494 ARG cc_start: 0.6634 (OUTLIER) cc_final: 0.6267 (mtm110) REVERT: A 502 LYS cc_start: 0.8038 (OUTLIER) cc_final: 0.7573 (mtpt) REVERT: B 88 ARG cc_start: 0.7749 (mtp180) cc_final: 0.7425 (mtm-85) REVERT: B 137 ASN cc_start: 0.8762 (p0) cc_final: 0.8352 (p0) REVERT: B 203 ASP cc_start: 0.6862 (t70) cc_final: 0.6460 (p0) REVERT: B 257 MET cc_start: 0.8525 (mtm) cc_final: 0.8274 (mtp) REVERT: B 280 MET cc_start: 0.7447 (tpp) cc_final: 0.7179 (tpp) REVERT: B 320 ARG cc_start: 0.6582 (mmm160) cc_final: 0.6206 (tpp-160) REVERT: B 398 LYS cc_start: 0.8630 (tptm) cc_final: 0.8273 (tptt) REVERT: B 433 LYS cc_start: 0.8407 (tttt) cc_final: 0.7758 (tptt) REVERT: B 493 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7797 (mm-30) REVERT: B 517 LYS cc_start: 0.8004 (mptt) cc_final: 0.7336 (mmmt) REVERT: C 135 ASN cc_start: 0.8321 (m110) cc_final: 0.7965 (t0) REVERT: C 156 ARG cc_start: 0.8154 (mtp85) cc_final: 0.7829 (mtm180) REVERT: C 231 THR cc_start: 0.9143 (m) cc_final: 0.8791 (m) REVERT: C 232 ASP cc_start: 0.8337 (t70) cc_final: 0.7622 (t0) REVERT: C 263 GLU cc_start: 0.7437 (tp30) cc_final: 0.7073 (tp30) REVERT: C 309 MET cc_start: 0.8558 (OUTLIER) cc_final: 0.8282 (tpp) REVERT: C 334 LEU cc_start: 0.7683 (OUTLIER) cc_final: 0.7437 (mp) REVERT: C 337 ARG cc_start: 0.7213 (mtp85) cc_final: 0.6637 (tpp80) REVERT: C 376 ARG cc_start: 0.8278 (ttp-110) cc_final: 0.7849 (ptp-110) REVERT: C 410 ASN cc_start: 0.8323 (p0) cc_final: 0.8030 (p0) REVERT: C 462 LYS cc_start: 0.8399 (mttm) cc_final: 0.8069 (mttp) REVERT: C 487 ASP cc_start: 0.7284 (m-30) cc_final: 0.6660 (t0) REVERT: D 208 ASP cc_start: 0.7385 (OUTLIER) cc_final: 0.6635 (p0) REVERT: D 227 ASP cc_start: 0.7955 (m-30) cc_final: 0.7571 (t0) REVERT: D 320 ARG cc_start: 0.6025 (mmm160) cc_final: 0.5503 (mtt90) REVERT: D 355 THR cc_start: 0.7823 (OUTLIER) cc_final: 0.7438 (p) REVERT: D 467 LYS cc_start: 0.7880 (mttt) cc_final: 0.7348 (mtpm) outliers start: 36 outliers final: 19 residues processed: 210 average time/residue: 0.6580 time to fit residues: 149.8795 Evaluate side-chains 218 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 188 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 156 ARG Chi-restraints excluded: chain A residue 263 GLU Chi-restraints excluded: chain A residue 306 ARG Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 488 ASN Chi-restraints excluded: chain A residue 494 ARG Chi-restraints excluded: chain A residue 502 LYS Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 493 GLU Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 242 MET Chi-restraints excluded: chain C residue 309 MET Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 208 ASP Chi-restraints excluded: chain D residue 242 SER Chi-restraints excluded: chain D residue 280 MET Chi-restraints excluded: chain D residue 355 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 132 optimal weight: 0.6980 chunk 160 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 125 optimal weight: 0.1980 chunk 56 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 161 optimal weight: 0.8980 chunk 131 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 81 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 146 ASN A 151 ASN B 144 GLN D 146 ASN D 177 GLN D 347 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.164863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.118856 restraints weight = 14402.131| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.27 r_work: 0.3157 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13673 Z= 0.107 Angle : 0.518 12.694 18514 Z= 0.260 Chirality : 0.047 0.144 2080 Planarity : 0.003 0.034 2398 Dihedral : 4.103 26.249 1876 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.35 % Favored : 95.59 % Rotamer: Outliers : 2.29 % Allowed : 19.74 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.21), residues: 1700 helix: -0.02 (0.27), residues: 382 sheet: -0.95 (0.24), residues: 432 loop : -0.53 (0.22), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 318 TYR 0.011 0.001 TYR C 357 PHE 0.013 0.001 PHE B 308 TRP 0.006 0.001 TRP A 185 HIS 0.003 0.001 HIS D 232 Details of bonding type rmsd covalent geometry : bond 0.00259 (13672) covalent geometry : angle 0.51753 (18512) SS BOND : bond 0.00056 ( 1) SS BOND : angle 0.22830 ( 2) hydrogen bonds : bond 0.02883 ( 308) hydrogen bonds : angle 4.70932 ( 825) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5152.43 seconds wall clock time: 88 minutes 28.74 seconds (5308.74 seconds total)