Starting phenix.real_space_refine on Sun May 3 14:14:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xuk_67269/05_2026/9xuk_67269.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xuk_67269/05_2026/9xuk_67269.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9xuk_67269/05_2026/9xuk_67269.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xuk_67269/05_2026/9xuk_67269.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9xuk_67269/05_2026/9xuk_67269.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xuk_67269/05_2026/9xuk_67269.map" } resolution = 2.95 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= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 50 5.16 5 C 8510 2.51 5 N 2288 2.21 5 O 2562 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 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: 13410 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3367 Classifications: {'peptide': 435} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 414} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 3347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3347 Classifications: {'peptide': 429} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 413} Chain breaks: 1 Chain: "D" Number of atoms: 3329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3329 Classifications: {'peptide': 427} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 411} Chain breaks: 1 Chain: "C" Number of atoms: 3367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3367 Classifications: {'peptide': 435} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 414} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 3.59, per 1000 atoms: 0.27 Number of scatterers: 13410 At special positions: 0 Unit cell: (108.112, 95.996, 107.18, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 50 16.00 O 2562 8.00 N 2288 7.00 C 8510 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: 1.02 Conformation dependent library (CDL) restraints added in 698.2 milliseconds 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 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: 56 helices and 24 sheets defined 26.8% alpha, 14.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 85 through 89 Processing helix chain 'A' and resid 103 through 107 Processing helix chain 'A' and resid 111 through 114 Processing helix chain 'A' and resid 124 through 134 Processing helix chain 'A' and resid 147 through 158 Processing helix chain 'A' and resid 188 through 196 removed outlier: 3.639A pdb=" N TYR A 196 " --> pdb=" O ALA A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 202 removed outlier: 3.621A pdb=" N GLU A 202 " --> pdb=" O TRP A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 231 removed outlier: 3.830A pdb=" N PHE A 224 " --> pdb=" O ASP A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 275 Processing helix chain 'A' and resid 286 through 293 removed outlier: 3.551A pdb=" N GLU A 292 " --> pdb=" O GLN A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 315 removed outlier: 3.829A pdb=" N LEU A 310 " --> pdb=" O ARG A 306 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ASP A 311 " --> pdb=" O ASP A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 333 removed outlier: 3.932A pdb=" N THR A 332 " --> pdb=" O ILE A 328 " (cutoff:3.500A) removed outlier: 4.046A 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 449 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 removed outlier: 3.510A pdb=" N ASN B 151 " --> pdb=" O SER B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 197 removed outlier: 3.719A pdb=" N PHE B 197 " --> pdb=" O ALA B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 236 removed outlier: 3.883A pdb=" N PHE B 228 " --> pdb=" O ASP B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 280 removed outlier: 3.905A pdb=" N MET B 280 " --> pdb=" O ASP B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 297 Processing helix chain 'B' and resid 311 through 318 Processing helix chain 'B' and resid 330 through 336 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 'B' and resid 503 through 507 Processing helix chain 'D' and resid 100 through 104 Processing helix chain 'D' and resid 111 through 114 Processing helix chain 'D' and resid 124 through 134 Processing helix chain 'D' and resid 148 through 158 Processing helix chain 'D' and resid 190 through 196 Processing helix chain 'D' and resid 224 through 233 removed outlier: 3.812A pdb=" N PHE D 228 " --> pdb=" O ASP D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 279 Processing helix chain 'D' and resid 291 through 297 Processing helix chain 'D' and resid 310 through 319 removed outlier: 3.547A pdb=" N LEU D 317 " --> pdb=" O LEU D 313 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG D 318 " --> pdb=" O LEU D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 338 Proline residue: D 333 - end of helix 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 456 Processing helix chain 'C' and resid 85 through 88 Processing helix chain 'C' and resid 104 through 108 removed outlier: 4.024A pdb=" N LYS C 108 " --> pdb=" O PRO C 105 " (cutoff:3.500A) 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 Processing helix chain 'C' and resid 188 through 196 removed outlier: 3.797A pdb=" N TYR C 196 " --> pdb=" O ALA C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 202 removed outlier: 3.981A pdb=" N GLU C 202 " --> pdb=" O TRP C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 231 removed outlier: 3.689A pdb=" N PHE C 224 " --> pdb=" O ASP C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 275 removed outlier: 3.978A pdb=" N LYS C 274 " --> pdb=" O GLY C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 293 Processing helix chain 'C' and resid 307 through 315 Processing helix chain 'C' and resid 322 through 333 removed outlier: 4.951A pdb=" N ILE C 328 " --> pdb=" O GLY C 324 " (cutoff:3.500A) Proline residue: C 329 - end of helix removed outlier: 3.631A pdb=" N SER C 333 " --> pdb=" O PRO C 329 " (cutoff:3.500A) 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 454 removed outlier: 3.613A pdb=" N LEU C 449 " --> pdb=" O THR C 445 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N SER C 451 " --> pdb=" O LYS C 447 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ALA C 452 " --> pdb=" O SER C 448 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 170 through 174 removed outlier: 4.695A pdb=" N LYS A 138 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA A 297 " --> pdb=" O LEU A 240 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N ALA A 238 " --> pdb=" O MET A 299 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ILE A 301 " --> pdb=" O THR A 236 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N THR A 236 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ILE A 235 " --> pdb=" O GLN A 339 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N TYR A 341 " --> pdb=" O ILE A 235 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N VAL A 237 " --> pdb=" O TYR A 341 " (cutoff:3.500A) 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 253 through 255 removed outlier: 7.080A pdb=" N LYS A 254 " --> pdb=" O ILE A 262 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 390 through 395 removed outlier: 6.013A pdb=" N LYS A 391 " --> pdb=" O ILE A 408 " (cutoff:3.500A) removed outlier: 6.678A 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: 9.085A pdb=" N VAL B 430 " --> pdb=" O LYS B 467 " (cutoff:3.500A) removed outlier: 9.930A pdb=" N GLN B 469 " --> pdb=" O VAL B 430 " (cutoff:3.500A) removed outlier: 9.050A pdb=" N LEU B 432 " --> pdb=" O GLN B 469 " (cutoff:3.500A) removed outlier: 9.201A pdb=" N CYS B 471 " --> pdb=" O LEU B 432 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ASP B 434 " --> pdb=" O CYS B 471 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N ILE B 473 " --> pdb=" O ASP B 434 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N VAL B 436 " --> pdb=" O ILE B 473 " (cutoff:3.500A) removed outlier: 6.414A 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=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 434 through 435 removed outlier: 5.919A pdb=" N VAL A 417 " --> pdb=" O LEU A 435 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N VAL A 401 " --> pdb=" O VAL A 418 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 412 through 414 removed outlier: 6.187A pdb=" N LYS A 412 " --> pdb=" O ILE A 430 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ILE A 429 " --> pdb=" O ILE A 466 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 476 through 477 removed outlier: 6.217A pdb=" N ARG A 476 " --> pdb=" O ILE A 514 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 92 through 95 removed outlier: 6.173A pdb=" N ILE B 93 " --> pdb=" O LEU B 215 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SER B 216 " --> pdb=" O GLY B 304 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N GLY B 304 " --> pdb=" O SER B 216 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR B 299 " --> pdb=" O ILE B 246 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N SER B 242 " --> pdb=" O MET B 303 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N VAL B 305 " --> pdb=" O SER B 240 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N SER B 240 " --> pdb=" O VAL B 305 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N TYR B 344 " --> pdb=" O ILE B 239 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ILE B 241 " --> pdb=" O TYR B 344 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 116 through 117 Processing sheet with id=AB2, first strand: chain 'B' and resid 219 through 221 Processing sheet with id=AB3, first strand: chain 'B' and resid 256 through 259 removed outlier: 6.734A pdb=" N LEU B 256 " --> pdb=" O PHE B 268 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N PHE B 268 " --> pdb=" O LEU B 256 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N LYS B 258 " --> pdb=" O ILE B 266 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 461 through 462 removed outlier: 5.694A pdb=" N GLY B 461 " --> pdb=" O VAL B 479 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ARG B 478 " --> pdb=" O ILE B 516 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'D' and resid 171 through 172 removed outlier: 6.382A pdb=" N VAL D 139 " --> pdb=" O GLU D 171 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N SER D 216 " --> pdb=" O GLY D 304 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N GLY D 304 " --> pdb=" O SER D 216 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N MET D 303 " --> pdb=" O ILE D 244 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N ILE D 244 " --> pdb=" O MET D 303 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N VAL D 305 " --> pdb=" O SER D 242 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR D 344 " --> pdb=" O ILE D 241 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 116 through 117 Processing sheet with id=AB7, first strand: chain 'D' and resid 219 through 220 Processing sheet with id=AB8, first strand: chain 'D' and resid 425 through 426 removed outlier: 6.474A pdb=" N PHE D 409 " --> pdb=" O VAL D 426 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N LYS D 393 " --> pdb=" O LEU D 410 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL C 401 " --> pdb=" O VAL C 418 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N VAL C 417 " --> pdb=" O LEU C 435 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LEU C 434 " --> pdb=" O ILE C 471 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 398 through 404 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 414 through 416 current: chain 'D' and resid 431 through 437 removed outlier: 9.121A pdb=" N LEU D 432 " --> pdb=" O GLN D 469 " (cutoff:3.500A) removed outlier: 9.252A pdb=" N CYS D 471 " --> pdb=" O LEU D 432 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ASP D 434 " --> pdb=" O CYS D 471 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N ILE D 473 " --> pdb=" O ASP D 434 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N VAL D 436 " --> pdb=" O ILE D 473 " (cutoff:3.500A) removed outlier: 6.649A 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 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 508 through 510 current: chain 'C' and resid 407 through 408 removed outlier: 6.422A pdb=" N VAL C 407 " --> pdb=" O ILE C 424 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 461 through 462 removed outlier: 5.619A pdb=" N GLY D 461 " --> pdb=" O VAL D 479 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ARG D 478 " --> pdb=" O ILE D 516 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'C' and resid 90 through 96 removed outlier: 7.142A pdb=" N VAL C 90 " --> pdb=" O LYS C 138 " (cutoff:3.500A) removed outlier: 8.504A pdb=" N TYR C 140 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N GLY C 92 " --> pdb=" O TYR C 140 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N LEU C 142 " --> pdb=" O GLY C 92 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ILE C 94 " --> pdb=" O LEU C 142 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ILE C 139 " --> pdb=" O GLU C 172 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N LEU C 174 " --> pdb=" O ILE C 139 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N VAL C 141 " --> pdb=" O LEU C 174 " (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 No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'C' and resid 116 through 117 Processing sheet with id=AC4, first strand: chain 'C' and resid 215 through 217 Processing sheet with id=AC5, first strand: chain 'C' and resid 412 through 414 removed outlier: 6.442A pdb=" N ILE C 429 " --> pdb=" O ILE C 466 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N HIS C 465 " --> pdb=" O ILE C 483 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 476 through 477 removed outlier: 6.784A pdb=" N ARG C 476 " --> pdb=" O ILE C 514 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 303 hydrogen bonds defined for protein. 837 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: 2.02 Time building geometry restraints manager: 1.43 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: 4437 1.34 - 1.46: 2004 1.46 - 1.57: 7141 1.57 - 1.69: 0 1.69 - 1.81: 82 Bond restraints: 13664 Sorted by residual: bond pdb=" CA THR A 80 " pdb=" C THR A 80 " ideal model delta sigma weight residual 1.520 1.497 0.023 1.20e-02 6.94e+03 3.64e+00 bond pdb=" CG1 ILE D 132 " pdb=" CD1 ILE D 132 " ideal model delta sigma weight residual 1.513 1.443 0.070 3.90e-02 6.57e+02 3.24e+00 bond pdb=" C THR C 80 " pdb=" N CYS C 81 " ideal model delta sigma weight residual 1.331 1.309 0.022 1.43e-02 4.89e+03 2.40e+00 bond pdb=" C LYS A 112 " pdb=" N PRO A 113 " ideal model delta sigma weight residual 1.334 1.369 -0.035 2.34e-02 1.83e+03 2.27e+00 bond pdb=" CB GLU C 495 " pdb=" CG GLU C 495 " ideal model delta sigma weight residual 1.520 1.561 -0.041 3.00e-02 1.11e+03 1.90e+00 ... (remaining 13659 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.44: 18414 3.44 - 6.88: 71 6.88 - 10.32: 7 10.32 - 13.76: 2 13.76 - 17.20: 2 Bond angle restraints: 18496 Sorted by residual: angle pdb=" N ASP D 231 " pdb=" CA ASP D 231 " pdb=" C ASP D 231 " ideal model delta sigma weight residual 114.75 106.53 8.22 1.26e+00 6.30e-01 4.25e+01 angle pdb=" C LYS B 310 " pdb=" N GLU B 311 " pdb=" CA GLU B 311 " ideal model delta sigma weight residual 121.54 132.39 -10.85 1.91e+00 2.74e-01 3.22e+01 angle pdb=" CA GLU B 311 " pdb=" CB GLU B 311 " pdb=" CG GLU B 311 " ideal model delta sigma weight residual 114.10 124.55 -10.45 2.00e+00 2.50e-01 2.73e+01 angle pdb=" CA LEU A 449 " pdb=" CB LEU A 449 " pdb=" CG LEU A 449 " ideal model delta sigma weight residual 116.30 133.50 -17.20 3.50e+00 8.16e-02 2.42e+01 angle pdb=" CA LEU A 312 " pdb=" CB LEU A 312 " pdb=" CG LEU A 312 " ideal model delta sigma weight residual 116.30 131.18 -14.88 3.50e+00 8.16e-02 1.81e+01 ... (remaining 18491 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 6924 17.90 - 35.81: 945 35.81 - 53.71: 297 53.71 - 71.61: 63 71.61 - 89.51: 16 Dihedral angle restraints: 8245 sinusoidal: 3271 harmonic: 4974 Sorted by residual: dihedral pdb=" CB CYS A 81 " pdb=" SG CYS A 81 " pdb=" SG CYS C 81 " pdb=" CB CYS C 81 " ideal model delta sinusoidal sigma weight residual -86.00 -157.35 71.35 1 1.00e+01 1.00e-02 6.53e+01 dihedral pdb=" CA ASP A 472 " pdb=" C ASP A 472 " pdb=" N LYS A 473 " pdb=" CA LYS A 473 " ideal model delta harmonic sigma weight residual 180.00 151.01 28.99 0 5.00e+00 4.00e-02 3.36e+01 dihedral pdb=" CA GLN D 230 " pdb=" C GLN D 230 " pdb=" N ASP D 231 " pdb=" CA ASP D 231 " ideal model delta harmonic sigma weight residual 180.00 156.63 23.37 0 5.00e+00 4.00e-02 2.18e+01 ... (remaining 8242 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1576 0.049 - 0.098: 339 0.098 - 0.148: 159 0.148 - 0.197: 5 0.197 - 0.246: 1 Chirality restraints: 2080 Sorted by residual: chirality pdb=" CB ILE A 94 " pdb=" CA ILE A 94 " pdb=" CG1 ILE A 94 " pdb=" CG2 ILE A 94 " both_signs ideal model delta sigma weight residual False 2.64 2.89 -0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CB ILE B 209 " pdb=" CA ILE B 209 " pdb=" CG1 ILE B 209 " pdb=" CG2 ILE B 209 " both_signs ideal model delta sigma weight residual False 2.64 2.80 -0.16 2.00e-01 2.50e+01 6.36e-01 chirality pdb=" CA PHE D 197 " pdb=" N PHE D 197 " pdb=" C PHE D 197 " pdb=" CB PHE D 197 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.35e-01 ... (remaining 2077 not shown) Planarity restraints: 2402 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 386 " 0.124 9.50e-02 1.11e+02 5.62e-02 2.81e+00 pdb=" NE ARG B 386 " -0.013 2.00e-02 2.50e+03 pdb=" CZ ARG B 386 " 0.015 2.00e-02 2.50e+03 pdb=" NH1 ARG B 386 " -0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG B 386 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 284 " -0.008 2.00e-02 2.50e+03 1.67e-02 2.78e+00 pdb=" C THR B 284 " 0.029 2.00e-02 2.50e+03 pdb=" O THR B 284 " -0.011 2.00e-02 2.50e+03 pdb=" N THR B 285 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 115 " -0.026 5.00e-02 4.00e+02 3.89e-02 2.43e+00 pdb=" N PRO A 116 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 116 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 116 " -0.022 5.00e-02 4.00e+02 ... (remaining 2399 not shown) Histogram of nonbonded interaction distances: 2.48 - 2.96: 6412 2.96 - 3.45: 13230 3.45 - 3.93: 21894 3.93 - 4.42: 25492 4.42 - 4.90: 42697 Nonbonded interactions: 109725 Sorted by model distance: nonbonded pdb=" O THR D 107 " pdb=" OG1 THR D 107 " model vdw 2.478 3.040 nonbonded pdb=" O THR B 107 " pdb=" OG1 THR B 107 " model vdw 2.490 3.040 nonbonded pdb=" N GLU A 258 " pdb=" OE1 GLU A 258 " model vdw 2.538 3.120 nonbonded pdb=" N ASP C 83 " pdb=" OD1 ASP C 83 " model vdw 2.541 3.120 nonbonded pdb=" O LYS B 310 " pdb=" OE2 GLU B 311 " model vdw 2.545 3.040 ... (remaining 109720 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = (chain 'B' and (resid 84 through 176 or resid 189 through 522)) 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: 1.360 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: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.820 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 13665 Z= 0.121 Angle : 0.620 17.200 18498 Z= 0.314 Chirality : 0.048 0.246 2080 Planarity : 0.003 0.056 2402 Dihedral : 18.352 89.515 5058 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.91 % Favored : 94.04 % Rotamer: Outliers : 4.23 % Allowed : 35.78 % Favored : 59.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.20), residues: 1710 helix: -0.13 (0.27), residues: 377 sheet: -0.78 (0.26), residues: 394 loop : -1.16 (0.21), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B 386 TYR 0.011 0.001 TYR B 158 PHE 0.019 0.001 PHE C 317 TRP 0.007 0.001 TRP C 198 HIS 0.004 0.001 HIS B 369 Details of bonding type rmsd covalent geometry : bond 0.00272 (13664) covalent geometry : angle 0.61979 (18496) SS BOND : bond 0.00090 ( 1) SS BOND : angle 0.94592 ( 2) hydrogen bonds : bond 0.19702 ( 303) hydrogen bonds : angle 8.36933 ( 837) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 255 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 ASP cc_start: 0.8041 (p0) cc_final: 0.7837 (p0) REVERT: A 144 GLN cc_start: 0.8424 (tt0) cc_final: 0.8157 (tt0) REVERT: A 191 ASP cc_start: 0.7831 (t70) cc_final: 0.7370 (t0) REVERT: A 206 LEU cc_start: 0.7962 (mm) cc_final: 0.7720 (mt) REVERT: A 214 ASP cc_start: 0.7704 (p0) cc_final: 0.7206 (p0) REVERT: A 232 ASP cc_start: 0.7412 (t0) cc_final: 0.7172 (m-30) REVERT: A 311 ASP cc_start: 0.7286 (m-30) cc_final: 0.6956 (t0) REVERT: A 322 ASP cc_start: 0.7134 (t70) cc_final: 0.6398 (t70) REVERT: A 325 SER cc_start: 0.8581 (m) cc_final: 0.8192 (p) REVERT: A 337 ARG cc_start: 0.7876 (ttt90) cc_final: 0.7040 (ttm-80) REVERT: A 396 ASP cc_start: 0.8681 (OUTLIER) cc_final: 0.8250 (m-30) REVERT: A 443 THR cc_start: 0.8278 (m) cc_final: 0.7645 (p) REVERT: A 446 GLU cc_start: 0.6912 (mt-10) cc_final: 0.6372 (mp0) REVERT: A 484 ILE cc_start: 0.8046 (tt) cc_final: 0.7749 (pt) REVERT: B 88 ARG cc_start: 0.7772 (ttm-80) cc_final: 0.7249 (ttp-110) REVERT: B 95 LEU cc_start: 0.8679 (tt) cc_final: 0.7878 (mt) REVERT: B 109 ARG cc_start: 0.7631 (OUTLIER) cc_final: 0.7247 (pmt170) REVERT: B 137 ASN cc_start: 0.8362 (p0) cc_final: 0.7944 (p0) REVERT: B 156 ARG cc_start: 0.8053 (ttp-170) cc_final: 0.7718 (ttt180) REVERT: B 171 GLU cc_start: 0.7236 (mm-30) cc_final: 0.6761 (mm-30) REVERT: B 231 ASP cc_start: 0.7619 (OUTLIER) cc_final: 0.6945 (t70) REVERT: B 256 LEU cc_start: 0.6941 (OUTLIER) cc_final: 0.6115 (mt) REVERT: B 257 MET cc_start: 0.6582 (mtm) cc_final: 0.5777 (mtp) REVERT: B 258 LYS cc_start: 0.6638 (ttmt) cc_final: 0.6105 (tmtt) REVERT: B 264 ARG cc_start: 0.6859 (ttp80) cc_final: 0.6355 (ttm-80) REVERT: B 280 MET cc_start: 0.6327 (mmm) cc_final: 0.6046 (mmm) REVERT: B 296 LYS cc_start: 0.7902 (tppp) cc_final: 0.7646 (ttpt) REVERT: B 358 SER cc_start: 0.8746 (OUTLIER) cc_final: 0.8515 (t) REVERT: B 393 LYS cc_start: 0.8750 (ttmt) cc_final: 0.8195 (tttp) REVERT: B 409 PHE cc_start: 0.8789 (m-80) cc_final: 0.8441 (m-10) REVERT: B 428 SER cc_start: 0.8342 (m) cc_final: 0.7717 (t) REVERT: B 452 LEU cc_start: 0.7022 (mt) cc_final: 0.6765 (mp) REVERT: B 467 LYS cc_start: 0.7294 (mtmt) cc_final: 0.6905 (mttp) REVERT: B 484 ILE cc_start: 0.7983 (mt) cc_final: 0.7581 (mm) REVERT: D 102 ARG cc_start: 0.8281 (mtm180) cc_final: 0.7977 (mtm180) REVERT: D 152 ARG cc_start: 0.8097 (tpp80) cc_final: 0.7876 (ttm110) REVERT: D 156 ARG cc_start: 0.7892 (ttp80) cc_final: 0.7494 (tpp-160) REVERT: D 163 LEU cc_start: 0.6475 (OUTLIER) cc_final: 0.5935 (mp) REVERT: D 171 GLU cc_start: 0.7429 (tt0) cc_final: 0.7002 (mt-10) REVERT: D 173 LEU cc_start: 0.8378 (pt) cc_final: 0.8103 (pp) REVERT: D 195 ARG cc_start: 0.5220 (OUTLIER) cc_final: 0.4555 (ptm160) REVERT: D 230 GLN cc_start: 0.7236 (tm-30) cc_final: 0.6914 (tm-30) REVERT: D 231 ASP cc_start: 0.7176 (t70) cc_final: 0.6743 (t0) REVERT: D 258 LYS cc_start: 0.7371 (OUTLIER) cc_final: 0.7150 (mmmm) REVERT: D 348 ASP cc_start: 0.7608 (t70) cc_final: 0.6926 (m-30) REVERT: D 351 GLU cc_start: 0.7304 (tp30) cc_final: 0.7000 (tp30) REVERT: D 368 GLU cc_start: 0.8317 (mt-10) cc_final: 0.7854 (mm-30) REVERT: D 393 LYS cc_start: 0.8417 (ttmt) cc_final: 0.7983 (tttt) REVERT: D 412 ASN cc_start: 0.8134 (t0) cc_final: 0.7532 (m110) REVERT: D 429 ASN cc_start: 0.8144 (t0) cc_final: 0.7898 (m110) REVERT: D 433 LYS cc_start: 0.7661 (ttmm) cc_final: 0.7297 (tttm) REVERT: D 452 LEU cc_start: 0.7596 (mt) cc_final: 0.7348 (mp) REVERT: C 102 ARG cc_start: 0.7023 (mtp180) cc_final: 0.6481 (mtm180) REVERT: C 144 GLN cc_start: 0.8202 (tt0) cc_final: 0.7455 (mm-40) REVERT: C 147 SER cc_start: 0.8578 (t) cc_final: 0.8316 (p) REVERT: C 151 ASN cc_start: 0.8184 (m-40) cc_final: 0.7953 (m110) REVERT: C 168 GLU cc_start: 0.6293 (OUTLIER) cc_final: 0.5989 (pm20) REVERT: C 174 LEU cc_start: 0.7583 (OUTLIER) cc_final: 0.6649 (pp) REVERT: C 201 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7373 (mt-10) REVERT: C 206 LEU cc_start: 0.7936 (mt) cc_final: 0.7669 (mp) REVERT: C 293 MET cc_start: 0.7078 (mtt) cc_final: 0.6675 (ptp) REVERT: C 295 PHE cc_start: 0.6524 (m-80) cc_final: 0.6108 (m-80) REVERT: C 306 ARG cc_start: 0.7799 (ptm-80) cc_final: 0.7174 (ptm-80) REVERT: C 325 SER cc_start: 0.8503 (OUTLIER) cc_final: 0.8169 (p) REVERT: C 348 GLU cc_start: 0.7911 (tp30) cc_final: 0.7149 (tt0) REVERT: C 365 LYS cc_start: 0.8133 (ttmm) cc_final: 0.7525 (mtpt) REVERT: C 487 ASP cc_start: 0.7388 (m-30) cc_final: 0.7157 (t0) REVERT: C 488 ASN cc_start: 0.7742 (t0) cc_final: 0.7515 (t0) outliers start: 61 outliers final: 30 residues processed: 301 average time/residue: 0.5544 time to fit residues: 183.0986 Evaluate side-chains 271 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 229 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 109 ARG Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 231 ASP Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 306 TYR Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 406 HIS Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 195 ARG Chi-restraints excluded: chain D residue 258 LYS Chi-restraints excluded: chain D residue 266 ILE Chi-restraints excluded: chain D residue 411 THR Chi-restraints excluded: chain D residue 419 ILE Chi-restraints excluded: chain D residue 428 SER Chi-restraints excluded: chain C residue 156 ARG Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 315 ASN Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 519 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 9.9990 chunk 149 optimal weight: 8.9990 overall best weight: 2.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 219 HIS ** D 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 79 GLN C 146 ASN C 226 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.169071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.114331 restraints weight = 14339.422| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 2.56 r_work: 0.3007 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 13665 Z= 0.242 Angle : 0.660 12.746 18498 Z= 0.334 Chirality : 0.051 0.174 2080 Planarity : 0.004 0.054 2402 Dihedral : 7.283 74.282 1957 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.37 % Favored : 92.57 % Rotamer: Outliers : 9.22 % Allowed : 28.57 % Favored : 62.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.50 (0.20), residues: 1710 helix: -0.24 (0.26), residues: 399 sheet: -0.86 (0.26), residues: 382 loop : -1.38 (0.21), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 386 TYR 0.017 0.002 TYR B 349 PHE 0.020 0.002 PHE D 197 TRP 0.013 0.001 TRP D 199 HIS 0.007 0.002 HIS B 369 Details of bonding type rmsd covalent geometry : bond 0.00601 (13664) covalent geometry : angle 0.65990 (18496) SS BOND : bond 0.00273 ( 1) SS BOND : angle 0.74857 ( 2) hydrogen bonds : bond 0.04259 ( 303) hydrogen bonds : angle 6.16675 ( 837) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 235 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 ASP cc_start: 0.8117 (p0) cc_final: 0.7790 (p0) REVERT: A 174 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8126 (pp) REVERT: A 191 ASP cc_start: 0.8232 (t70) cc_final: 0.7820 (t0) REVERT: A 232 ASP cc_start: 0.7525 (t0) cc_final: 0.7187 (m-30) REVERT: A 311 ASP cc_start: 0.7311 (m-30) cc_final: 0.6903 (t0) REVERT: A 316 GLN cc_start: 0.7994 (mp10) cc_final: 0.7447 (mp10) REVERT: A 322 ASP cc_start: 0.7367 (t70) cc_final: 0.6795 (t70) REVERT: A 337 ARG cc_start: 0.7923 (ttt90) cc_final: 0.7254 (mtp85) REVERT: A 350 ILE cc_start: 0.7668 (mm) cc_final: 0.7431 (mt) REVERT: A 446 GLU cc_start: 0.7419 (mt-10) cc_final: 0.7087 (mp0) REVERT: A 500 PHE cc_start: 0.7990 (t80) cc_final: 0.7762 (t80) REVERT: B 88 ARG cc_start: 0.7845 (ttm-80) cc_final: 0.7302 (ttp-110) REVERT: B 95 LEU cc_start: 0.8819 (tt) cc_final: 0.8067 (mt) REVERT: B 137 ASN cc_start: 0.8430 (p0) cc_final: 0.7907 (p0) REVERT: B 170 VAL cc_start: 0.8256 (m) cc_final: 0.7872 (t) REVERT: B 171 GLU cc_start: 0.7532 (mm-30) cc_final: 0.6970 (mm-30) REVERT: B 257 MET cc_start: 0.7266 (mtm) cc_final: 0.6655 (mtp) REVERT: B 258 LYS cc_start: 0.6939 (ttmt) cc_final: 0.6293 (tmtm) REVERT: B 264 ARG cc_start: 0.7099 (ttp80) cc_final: 0.6830 (ttm-80) REVERT: B 269 SER cc_start: 0.6468 (OUTLIER) cc_final: 0.6115 (p) REVERT: B 280 MET cc_start: 0.6590 (mmm) cc_final: 0.6349 (mmm) REVERT: B 296 LYS cc_start: 0.7939 (tppp) cc_final: 0.7717 (ttpt) REVERT: B 326 ASP cc_start: 0.7028 (t70) cc_final: 0.6715 (t70) REVERT: B 327 PHE cc_start: 0.6842 (OUTLIER) cc_final: 0.6641 (t80) REVERT: B 338 GLU cc_start: 0.6799 (OUTLIER) cc_final: 0.6555 (pm20) REVERT: B 357 ARG cc_start: 0.8481 (OUTLIER) cc_final: 0.7007 (tpp-160) REVERT: B 393 LYS cc_start: 0.8870 (ttmt) cc_final: 0.8344 (tttm) REVERT: B 399 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8540 (mp) REVERT: B 428 SER cc_start: 0.8451 (OUTLIER) cc_final: 0.7860 (t) REVERT: B 467 LYS cc_start: 0.7579 (mtmt) cc_final: 0.7105 (mtpp) REVERT: D 103 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7875 (mt) REVERT: D 156 ARG cc_start: 0.8048 (ttp80) cc_final: 0.7559 (tpp-160) REVERT: D 170 VAL cc_start: 0.7294 (OUTLIER) cc_final: 0.6950 (p) REVERT: D 171 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7130 (mt-10) REVERT: D 173 LEU cc_start: 0.8642 (pt) cc_final: 0.8337 (pp) REVERT: D 195 ARG cc_start: 0.5590 (OUTLIER) cc_final: 0.4813 (ptm160) REVERT: D 230 GLN cc_start: 0.7386 (tm-30) cc_final: 0.7080 (tm-30) REVERT: D 231 ASP cc_start: 0.7588 (t70) cc_final: 0.7046 (t0) REVERT: D 258 LYS cc_start: 0.7458 (mptm) cc_final: 0.7042 (mmmm) REVERT: D 348 ASP cc_start: 0.7851 (t70) cc_final: 0.7354 (m-30) REVERT: D 351 GLU cc_start: 0.7625 (tp30) cc_final: 0.7284 (tp30) REVERT: D 393 LYS cc_start: 0.8690 (ttmt) cc_final: 0.8205 (tttt) REVERT: D 412 ASN cc_start: 0.8335 (t0) cc_final: 0.7671 (m110) REVERT: D 429 ASN cc_start: 0.8418 (t0) cc_final: 0.8146 (m110) REVERT: D 431 GLN cc_start: 0.8426 (mt0) cc_final: 0.7866 (mt0) REVERT: D 433 LYS cc_start: 0.7844 (ttmm) cc_final: 0.7412 (tttp) REVERT: C 108 LYS cc_start: 0.8705 (tttp) cc_final: 0.8387 (ttmt) REVERT: C 144 GLN cc_start: 0.8240 (tt0) cc_final: 0.7477 (tp-100) REVERT: C 152 ARG cc_start: 0.8383 (tmm160) cc_final: 0.7762 (tmt-80) REVERT: C 172 GLU cc_start: 0.7590 (mm-30) cc_final: 0.7390 (tp30) REVERT: C 177 GLN cc_start: 0.7310 (tp40) cc_final: 0.6616 (mt0) REVERT: C 201 GLU cc_start: 0.7853 (mm-30) cc_final: 0.7425 (mt-10) REVERT: C 206 LEU cc_start: 0.7876 (mt) cc_final: 0.7574 (mp) REVERT: C 242 MET cc_start: 0.6416 (OUTLIER) cc_final: 0.6127 (ttm) REVERT: C 293 MET cc_start: 0.6881 (mtt) cc_final: 0.6570 (ptp) REVERT: C 306 ARG cc_start: 0.7904 (ptm-80) cc_final: 0.7569 (ptm-80) REVERT: C 316 GLN cc_start: 0.7857 (OUTLIER) cc_final: 0.7427 (mt0) REVERT: C 348 GLU cc_start: 0.8151 (tp30) cc_final: 0.7384 (tt0) REVERT: C 365 LYS cc_start: 0.8190 (ttmm) cc_final: 0.7541 (mtpt) REVERT: C 402 ILE cc_start: 0.8949 (OUTLIER) cc_final: 0.8715 (mm) REVERT: C 412 LYS cc_start: 0.8593 (OUTLIER) cc_final: 0.8227 (tptt) REVERT: C 425 SER cc_start: 0.8737 (OUTLIER) cc_final: 0.8293 (t) REVERT: C 487 ASP cc_start: 0.7482 (m-30) cc_final: 0.7255 (t0) outliers start: 133 outliers final: 55 residues processed: 329 average time/residue: 0.4904 time to fit residues: 179.0074 Evaluate side-chains 290 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 219 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 416 SER Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 246 ILE Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 306 TYR Chi-restraints excluded: chain B residue 327 PHE Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 406 HIS Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 441 ASP Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 195 ARG Chi-restraints excluded: chain D residue 201 PHE Chi-restraints excluded: chain D residue 240 SER Chi-restraints excluded: chain D residue 254 PHE Chi-restraints excluded: chain D residue 266 ILE Chi-restraints excluded: chain D residue 303 MET Chi-restraints excluded: chain D residue 411 THR Chi-restraints excluded: chain D residue 507 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 156 ARG Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 242 MET Chi-restraints excluded: chain C residue 316 GLN Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 390 SER Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 412 LYS Chi-restraints excluded: chain C residue 416 SER Chi-restraints excluded: chain C residue 425 SER Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 496 THR Chi-restraints excluded: chain C residue 519 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 88 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 134 optimal weight: 3.9990 chunk 146 optimal weight: 2.9990 chunk 115 optimal weight: 4.9990 chunk 152 optimal weight: 4.9990 chunk 18 optimal weight: 10.0000 chunk 133 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 81 optimal weight: 0.9980 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 GLN A 410 ASN B 219 HIS C 178 GLN C 465 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.168728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.114332 restraints weight = 14452.097| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.56 r_work: 0.3168 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 13665 Z= 0.196 Angle : 0.601 13.347 18498 Z= 0.306 Chirality : 0.050 0.184 2080 Planarity : 0.004 0.046 2402 Dihedral : 6.191 58.504 1923 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.19 % Favored : 92.75 % Rotamer: Outliers : 8.32 % Allowed : 28.92 % Favored : 62.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.20), residues: 1710 helix: -0.20 (0.26), residues: 401 sheet: -0.99 (0.25), residues: 392 loop : -1.44 (0.21), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 386 TYR 0.013 0.001 TYR B 158 PHE 0.016 0.002 PHE B 360 TRP 0.006 0.001 TRP D 199 HIS 0.006 0.001 HIS B 369 Details of bonding type rmsd covalent geometry : bond 0.00486 (13664) covalent geometry : angle 0.60133 (18496) SS BOND : bond 0.00254 ( 1) SS BOND : angle 0.64195 ( 2) hydrogen bonds : bond 0.03909 ( 303) hydrogen bonds : angle 5.80117 ( 837) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 210 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8210 (pp) REVERT: A 191 ASP cc_start: 0.8338 (t70) cc_final: 0.7938 (t0) REVERT: A 232 ASP cc_start: 0.7676 (t0) cc_final: 0.7347 (m-30) REVERT: A 311 ASP cc_start: 0.7542 (m-30) cc_final: 0.7131 (t0) REVERT: A 316 GLN cc_start: 0.8091 (mp10) cc_final: 0.7581 (mp10) REVERT: A 322 ASP cc_start: 0.7405 (OUTLIER) cc_final: 0.6887 (t70) REVERT: A 350 ILE cc_start: 0.7775 (OUTLIER) cc_final: 0.7571 (mt) REVERT: A 446 GLU cc_start: 0.7480 (mt-10) cc_final: 0.7199 (mp0) REVERT: A 500 PHE cc_start: 0.8029 (t80) cc_final: 0.7771 (t80) REVERT: B 88 ARG cc_start: 0.7813 (ttm-80) cc_final: 0.7341 (ttp-110) REVERT: B 95 LEU cc_start: 0.8885 (tt) cc_final: 0.8213 (mt) REVERT: B 137 ASN cc_start: 0.8560 (p0) cc_final: 0.8190 (p0) REVERT: B 170 VAL cc_start: 0.8297 (m) cc_final: 0.7979 (t) REVERT: B 171 GLU cc_start: 0.7446 (mm-30) cc_final: 0.7091 (mm-30) REVERT: B 233 ARG cc_start: 0.7197 (OUTLIER) cc_final: 0.6768 (mpt-90) REVERT: B 257 MET cc_start: 0.7344 (mtm) cc_final: 0.6890 (mtp) REVERT: B 258 LYS cc_start: 0.7182 (ttmt) cc_final: 0.6436 (tmtm) REVERT: B 264 ARG cc_start: 0.7380 (ttp80) cc_final: 0.7157 (ttm-80) REVERT: B 269 SER cc_start: 0.6598 (OUTLIER) cc_final: 0.6240 (p) REVERT: B 280 MET cc_start: 0.6691 (mmm) cc_final: 0.6455 (mmm) REVERT: B 326 ASP cc_start: 0.7182 (t70) cc_final: 0.6821 (t70) REVERT: B 338 GLU cc_start: 0.6892 (OUTLIER) cc_final: 0.6620 (pm20) REVERT: B 357 ARG cc_start: 0.8748 (OUTLIER) cc_final: 0.7341 (tpp-160) REVERT: B 393 LYS cc_start: 0.9007 (ttmt) cc_final: 0.8567 (tttm) REVERT: B 399 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8677 (mp) REVERT: B 428 SER cc_start: 0.8688 (OUTLIER) cc_final: 0.8159 (t) REVERT: D 103 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8292 (mt) REVERT: D 156 ARG cc_start: 0.8144 (ttp80) cc_final: 0.7726 (tpp-160) REVERT: D 170 VAL cc_start: 0.7669 (OUTLIER) cc_final: 0.7286 (p) REVERT: D 171 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7306 (mt-10) REVERT: D 173 LEU cc_start: 0.8822 (pt) cc_final: 0.8553 (pp) REVERT: D 195 ARG cc_start: 0.5595 (OUTLIER) cc_final: 0.4881 (ptp-110) REVERT: D 231 ASP cc_start: 0.7859 (t70) cc_final: 0.7324 (t0) REVERT: D 258 LYS cc_start: 0.7563 (mptm) cc_final: 0.7148 (mmmm) REVERT: D 348 ASP cc_start: 0.7956 (t70) cc_final: 0.7459 (m-30) REVERT: D 351 GLU cc_start: 0.7769 (tp30) cc_final: 0.7552 (tp30) REVERT: D 393 LYS cc_start: 0.8788 (ttmt) cc_final: 0.8417 (tttt) REVERT: D 412 ASN cc_start: 0.8568 (t0) cc_final: 0.7980 (m110) REVERT: D 429 ASN cc_start: 0.8443 (t0) cc_final: 0.8219 (m110) REVERT: D 431 GLN cc_start: 0.8594 (mt0) cc_final: 0.8113 (mt0) REVERT: D 433 LYS cc_start: 0.8203 (ttmm) cc_final: 0.7799 (tttm) REVERT: D 493 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.7577 (mp0) REVERT: C 108 LYS cc_start: 0.8826 (tttp) cc_final: 0.8448 (ttmt) REVERT: C 144 GLN cc_start: 0.8228 (tt0) cc_final: 0.7629 (tp-100) REVERT: C 177 GLN cc_start: 0.7435 (tp40) cc_final: 0.6771 (mt0) REVERT: C 201 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7627 (mt-10) REVERT: C 206 LEU cc_start: 0.8033 (mt) cc_final: 0.7826 (mp) REVERT: C 223 LYS cc_start: 0.8692 (OUTLIER) cc_final: 0.8341 (mtmm) REVERT: C 293 MET cc_start: 0.7175 (mtt) cc_final: 0.6911 (ptp) REVERT: C 306 ARG cc_start: 0.8072 (ptm-80) cc_final: 0.7726 (ptm-80) REVERT: C 316 GLN cc_start: 0.7996 (OUTLIER) cc_final: 0.7511 (mt0) REVERT: C 348 GLU cc_start: 0.8332 (tp30) cc_final: 0.7617 (tt0) REVERT: C 402 ILE cc_start: 0.9094 (OUTLIER) cc_final: 0.8811 (mm) REVERT: C 412 LYS cc_start: 0.8731 (OUTLIER) cc_final: 0.8377 (tptt) REVERT: C 425 SER cc_start: 0.8832 (OUTLIER) cc_final: 0.8416 (t) REVERT: C 487 ASP cc_start: 0.7482 (m-30) cc_final: 0.7266 (t0) REVERT: C 497 ASP cc_start: 0.8724 (m-30) cc_final: 0.8444 (m-30) outliers start: 120 outliers final: 62 residues processed: 296 average time/residue: 0.5005 time to fit residues: 163.7350 Evaluate side-chains 288 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 206 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 120 ASN Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 416 SER Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 146 ASN Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 233 ARG Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 246 ILE Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 306 TYR Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 406 HIS Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 441 ASP Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 195 ARG Chi-restraints excluded: chain D residue 201 PHE Chi-restraints excluded: chain D residue 266 ILE Chi-restraints excluded: chain D residue 303 MET Chi-restraints excluded: chain D residue 411 THR Chi-restraints excluded: chain D residue 481 LYS Chi-restraints excluded: chain D residue 493 GLU Chi-restraints excluded: chain D residue 507 ILE Chi-restraints excluded: chain D residue 508 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 156 ARG Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 223 LYS Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 316 GLN Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 390 SER Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 412 LYS Chi-restraints excluded: chain C residue 416 SER Chi-restraints excluded: chain C residue 425 SER Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 496 THR Chi-restraints excluded: chain C residue 519 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 110 optimal weight: 0.9990 chunk 70 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 9 optimal weight: 30.0000 chunk 98 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 111 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 129 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 GLN B 219 HIS B 347 ASN C 226 GLN C 383 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.171204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.116801 restraints weight = 14272.613| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 2.57 r_work: 0.3201 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13665 Z= 0.123 Angle : 0.554 13.231 18498 Z= 0.282 Chirality : 0.048 0.241 2080 Planarity : 0.003 0.043 2402 Dihedral : 5.960 59.072 1923 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.84 % Favored : 93.10 % Rotamer: Outliers : 7.42 % Allowed : 30.31 % Favored : 62.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.20), residues: 1710 helix: 0.02 (0.26), residues: 400 sheet: -0.97 (0.25), residues: 399 loop : -1.39 (0.21), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 386 TYR 0.012 0.001 TYR A 357 PHE 0.015 0.001 PHE B 360 TRP 0.005 0.001 TRP D 199 HIS 0.004 0.001 HIS B 369 Details of bonding type rmsd covalent geometry : bond 0.00302 (13664) covalent geometry : angle 0.55425 (18496) SS BOND : bond 0.00149 ( 1) SS BOND : angle 0.50373 ( 2) hydrogen bonds : bond 0.03360 ( 303) hydrogen bonds : angle 5.48834 ( 837) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 214 time to evaluate : 0.511 Fit side-chains revert: symmetry clash REVERT: A 174 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.7948 (pp) REVERT: A 191 ASP cc_start: 0.8305 (t70) cc_final: 0.7874 (t0) REVERT: A 311 ASP cc_start: 0.7558 (m-30) cc_final: 0.7142 (t0) REVERT: A 316 GLN cc_start: 0.8072 (mp10) cc_final: 0.7552 (mp10) REVERT: A 322 ASP cc_start: 0.7383 (t70) cc_final: 0.6878 (t70) REVERT: A 337 ARG cc_start: 0.8141 (ttt90) cc_final: 0.7442 (mtp85) REVERT: A 350 ILE cc_start: 0.7598 (OUTLIER) cc_final: 0.7382 (mt) REVERT: A 446 GLU cc_start: 0.7329 (mt-10) cc_final: 0.7099 (mp0) REVERT: A 500 PHE cc_start: 0.7992 (t80) cc_final: 0.7762 (t80) REVERT: B 88 ARG cc_start: 0.7781 (ttm-80) cc_final: 0.7317 (ttp-110) REVERT: B 95 LEU cc_start: 0.8876 (tt) cc_final: 0.8351 (mp) REVERT: B 137 ASN cc_start: 0.8593 (p0) cc_final: 0.8224 (p0) REVERT: B 170 VAL cc_start: 0.8205 (m) cc_final: 0.7933 (t) REVERT: B 171 GLU cc_start: 0.7397 (mm-30) cc_final: 0.7066 (mm-30) REVERT: B 233 ARG cc_start: 0.7152 (OUTLIER) cc_final: 0.6128 (mpt-90) REVERT: B 256 LEU cc_start: 0.7517 (OUTLIER) cc_final: 0.6963 (mt) REVERT: B 257 MET cc_start: 0.7161 (mtm) cc_final: 0.6849 (mtp) REVERT: B 258 LYS cc_start: 0.7145 (ttmt) cc_final: 0.6424 (tmtm) REVERT: B 264 ARG cc_start: 0.7337 (ttp80) cc_final: 0.7127 (ttm-80) REVERT: B 269 SER cc_start: 0.6571 (OUTLIER) cc_final: 0.6314 (p) REVERT: B 326 ASP cc_start: 0.7057 (t70) cc_final: 0.6701 (t70) REVERT: B 338 GLU cc_start: 0.6799 (OUTLIER) cc_final: 0.6505 (pm20) REVERT: B 357 ARG cc_start: 0.8731 (OUTLIER) cc_final: 0.7337 (tpp-160) REVERT: B 393 LYS cc_start: 0.8951 (ttmt) cc_final: 0.8523 (tttm) REVERT: B 395 ASP cc_start: 0.8322 (p0) cc_final: 0.8008 (p0) REVERT: B 399 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8650 (mp) REVERT: B 428 SER cc_start: 0.8643 (OUTLIER) cc_final: 0.8103 (t) REVERT: B 481 LYS cc_start: 0.8138 (OUTLIER) cc_final: 0.7915 (pttm) REVERT: D 103 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8294 (mt) REVERT: D 151 ASN cc_start: 0.8543 (OUTLIER) cc_final: 0.8068 (m110) REVERT: D 156 ARG cc_start: 0.8128 (ttp80) cc_final: 0.7695 (tpp-160) REVERT: D 170 VAL cc_start: 0.7628 (OUTLIER) cc_final: 0.7229 (p) REVERT: D 171 GLU cc_start: 0.7984 (tt0) cc_final: 0.7288 (mt-10) REVERT: D 173 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8491 (pp) REVERT: D 195 ARG cc_start: 0.5482 (OUTLIER) cc_final: 0.4844 (ptp-110) REVERT: D 231 ASP cc_start: 0.7948 (t70) cc_final: 0.7305 (t0) REVERT: D 258 LYS cc_start: 0.7511 (mptm) cc_final: 0.7159 (mmmm) REVERT: D 348 ASP cc_start: 0.7882 (t70) cc_final: 0.7374 (m-30) REVERT: D 351 GLU cc_start: 0.7742 (tp30) cc_final: 0.7527 (tp30) REVERT: D 393 LYS cc_start: 0.8752 (ttmt) cc_final: 0.8414 (tttt) REVERT: D 412 ASN cc_start: 0.8550 (t0) cc_final: 0.7957 (m110) REVERT: D 429 ASN cc_start: 0.8427 (t0) cc_final: 0.8207 (m110) REVERT: D 433 LYS cc_start: 0.8140 (ttmm) cc_final: 0.7743 (tttm) REVERT: D 452 LEU cc_start: 0.7819 (mt) cc_final: 0.7482 (mp) REVERT: C 108 LYS cc_start: 0.8819 (tttp) cc_final: 0.8483 (ttmt) REVERT: C 144 GLN cc_start: 0.8214 (tt0) cc_final: 0.7640 (tp-100) REVERT: C 177 GLN cc_start: 0.7418 (tp40) cc_final: 0.6720 (mt0) REVERT: C 201 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7511 (mt-10) REVERT: C 223 LYS cc_start: 0.8652 (OUTLIER) cc_final: 0.8309 (mtmm) REVERT: C 293 MET cc_start: 0.7175 (mtt) cc_final: 0.6905 (ptp) REVERT: C 306 ARG cc_start: 0.8034 (ptm-80) cc_final: 0.7735 (ptm-80) REVERT: C 316 GLN cc_start: 0.7895 (OUTLIER) cc_final: 0.7413 (mt0) REVERT: C 348 GLU cc_start: 0.8323 (tp30) cc_final: 0.7588 (tt0) REVERT: C 402 ILE cc_start: 0.9090 (OUTLIER) cc_final: 0.8792 (mm) REVERT: C 412 LYS cc_start: 0.8734 (OUTLIER) cc_final: 0.8393 (tptt) REVERT: C 425 SER cc_start: 0.8734 (OUTLIER) cc_final: 0.8325 (t) REVERT: C 497 ASP cc_start: 0.8724 (m-30) cc_final: 0.8437 (m-30) outliers start: 107 outliers final: 59 residues processed: 288 average time/residue: 0.5174 time to fit residues: 164.9144 Evaluate side-chains 290 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 210 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 120 ASN Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 416 SER Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 233 ARG Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 246 ILE Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 306 TYR Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 406 HIS Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 441 ASP Chi-restraints excluded: chain B residue 481 LYS Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain D residue 151 ASN Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 195 ARG Chi-restraints excluded: chain D residue 201 PHE Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 240 SER Chi-restraints excluded: chain D residue 266 ILE Chi-restraints excluded: chain D residue 340 TYR Chi-restraints excluded: chain D residue 411 THR Chi-restraints excluded: chain D residue 481 LYS Chi-restraints excluded: chain D residue 507 ILE Chi-restraints excluded: chain D residue 508 THR Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 156 ARG Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 223 LYS Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 316 GLN Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 412 LYS Chi-restraints excluded: chain C residue 425 SER Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 496 THR Chi-restraints excluded: chain C residue 519 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 101 optimal weight: 20.0000 chunk 52 optimal weight: 20.0000 chunk 130 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 chunk 151 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 chunk 6 optimal weight: 0.9990 chunk 122 optimal weight: 6.9990 chunk 131 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 GLN A 146 ASN B 219 HIS ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 ASN C 178 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.169272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.116680 restraints weight = 14353.497| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.66 r_work: 0.3168 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13665 Z= 0.180 Angle : 0.592 13.252 18498 Z= 0.299 Chirality : 0.049 0.188 2080 Planarity : 0.004 0.046 2402 Dihedral : 6.045 56.815 1922 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.66 % Favored : 92.28 % Rotamer: Outliers : 8.32 % Allowed : 29.13 % Favored : 62.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.20), residues: 1710 helix: 0.11 (0.26), residues: 401 sheet: -1.00 (0.25), residues: 403 loop : -1.43 (0.21), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 386 TYR 0.012 0.001 TYR B 158 PHE 0.016 0.001 PHE B 360 TRP 0.006 0.001 TRP D 199 HIS 0.006 0.001 HIS B 369 Details of bonding type rmsd covalent geometry : bond 0.00449 (13664) covalent geometry : angle 0.59172 (18496) SS BOND : bond 0.00176 ( 1) SS BOND : angle 0.59681 ( 2) hydrogen bonds : bond 0.03524 ( 303) hydrogen bonds : angle 5.46246 ( 837) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 201 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 174 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8116 (pp) REVERT: A 191 ASP cc_start: 0.8318 (t70) cc_final: 0.7907 (t0) REVERT: A 311 ASP cc_start: 0.7571 (m-30) cc_final: 0.7152 (t0) REVERT: A 316 GLN cc_start: 0.8040 (mp10) cc_final: 0.7531 (mp10) REVERT: A 322 ASP cc_start: 0.7429 (OUTLIER) cc_final: 0.6910 (t70) REVERT: A 337 ARG cc_start: 0.8098 (ttt90) cc_final: 0.7411 (mtp85) REVERT: A 350 ILE cc_start: 0.7798 (OUTLIER) cc_final: 0.7596 (mt) REVERT: A 436 MET cc_start: 0.9147 (OUTLIER) cc_final: 0.8431 (mtm) REVERT: A 446 GLU cc_start: 0.7388 (mt-10) cc_final: 0.7113 (mp0) REVERT: B 88 ARG cc_start: 0.7813 (ttm-80) cc_final: 0.7346 (ttp-110) REVERT: B 95 LEU cc_start: 0.8883 (tt) cc_final: 0.8391 (mp) REVERT: B 137 ASN cc_start: 0.8585 (p0) cc_final: 0.8214 (p0) REVERT: B 170 VAL cc_start: 0.8226 (m) cc_final: 0.7977 (t) REVERT: B 171 GLU cc_start: 0.7424 (mm-30) cc_final: 0.7042 (mm-30) REVERT: B 233 ARG cc_start: 0.7195 (OUTLIER) cc_final: 0.6950 (mpt-90) REVERT: B 256 LEU cc_start: 0.7726 (OUTLIER) cc_final: 0.7460 (mt) REVERT: B 258 LYS cc_start: 0.7212 (ttmt) cc_final: 0.6507 (tmtm) REVERT: B 264 ARG cc_start: 0.7426 (ttp80) cc_final: 0.7179 (ttm-80) REVERT: B 326 ASP cc_start: 0.7054 (t70) cc_final: 0.6693 (t70) REVERT: B 338 GLU cc_start: 0.6781 (OUTLIER) cc_final: 0.6499 (pm20) REVERT: B 357 ARG cc_start: 0.8738 (OUTLIER) cc_final: 0.7346 (tpp-160) REVERT: B 393 LYS cc_start: 0.8965 (ttmt) cc_final: 0.8533 (tttm) REVERT: B 399 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8661 (mp) REVERT: B 428 SER cc_start: 0.8655 (OUTLIER) cc_final: 0.8114 (t) REVERT: B 481 LYS cc_start: 0.8177 (OUTLIER) cc_final: 0.7959 (pttm) REVERT: D 103 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8281 (mt) REVERT: D 156 ARG cc_start: 0.8128 (ttp80) cc_final: 0.7751 (ttp-170) REVERT: D 170 VAL cc_start: 0.7713 (OUTLIER) cc_final: 0.7340 (p) REVERT: D 171 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7340 (mt-10) REVERT: D 173 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8519 (pp) REVERT: D 195 ARG cc_start: 0.5524 (OUTLIER) cc_final: 0.4626 (mtt-85) REVERT: D 231 ASP cc_start: 0.7898 (t70) cc_final: 0.7247 (t0) REVERT: D 348 ASP cc_start: 0.7876 (t70) cc_final: 0.7405 (m-30) REVERT: D 351 GLU cc_start: 0.7796 (tp30) cc_final: 0.7549 (tp30) REVERT: D 393 LYS cc_start: 0.8759 (ttmt) cc_final: 0.8425 (tttt) REVERT: D 412 ASN cc_start: 0.8576 (t0) cc_final: 0.7996 (m110) REVERT: D 429 ASN cc_start: 0.8478 (t0) cc_final: 0.8249 (m110) REVERT: D 433 LYS cc_start: 0.8188 (ttmm) cc_final: 0.7800 (tttm) REVERT: D 452 LEU cc_start: 0.7803 (mt) cc_final: 0.7501 (mp) REVERT: D 493 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.7604 (mp0) REVERT: C 108 LYS cc_start: 0.8845 (tttp) cc_final: 0.8454 (tppt) REVERT: C 144 GLN cc_start: 0.8229 (tt0) cc_final: 0.7655 (tp40) REVERT: C 168 GLU cc_start: 0.6219 (OUTLIER) cc_final: 0.6009 (pm20) REVERT: C 201 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7627 (mt-10) REVERT: C 223 LYS cc_start: 0.8690 (OUTLIER) cc_final: 0.8335 (mtmm) REVERT: C 293 MET cc_start: 0.7213 (mtt) cc_final: 0.6921 (ptp) REVERT: C 306 ARG cc_start: 0.8064 (ptm-80) cc_final: 0.7751 (ptm-80) REVERT: C 309 MET cc_start: 0.7007 (OUTLIER) cc_final: 0.6555 (ttp) REVERT: C 316 GLN cc_start: 0.7948 (OUTLIER) cc_final: 0.7448 (mt0) REVERT: C 348 GLU cc_start: 0.8329 (tp30) cc_final: 0.7591 (tt0) REVERT: C 402 ILE cc_start: 0.9101 (OUTLIER) cc_final: 0.8823 (mm) REVERT: C 425 SER cc_start: 0.8841 (OUTLIER) cc_final: 0.8444 (t) REVERT: C 431 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.8394 (pt0) REVERT: C 497 ASP cc_start: 0.8683 (m-30) cc_final: 0.8404 (m-30) outliers start: 120 outliers final: 60 residues processed: 285 average time/residue: 0.5157 time to fit residues: 162.4016 Evaluate side-chains 287 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 202 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 416 SER Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 233 ARG Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 246 ILE Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 306 TYR Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 406 HIS Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 441 ASP Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 481 LYS Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 195 ARG Chi-restraints excluded: chain D residue 201 PHE Chi-restraints excluded: chain D residue 240 SER Chi-restraints excluded: chain D residue 266 ILE Chi-restraints excluded: chain D residue 411 THR Chi-restraints excluded: chain D residue 481 LYS Chi-restraints excluded: chain D residue 493 GLU Chi-restraints excluded: chain D residue 507 ILE Chi-restraints excluded: chain D residue 508 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 156 ARG Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 223 LYS Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 309 MET Chi-restraints excluded: chain C residue 316 GLN Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 390 SER Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 425 SER Chi-restraints excluded: chain C residue 431 GLU Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 519 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 63 optimal weight: 0.4980 chunk 24 optimal weight: 0.9980 chunk 120 optimal weight: 5.9990 chunk 101 optimal weight: 9.9990 chunk 52 optimal weight: 9.9990 chunk 94 optimal weight: 0.9980 chunk 40 optimal weight: 10.0000 chunk 57 optimal weight: 6.9990 chunk 108 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 chunk 43 optimal weight: 6.9990 overall best weight: 2.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 GLN B 219 HIS B 388 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.167535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.113174 restraints weight = 14425.379| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.56 r_work: 0.3207 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 13665 Z= 0.219 Angle : 0.621 13.390 18498 Z= 0.314 Chirality : 0.050 0.167 2080 Planarity : 0.004 0.047 2402 Dihedral : 6.234 58.276 1922 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.89 % Favored : 92.05 % Rotamer: Outliers : 8.60 % Allowed : 28.85 % Favored : 62.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.20), residues: 1710 helix: 0.04 (0.26), residues: 403 sheet: -0.94 (0.27), residues: 332 loop : -1.40 (0.20), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 386 TYR 0.013 0.001 TYR B 158 PHE 0.017 0.002 PHE B 360 TRP 0.007 0.001 TRP D 199 HIS 0.006 0.001 HIS B 369 Details of bonding type rmsd covalent geometry : bond 0.00546 (13664) covalent geometry : angle 0.62139 (18496) SS BOND : bond 0.00212 ( 1) SS BOND : angle 0.68976 ( 2) hydrogen bonds : bond 0.03645 ( 303) hydrogen bonds : angle 5.52462 ( 837) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 211 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 168 GLU cc_start: 0.5716 (OUTLIER) cc_final: 0.5486 (mt-10) REVERT: A 174 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8325 (pp) REVERT: A 191 ASP cc_start: 0.8418 (t70) cc_final: 0.8009 (t0) REVERT: A 311 ASP cc_start: 0.7663 (m-30) cc_final: 0.7241 (t0) REVERT: A 316 GLN cc_start: 0.8068 (mp10) cc_final: 0.7517 (mp10) REVERT: A 322 ASP cc_start: 0.7394 (OUTLIER) cc_final: 0.6914 (t70) REVERT: A 337 ARG cc_start: 0.8044 (ttt90) cc_final: 0.7353 (mtp85) REVERT: A 436 MET cc_start: 0.9156 (OUTLIER) cc_final: 0.8477 (mtm) REVERT: A 446 GLU cc_start: 0.7458 (mt-10) cc_final: 0.7199 (mp0) REVERT: B 88 ARG cc_start: 0.7852 (ttm-80) cc_final: 0.7419 (ttp-110) REVERT: B 95 LEU cc_start: 0.8953 (tt) cc_final: 0.8474 (mp) REVERT: B 109 ARG cc_start: 0.7877 (OUTLIER) cc_final: 0.7520 (pmt170) REVERT: B 137 ASN cc_start: 0.8598 (p0) cc_final: 0.8251 (p0) REVERT: B 170 VAL cc_start: 0.8300 (m) cc_final: 0.8030 (t) REVERT: B 192 ASP cc_start: 0.7018 (t0) cc_final: 0.6700 (t0) REVERT: B 256 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7731 (mt) REVERT: B 258 LYS cc_start: 0.7412 (ttmt) cc_final: 0.6600 (tmtm) REVERT: B 264 ARG cc_start: 0.7501 (ttp80) cc_final: 0.7104 (ttm-80) REVERT: B 296 LYS cc_start: 0.7968 (ttpt) cc_final: 0.7520 (tppt) REVERT: B 326 ASP cc_start: 0.7208 (t70) cc_final: 0.6867 (t70) REVERT: B 338 GLU cc_start: 0.6978 (OUTLIER) cc_final: 0.6697 (pm20) REVERT: B 357 ARG cc_start: 0.8845 (OUTLIER) cc_final: 0.7401 (tpp-160) REVERT: B 393 LYS cc_start: 0.8995 (ttmt) cc_final: 0.8582 (tttm) REVERT: B 399 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8772 (mp) REVERT: B 428 SER cc_start: 0.8774 (OUTLIER) cc_final: 0.8276 (t) REVERT: B 470 GLU cc_start: 0.8274 (tt0) cc_final: 0.7856 (tt0) REVERT: B 481 LYS cc_start: 0.8306 (OUTLIER) cc_final: 0.8092 (pttm) REVERT: D 103 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8440 (mt) REVERT: D 151 ASN cc_start: 0.8633 (OUTLIER) cc_final: 0.8260 (m-40) REVERT: D 156 ARG cc_start: 0.8249 (ttp80) cc_final: 0.7872 (ttp-170) REVERT: D 170 VAL cc_start: 0.7912 (OUTLIER) cc_final: 0.7517 (p) REVERT: D 171 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7402 (mt-10) REVERT: D 195 ARG cc_start: 0.5705 (OUTLIER) cc_final: 0.4791 (mtt-85) REVERT: D 230 GLN cc_start: 0.7361 (OUTLIER) cc_final: 0.6980 (tt0) REVERT: D 231 ASP cc_start: 0.7979 (t70) cc_final: 0.7375 (t0) REVERT: D 348 ASP cc_start: 0.7936 (t70) cc_final: 0.7500 (m-30) REVERT: D 393 LYS cc_start: 0.8784 (ttmt) cc_final: 0.8507 (tttt) REVERT: D 412 ASN cc_start: 0.8714 (t0) cc_final: 0.8171 (m110) REVERT: D 429 ASN cc_start: 0.8508 (t0) cc_final: 0.8276 (m110) REVERT: D 433 LYS cc_start: 0.8334 (ttmm) cc_final: 0.7990 (tttm) REVERT: D 452 LEU cc_start: 0.8034 (mt) cc_final: 0.7741 (mp) REVERT: D 493 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.7589 (mp0) REVERT: C 108 LYS cc_start: 0.8891 (tttp) cc_final: 0.7948 (tppt) REVERT: C 144 GLN cc_start: 0.8262 (tt0) cc_final: 0.7777 (tp-100) REVERT: C 168 GLU cc_start: 0.5989 (OUTLIER) cc_final: 0.5773 (pm20) REVERT: C 201 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7639 (mt-10) REVERT: C 223 LYS cc_start: 0.8821 (OUTLIER) cc_final: 0.8441 (mtmm) REVERT: C 293 MET cc_start: 0.7409 (mtt) cc_final: 0.7037 (ptp) REVERT: C 306 ARG cc_start: 0.8205 (ptm-80) cc_final: 0.7882 (ptm-80) REVERT: C 336 LEU cc_start: 0.7319 (OUTLIER) cc_final: 0.7025 (pp) REVERT: C 348 GLU cc_start: 0.8336 (tp30) cc_final: 0.7646 (tt0) REVERT: C 398 THR cc_start: 0.8933 (OUTLIER) cc_final: 0.8565 (p) REVERT: C 402 ILE cc_start: 0.9160 (OUTLIER) cc_final: 0.8886 (mm) REVERT: C 425 SER cc_start: 0.8912 (OUTLIER) cc_final: 0.8537 (t) REVERT: C 431 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.8438 (pt0) REVERT: C 484 ILE cc_start: 0.8816 (tp) cc_final: 0.8590 (pt) REVERT: C 495 GLU cc_start: 0.7370 (mm-30) cc_final: 0.5561 (mm-30) REVERT: C 497 ASP cc_start: 0.8733 (m-30) cc_final: 0.8470 (m-30) outliers start: 124 outliers final: 66 residues processed: 299 average time/residue: 0.5322 time to fit residues: 175.6438 Evaluate side-chains 294 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 202 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 144 GLN Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 416 SER Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 109 ARG Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 246 ILE Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 306 TYR Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 406 HIS Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 441 ASP Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 481 LYS Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain D residue 151 ASN Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 195 ARG Chi-restraints excluded: chain D residue 201 PHE Chi-restraints excluded: chain D residue 230 GLN Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 266 ILE Chi-restraints excluded: chain D residue 303 MET Chi-restraints excluded: chain D residue 340 TYR Chi-restraints excluded: chain D residue 411 THR Chi-restraints excluded: chain D residue 419 ILE Chi-restraints excluded: chain D residue 481 LYS Chi-restraints excluded: chain D residue 493 GLU Chi-restraints excluded: chain D residue 507 ILE Chi-restraints excluded: chain D residue 508 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 156 ARG Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 223 LYS Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 390 SER Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 416 SER Chi-restraints excluded: chain C residue 425 SER Chi-restraints excluded: chain C residue 431 GLU Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 486 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 2 optimal weight: 0.9990 chunk 130 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 133 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 42 optimal weight: 0.0170 chunk 144 optimal weight: 8.9990 chunk 58 optimal weight: 5.9990 chunk 115 optimal weight: 4.9990 chunk 168 optimal weight: 7.9990 overall best weight: 1.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 ASN A 414 HIS B 219 HIS B 347 ASN B 388 ASN C 178 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.169631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.115205 restraints weight = 14247.904| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 2.56 r_work: 0.3154 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13665 Z= 0.145 Angle : 0.576 9.557 18498 Z= 0.294 Chirality : 0.048 0.170 2080 Planarity : 0.004 0.053 2402 Dihedral : 6.041 58.123 1921 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.25 % Favored : 92.69 % Rotamer: Outliers : 7.77 % Allowed : 29.89 % Favored : 62.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.20), residues: 1710 helix: 0.17 (0.26), residues: 402 sheet: -1.11 (0.24), residues: 413 loop : -1.46 (0.21), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 386 TYR 0.012 0.001 TYR A 357 PHE 0.019 0.001 PHE A 145 TRP 0.006 0.001 TRP D 199 HIS 0.005 0.001 HIS B 369 Details of bonding type rmsd covalent geometry : bond 0.00360 (13664) covalent geometry : angle 0.57629 (18496) SS BOND : bond 0.00131 ( 1) SS BOND : angle 0.44095 ( 2) hydrogen bonds : bond 0.03320 ( 303) hydrogen bonds : angle 5.38261 ( 837) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 206 time to evaluate : 0.434 Fit side-chains revert: symmetry clash REVERT: A 174 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.7953 (pp) REVERT: A 191 ASP cc_start: 0.8296 (t70) cc_final: 0.7886 (t0) REVERT: A 311 ASP cc_start: 0.7497 (m-30) cc_final: 0.7057 (t0) REVERT: A 316 GLN cc_start: 0.7900 (mp10) cc_final: 0.7331 (mp10) REVERT: A 322 ASP cc_start: 0.7287 (OUTLIER) cc_final: 0.6766 (t70) REVERT: A 337 ARG cc_start: 0.7893 (ttt90) cc_final: 0.7152 (mtp85) REVERT: A 436 MET cc_start: 0.9131 (OUTLIER) cc_final: 0.8418 (mtm) REVERT: A 446 GLU cc_start: 0.7336 (mt-10) cc_final: 0.7124 (mp0) REVERT: B 88 ARG cc_start: 0.7798 (ttm-80) cc_final: 0.7330 (ttp-110) REVERT: B 95 LEU cc_start: 0.8842 (tt) cc_final: 0.8362 (mp) REVERT: B 109 ARG cc_start: 0.7897 (OUTLIER) cc_final: 0.7451 (pmt170) REVERT: B 137 ASN cc_start: 0.8546 (p0) cc_final: 0.8146 (p0) REVERT: B 170 VAL cc_start: 0.8191 (m) cc_final: 0.7978 (t) REVERT: B 256 LEU cc_start: 0.7915 (OUTLIER) cc_final: 0.7585 (mt) REVERT: B 258 LYS cc_start: 0.7274 (ttmt) cc_final: 0.6502 (tmtm) REVERT: B 264 ARG cc_start: 0.7089 (ttp80) cc_final: 0.6744 (ttt90) REVERT: B 296 LYS cc_start: 0.7988 (ttpt) cc_final: 0.7526 (tppt) REVERT: B 326 ASP cc_start: 0.7010 (t70) cc_final: 0.6651 (t70) REVERT: B 338 GLU cc_start: 0.6855 (OUTLIER) cc_final: 0.6572 (pm20) REVERT: B 357 ARG cc_start: 0.8695 (OUTLIER) cc_final: 0.7278 (tpp-160) REVERT: B 393 LYS cc_start: 0.8952 (ttmt) cc_final: 0.8489 (tttm) REVERT: B 399 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8624 (mp) REVERT: B 428 SER cc_start: 0.8655 (OUTLIER) cc_final: 0.8113 (t) REVERT: B 470 GLU cc_start: 0.8142 (tt0) cc_final: 0.7697 (tt0) REVERT: B 481 LYS cc_start: 0.8126 (OUTLIER) cc_final: 0.7917 (pttm) REVERT: D 103 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8227 (mt) REVERT: D 151 ASN cc_start: 0.8556 (OUTLIER) cc_final: 0.8057 (m110) REVERT: D 156 ARG cc_start: 0.8131 (ttp80) cc_final: 0.7700 (ttp-170) REVERT: D 170 VAL cc_start: 0.7757 (OUTLIER) cc_final: 0.7377 (p) REVERT: D 171 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7267 (mt-10) REVERT: D 173 LEU cc_start: 0.8675 (pt) cc_final: 0.8410 (pp) REVERT: D 195 ARG cc_start: 0.5611 (OUTLIER) cc_final: 0.4626 (mtp85) REVERT: D 230 GLN cc_start: 0.7259 (OUTLIER) cc_final: 0.6908 (tt0) REVERT: D 231 ASP cc_start: 0.7821 (t70) cc_final: 0.7204 (t0) REVERT: D 348 ASP cc_start: 0.7923 (t70) cc_final: 0.7420 (m-30) REVERT: D 393 LYS cc_start: 0.8728 (ttmt) cc_final: 0.8368 (tttt) REVERT: D 412 ASN cc_start: 0.8619 (t0) cc_final: 0.7991 (m-40) REVERT: D 429 ASN cc_start: 0.8475 (t0) cc_final: 0.8231 (m110) REVERT: D 433 LYS cc_start: 0.8149 (ttmm) cc_final: 0.7736 (tttm) REVERT: D 452 LEU cc_start: 0.7788 (mt) cc_final: 0.7493 (mp) REVERT: C 108 LYS cc_start: 0.8813 (tttp) cc_final: 0.8397 (tppt) REVERT: C 144 GLN cc_start: 0.8280 (tt0) cc_final: 0.7711 (tp40) REVERT: C 152 ARG cc_start: 0.8484 (tmm160) cc_final: 0.8075 (tmt-80) REVERT: C 201 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7551 (mt-10) REVERT: C 223 LYS cc_start: 0.8627 (OUTLIER) cc_final: 0.8275 (mtmm) REVERT: C 256 ASP cc_start: 0.6862 (t0) cc_final: 0.6448 (t0) REVERT: C 293 MET cc_start: 0.7237 (mtt) cc_final: 0.6834 (ptp) REVERT: C 306 ARG cc_start: 0.8065 (ptm-80) cc_final: 0.7740 (ptm-80) REVERT: C 316 GLN cc_start: 0.7939 (OUTLIER) cc_final: 0.7406 (mt0) REVERT: C 348 GLU cc_start: 0.8233 (tp30) cc_final: 0.7468 (tt0) REVERT: C 398 THR cc_start: 0.8816 (OUTLIER) cc_final: 0.8440 (p) REVERT: C 402 ILE cc_start: 0.9084 (OUTLIER) cc_final: 0.8798 (mm) REVERT: C 425 SER cc_start: 0.8756 (OUTLIER) cc_final: 0.8359 (t) REVERT: C 431 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8348 (pt0) REVERT: C 484 ILE cc_start: 0.8650 (tp) cc_final: 0.8438 (pt) REVERT: C 497 ASP cc_start: 0.8683 (m-30) cc_final: 0.8393 (m-30) outliers start: 112 outliers final: 64 residues processed: 284 average time/residue: 0.5176 time to fit residues: 162.6102 Evaluate side-chains 291 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 204 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 120 ASN Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 416 SER Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 109 ARG Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 246 ILE Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 306 TYR Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 406 HIS Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 441 ASP Chi-restraints excluded: chain B residue 481 LYS Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain D residue 151 ASN Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 195 ARG Chi-restraints excluded: chain D residue 201 PHE Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 230 GLN Chi-restraints excluded: chain D residue 240 SER Chi-restraints excluded: chain D residue 266 ILE Chi-restraints excluded: chain D residue 340 TYR Chi-restraints excluded: chain D residue 411 THR Chi-restraints excluded: chain D residue 481 LYS Chi-restraints excluded: chain D residue 507 ILE Chi-restraints excluded: chain D residue 508 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 156 ARG Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 223 LYS Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 307 ASP Chi-restraints excluded: chain C residue 316 GLN Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 390 SER Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 425 SER Chi-restraints excluded: chain C residue 431 GLU Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 519 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 148 optimal weight: 0.5980 chunk 73 optimal weight: 1.9990 chunk 24 optimal weight: 0.4980 chunk 1 optimal weight: 0.0770 chunk 29 optimal weight: 0.9990 chunk 153 optimal weight: 0.4980 chunk 45 optimal weight: 1.9990 chunk 67 optimal weight: 0.0470 chunk 149 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 87 optimal weight: 0.9980 overall best weight: 0.3436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 GLN A 146 ASN B 219 HIS B 347 ASN C 178 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.173261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.119124 restraints weight = 14190.780| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.56 r_work: 0.3234 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 13665 Z= 0.103 Angle : 0.547 12.423 18498 Z= 0.279 Chirality : 0.047 0.184 2080 Planarity : 0.004 0.057 2402 Dihedral : 5.733 56.711 1921 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.61 % Favored : 93.33 % Rotamer: Outliers : 5.55 % Allowed : 32.32 % Favored : 62.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.21), residues: 1710 helix: 0.17 (0.27), residues: 404 sheet: -1.00 (0.25), residues: 415 loop : -1.38 (0.22), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 386 TYR 0.013 0.001 TYR A 357 PHE 0.014 0.001 PHE B 360 TRP 0.005 0.001 TRP A 185 HIS 0.003 0.001 HIS B 369 Details of bonding type rmsd covalent geometry : bond 0.00244 (13664) covalent geometry : angle 0.54739 (18496) SS BOND : bond 0.00113 ( 1) SS BOND : angle 0.28279 ( 2) hydrogen bonds : bond 0.03054 ( 303) hydrogen bonds : angle 5.20123 ( 837) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 215 time to evaluate : 0.540 Fit side-chains revert: symmetry clash REVERT: A 174 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.7675 (pp) REVERT: A 191 ASP cc_start: 0.8275 (t70) cc_final: 0.7836 (t0) REVERT: A 311 ASP cc_start: 0.7551 (m-30) cc_final: 0.7191 (t0) REVERT: A 316 GLN cc_start: 0.7871 (mp10) cc_final: 0.7574 (mp10) REVERT: A 322 ASP cc_start: 0.7275 (t70) cc_final: 0.6778 (t70) REVERT: A 337 ARG cc_start: 0.8040 (ttt90) cc_final: 0.7333 (mtp85) REVERT: A 436 MET cc_start: 0.9017 (OUTLIER) cc_final: 0.8714 (mtt) REVERT: A 446 GLU cc_start: 0.7363 (mt-10) cc_final: 0.7146 (mp0) REVERT: B 88 ARG cc_start: 0.7742 (ttm-80) cc_final: 0.7334 (ttp-110) REVERT: B 95 LEU cc_start: 0.8867 (tt) cc_final: 0.8329 (mp) REVERT: B 109 ARG cc_start: 0.7851 (OUTLIER) cc_final: 0.7404 (pmt170) REVERT: B 137 ASN cc_start: 0.8624 (p0) cc_final: 0.8286 (p0) REVERT: B 171 GLU cc_start: 0.7412 (mm-30) cc_final: 0.7051 (mm-30) REVERT: B 256 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7888 (mt) REVERT: B 258 LYS cc_start: 0.7230 (ttmt) cc_final: 0.6496 (tmtm) REVERT: B 264 ARG cc_start: 0.7089 (ttp80) cc_final: 0.6694 (ttt180) REVERT: B 296 LYS cc_start: 0.8041 (ttpt) cc_final: 0.7565 (tppt) REVERT: B 311 GLU cc_start: 0.7280 (pm20) cc_final: 0.7011 (pm20) REVERT: B 334 PHE cc_start: 0.6961 (m-10) cc_final: 0.6745 (m-10) REVERT: B 338 GLU cc_start: 0.6724 (OUTLIER) cc_final: 0.6439 (pm20) REVERT: B 393 LYS cc_start: 0.8966 (ttmt) cc_final: 0.8545 (tttm) REVERT: B 395 ASP cc_start: 0.8210 (p0) cc_final: 0.7867 (p0) REVERT: B 399 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8654 (mp) REVERT: B 428 SER cc_start: 0.8685 (OUTLIER) cc_final: 0.8148 (t) REVERT: D 151 ASN cc_start: 0.8493 (OUTLIER) cc_final: 0.8005 (m110) REVERT: D 156 ARG cc_start: 0.8110 (ttp80) cc_final: 0.7735 (tpp-160) REVERT: D 170 VAL cc_start: 0.7730 (OUTLIER) cc_final: 0.7332 (p) REVERT: D 171 GLU cc_start: 0.7881 (tt0) cc_final: 0.7224 (mt-10) REVERT: D 173 LEU cc_start: 0.8688 (pt) cc_final: 0.8417 (pp) REVERT: D 195 ARG cc_start: 0.5426 (OUTLIER) cc_final: 0.4536 (mtp85) REVERT: D 230 GLN cc_start: 0.7057 (OUTLIER) cc_final: 0.6751 (tt0) REVERT: D 231 ASP cc_start: 0.7835 (t70) cc_final: 0.7268 (t0) REVERT: D 348 ASP cc_start: 0.7875 (t70) cc_final: 0.7173 (m-30) REVERT: D 393 LYS cc_start: 0.8748 (ttmt) cc_final: 0.8391 (tttt) REVERT: D 412 ASN cc_start: 0.8586 (t0) cc_final: 0.7929 (m-40) REVERT: D 429 ASN cc_start: 0.8451 (t0) cc_final: 0.8247 (m110) REVERT: D 433 LYS cc_start: 0.8191 (ttmm) cc_final: 0.7818 (tttm) REVERT: D 452 LEU cc_start: 0.7782 (mt) cc_final: 0.7500 (mp) REVERT: C 108 LYS cc_start: 0.8747 (tttp) cc_final: 0.8355 (tppt) REVERT: C 144 GLN cc_start: 0.8213 (tt0) cc_final: 0.7665 (tp40) REVERT: C 152 ARG cc_start: 0.8534 (tmm160) cc_final: 0.8092 (tmt-80) REVERT: C 201 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7413 (mt-10) REVERT: C 256 ASP cc_start: 0.6898 (t0) cc_final: 0.6585 (t0) REVERT: C 293 MET cc_start: 0.7201 (mtt) cc_final: 0.6922 (ptp) REVERT: C 306 ARG cc_start: 0.7996 (ptm-80) cc_final: 0.7412 (ptm-80) REVERT: C 348 GLU cc_start: 0.8283 (tp30) cc_final: 0.7547 (tt0) REVERT: C 365 LYS cc_start: 0.8211 (ttmm) cc_final: 0.7629 (mtpt) REVERT: C 425 SER cc_start: 0.8687 (OUTLIER) cc_final: 0.8267 (t) REVERT: C 484 ILE cc_start: 0.8660 (tp) cc_final: 0.8449 (pt) REVERT: C 487 ASP cc_start: 0.7389 (t0) cc_final: 0.7095 (OUTLIER) REVERT: C 497 ASP cc_start: 0.8669 (m-30) cc_final: 0.8381 (m-30) outliers start: 80 outliers final: 44 residues processed: 268 average time/residue: 0.5508 time to fit residues: 162.9544 Evaluate side-chains 258 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 202 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 109 ARG Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 306 TYR Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 406 HIS Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 441 ASP Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain D residue 151 ASN Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 195 ARG Chi-restraints excluded: chain D residue 201 PHE Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 230 GLN Chi-restraints excluded: chain D residue 240 SER Chi-restraints excluded: chain D residue 340 TYR Chi-restraints excluded: chain D residue 411 THR Chi-restraints excluded: chain D residue 481 LYS Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 156 ARG Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 425 SER Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 519 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 6 optimal weight: 2.9990 chunk 53 optimal weight: 0.3980 chunk 23 optimal weight: 8.9990 chunk 58 optimal weight: 0.0870 chunk 138 optimal weight: 5.9990 chunk 91 optimal weight: 9.9990 chunk 107 optimal weight: 0.7980 chunk 116 optimal weight: 5.9990 chunk 135 optimal weight: 0.7980 chunk 71 optimal weight: 0.0020 chunk 38 optimal weight: 0.9980 overall best weight: 0.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 GLN B 188 GLN B 219 HIS B 347 ASN D 196 GLN D 406 HIS C 178 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.173788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.119698 restraints weight = 14300.943| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 2.56 r_work: 0.3301 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 13665 Z= 0.103 Angle : 0.553 12.984 18498 Z= 0.281 Chirality : 0.047 0.222 2080 Planarity : 0.004 0.056 2402 Dihedral : 5.535 56.587 1918 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.43 % Favored : 93.51 % Rotamer: Outliers : 5.34 % Allowed : 32.73 % Favored : 61.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.21), residues: 1710 helix: 0.28 (0.27), residues: 401 sheet: -0.90 (0.25), residues: 405 loop : -1.31 (0.21), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 386 TYR 0.012 0.001 TYR A 357 PHE 0.014 0.001 PHE B 268 TRP 0.005 0.001 TRP A 198 HIS 0.003 0.001 HIS B 369 Details of bonding type rmsd covalent geometry : bond 0.00246 (13664) covalent geometry : angle 0.55286 (18496) SS BOND : bond 0.00096 ( 1) SS BOND : angle 0.29840 ( 2) hydrogen bonds : bond 0.02975 ( 303) hydrogen bonds : angle 5.08321 ( 837) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 213 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 174 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7601 (pp) REVERT: A 191 ASP cc_start: 0.8288 (t70) cc_final: 0.7839 (t0) REVERT: A 311 ASP cc_start: 0.7624 (m-30) cc_final: 0.7277 (t0) REVERT: A 316 GLN cc_start: 0.7965 (mp10) cc_final: 0.7715 (mp10) REVERT: A 322 ASP cc_start: 0.7325 (t70) cc_final: 0.6836 (t70) REVERT: A 436 MET cc_start: 0.8972 (OUTLIER) cc_final: 0.8680 (mtt) REVERT: A 446 GLU cc_start: 0.7353 (mt-10) cc_final: 0.7150 (mp0) REVERT: B 88 ARG cc_start: 0.7727 (ttm-80) cc_final: 0.7316 (ttp-110) REVERT: B 95 LEU cc_start: 0.8861 (tt) cc_final: 0.8318 (mp) REVERT: B 109 ARG cc_start: 0.7726 (OUTLIER) cc_final: 0.7433 (pmt170) REVERT: B 137 ASN cc_start: 0.8624 (p0) cc_final: 0.8317 (p0) REVERT: B 171 GLU cc_start: 0.7447 (mm-30) cc_final: 0.7160 (mm-30) REVERT: B 256 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.8026 (mt) REVERT: B 258 LYS cc_start: 0.7186 (ttmt) cc_final: 0.6458 (tmtm) REVERT: B 264 ARG cc_start: 0.7078 (ttp80) cc_final: 0.6781 (ttt90) REVERT: B 296 LYS cc_start: 0.8073 (ttpt) cc_final: 0.7589 (tppt) REVERT: B 311 GLU cc_start: 0.7187 (pm20) cc_final: 0.6697 (pm20) REVERT: B 334 PHE cc_start: 0.7001 (m-10) cc_final: 0.6773 (m-10) REVERT: B 338 GLU cc_start: 0.6662 (OUTLIER) cc_final: 0.6343 (pm20) REVERT: B 393 LYS cc_start: 0.8950 (ttmt) cc_final: 0.8554 (tttm) REVERT: B 395 ASP cc_start: 0.8250 (p0) cc_final: 0.7916 (p0) REVERT: B 399 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8753 (mp) REVERT: B 428 SER cc_start: 0.8787 (OUTLIER) cc_final: 0.8275 (t) REVERT: B 484 ILE cc_start: 0.8379 (mt) cc_final: 0.8015 (mm) REVERT: D 151 ASN cc_start: 0.8546 (OUTLIER) cc_final: 0.8054 (m110) REVERT: D 156 ARG cc_start: 0.8156 (ttp80) cc_final: 0.7836 (tpp-160) REVERT: D 170 VAL cc_start: 0.7695 (OUTLIER) cc_final: 0.7261 (p) REVERT: D 171 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7228 (mt-10) REVERT: D 173 LEU cc_start: 0.8687 (pt) cc_final: 0.8413 (pt) REVERT: D 230 GLN cc_start: 0.7018 (OUTLIER) cc_final: 0.6734 (tt0) REVERT: D 231 ASP cc_start: 0.7856 (t70) cc_final: 0.7311 (t0) REVERT: D 258 LYS cc_start: 0.7551 (mptm) cc_final: 0.7168 (mmmm) REVERT: D 280 MET cc_start: 0.5628 (mtt) cc_final: 0.5071 (mtt) REVERT: D 348 ASP cc_start: 0.7894 (t70) cc_final: 0.7205 (m-30) REVERT: D 393 LYS cc_start: 0.8752 (ttmt) cc_final: 0.8422 (tttt) REVERT: D 412 ASN cc_start: 0.8583 (t0) cc_final: 0.7999 (m110) REVERT: D 433 LYS cc_start: 0.8240 (ttmm) cc_final: 0.7880 (tttm) REVERT: D 452 LEU cc_start: 0.7875 (mt) cc_final: 0.7597 (mp) REVERT: C 108 LYS cc_start: 0.8731 (tttp) cc_final: 0.8357 (tppt) REVERT: C 144 GLN cc_start: 0.8185 (tt0) cc_final: 0.7666 (tp-100) REVERT: C 152 ARG cc_start: 0.8550 (tmm160) cc_final: 0.8118 (tmt-80) REVERT: C 201 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7482 (mt-10) REVERT: C 256 ASP cc_start: 0.7085 (t0) cc_final: 0.6845 (t0) REVERT: C 293 MET cc_start: 0.7194 (mtt) cc_final: 0.6856 (ptp) REVERT: C 316 GLN cc_start: 0.7929 (OUTLIER) cc_final: 0.7354 (mt0) REVERT: C 348 GLU cc_start: 0.8328 (tp30) cc_final: 0.7628 (tt0) REVERT: C 365 LYS cc_start: 0.8256 (ttmm) cc_final: 0.7738 (mtpt) REVERT: C 425 SER cc_start: 0.8738 (OUTLIER) cc_final: 0.8339 (t) REVERT: C 487 ASP cc_start: 0.7426 (t0) cc_final: 0.7143 (OUTLIER) REVERT: C 497 ASP cc_start: 0.8696 (m-30) cc_final: 0.8392 (m-30) outliers start: 77 outliers final: 44 residues processed: 267 average time/residue: 0.5144 time to fit residues: 152.1061 Evaluate side-chains 261 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 204 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 109 ARG Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 406 HIS Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 441 ASP Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain D residue 151 ASN Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 201 PHE Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 230 GLN Chi-restraints excluded: chain D residue 240 SER Chi-restraints excluded: chain D residue 266 ILE Chi-restraints excluded: chain D residue 340 TYR Chi-restraints excluded: chain D residue 411 THR Chi-restraints excluded: chain D residue 481 LYS Chi-restraints excluded: chain D residue 507 ILE Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 156 ARG Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 316 GLN Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 425 SER Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 496 THR Chi-restraints excluded: chain C residue 519 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 69 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 153 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 99 optimal weight: 7.9990 chunk 127 optimal weight: 8.9990 chunk 64 optimal weight: 0.9980 chunk 96 optimal weight: 0.7980 chunk 169 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 GLN B 219 HIS B 347 ASN D 406 HIS C 178 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.168997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.114268 restraints weight = 14341.082| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.56 r_work: 0.3168 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 13665 Z= 0.196 Angle : 0.620 9.489 18498 Z= 0.313 Chirality : 0.050 0.234 2080 Planarity : 0.004 0.058 2402 Dihedral : 5.667 57.451 1912 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.54 % Favored : 92.40 % Rotamer: Outliers : 5.13 % Allowed : 33.22 % Favored : 61.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.21), residues: 1710 helix: 0.18 (0.27), residues: 400 sheet: -0.98 (0.25), residues: 404 loop : -1.40 (0.21), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG B 386 TYR 0.013 0.001 TYR B 306 PHE 0.018 0.001 PHE B 360 TRP 0.006 0.001 TRP B 199 HIS 0.006 0.001 HIS B 369 Details of bonding type rmsd covalent geometry : bond 0.00485 (13664) covalent geometry : angle 0.62047 (18496) SS BOND : bond 0.00154 ( 1) SS BOND : angle 0.56432 ( 2) hydrogen bonds : bond 0.03421 ( 303) hydrogen bonds : angle 5.34645 ( 837) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 206 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 191 ASP cc_start: 0.8331 (t70) cc_final: 0.7927 (t0) REVERT: A 311 ASP cc_start: 0.7528 (m-30) cc_final: 0.7194 (t0) REVERT: A 316 GLN cc_start: 0.7981 (mp10) cc_final: 0.7729 (mp10) REVERT: A 322 ASP cc_start: 0.7303 (OUTLIER) cc_final: 0.6789 (t70) REVERT: A 436 MET cc_start: 0.9131 (OUTLIER) cc_final: 0.8483 (mtm) REVERT: A 446 GLU cc_start: 0.7434 (mt-10) cc_final: 0.7170 (mp0) REVERT: B 88 ARG cc_start: 0.7829 (ttm-80) cc_final: 0.7396 (ttp-110) REVERT: B 95 LEU cc_start: 0.8949 (tt) cc_final: 0.8390 (mp) REVERT: B 109 ARG cc_start: 0.7894 (OUTLIER) cc_final: 0.7471 (pmt170) REVERT: B 137 ASN cc_start: 0.8580 (p0) cc_final: 0.8209 (p0) REVERT: B 171 GLU cc_start: 0.7418 (mm-30) cc_final: 0.7063 (mm-30) REVERT: B 256 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.8116 (mt) REVERT: B 258 LYS cc_start: 0.7100 (ttmt) cc_final: 0.6444 (tmtm) REVERT: B 264 ARG cc_start: 0.7082 (ttp80) cc_final: 0.6709 (ttt180) REVERT: B 296 LYS cc_start: 0.8050 (ttpt) cc_final: 0.7585 (tppt) REVERT: B 326 ASP cc_start: 0.7068 (t70) cc_final: 0.6705 (t70) REVERT: B 334 PHE cc_start: 0.6953 (m-10) cc_final: 0.6730 (m-10) REVERT: B 338 GLU cc_start: 0.6761 (OUTLIER) cc_final: 0.6478 (pm20) REVERT: B 393 LYS cc_start: 0.8962 (ttmt) cc_final: 0.8517 (tttm) REVERT: B 399 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8681 (mp) REVERT: B 406 HIS cc_start: 0.9072 (OUTLIER) cc_final: 0.8769 (m90) REVERT: B 428 SER cc_start: 0.8678 (OUTLIER) cc_final: 0.8137 (t) REVERT: D 151 ASN cc_start: 0.8611 (OUTLIER) cc_final: 0.8115 (m110) REVERT: D 156 ARG cc_start: 0.8212 (ttp80) cc_final: 0.7823 (ttp-170) REVERT: D 170 VAL cc_start: 0.7670 (OUTLIER) cc_final: 0.7295 (p) REVERT: D 171 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7290 (mt-10) REVERT: D 229 ILE cc_start: 0.7788 (mm) cc_final: 0.7521 (mp) REVERT: D 230 GLN cc_start: 0.7052 (OUTLIER) cc_final: 0.6730 (tt0) REVERT: D 231 ASP cc_start: 0.7841 (t70) cc_final: 0.7201 (t0) REVERT: D 280 MET cc_start: 0.5754 (mtt) cc_final: 0.5213 (mtt) REVERT: D 348 ASP cc_start: 0.8016 (t70) cc_final: 0.7535 (m-30) REVERT: D 393 LYS cc_start: 0.8748 (ttmt) cc_final: 0.8395 (tttt) REVERT: D 412 ASN cc_start: 0.8608 (t0) cc_final: 0.8023 (m-40) REVERT: D 433 LYS cc_start: 0.8206 (ttmm) cc_final: 0.7803 (tttm) REVERT: D 452 LEU cc_start: 0.7835 (mt) cc_final: 0.7566 (mp) REVERT: C 108 LYS cc_start: 0.8874 (tttp) cc_final: 0.8464 (tppt) REVERT: C 144 GLN cc_start: 0.8295 (tt0) cc_final: 0.7761 (tp-100) REVERT: C 152 ARG cc_start: 0.8525 (tmm160) cc_final: 0.8056 (tmt-80) REVERT: C 201 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7442 (mt-10) REVERT: C 256 ASP cc_start: 0.7070 (t0) cc_final: 0.6841 (t0) REVERT: C 293 MET cc_start: 0.7180 (mtt) cc_final: 0.6898 (ptp) REVERT: C 306 ARG cc_start: 0.8076 (ptm-80) cc_final: 0.7680 (ptm-80) REVERT: C 316 GLN cc_start: 0.7888 (OUTLIER) cc_final: 0.7338 (mt0) REVERT: C 334 LEU cc_start: 0.7480 (OUTLIER) cc_final: 0.7241 (tt) REVERT: C 348 GLU cc_start: 0.8287 (tp30) cc_final: 0.7536 (tt0) REVERT: C 398 THR cc_start: 0.8843 (OUTLIER) cc_final: 0.8461 (p) REVERT: C 425 SER cc_start: 0.8838 (OUTLIER) cc_final: 0.8419 (t) REVERT: C 436 MET cc_start: 0.9092 (mtt) cc_final: 0.8784 (mtt) REVERT: C 450 LEU cc_start: 0.7458 (OUTLIER) cc_final: 0.7085 (mp) REVERT: C 487 ASP cc_start: 0.7441 (t0) cc_final: 0.7092 (OUTLIER) REVERT: C 497 ASP cc_start: 0.8644 (m-30) cc_final: 0.8361 (m-30) outliers start: 74 outliers final: 44 residues processed: 255 average time/residue: 0.4944 time to fit residues: 139.6680 Evaluate side-chains 265 residues out of total 1444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 204 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 120 ASN Chi-restraints excluded: chain A residue 144 GLN Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 109 ARG Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 406 HIS Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 441 ASP Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain D residue 151 ASN Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 201 PHE Chi-restraints excluded: chain D residue 230 GLN Chi-restraints excluded: chain D residue 240 SER Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 411 THR Chi-restraints excluded: chain D residue 481 LYS Chi-restraints excluded: chain D residue 507 ILE Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 156 ARG Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 316 GLN Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 425 SER Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 519 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 112 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 153 optimal weight: 6.9990 chunk 90 optimal weight: 5.9990 chunk 116 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 111 optimal weight: 0.7980 chunk 126 optimal weight: 1.9990 chunk 59 optimal weight: 8.9990 chunk 148 optimal weight: 2.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 GLN B 219 HIS B 347 ASN D 406 HIS C 178 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.170679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.116042 restraints weight = 14419.400| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.57 r_work: 0.3199 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13665 Z= 0.140 Angle : 0.594 12.733 18498 Z= 0.298 Chirality : 0.049 0.234 2080 Planarity : 0.004 0.057 2402 Dihedral : 5.537 57.276 1912 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.96 % Favored : 92.98 % Rotamer: Outliers : 4.92 % Allowed : 33.22 % Favored : 61.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.20), residues: 1710 helix: 0.18 (0.27), residues: 401 sheet: -0.99 (0.25), residues: 404 loop : -1.40 (0.21), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG B 386 TYR 0.012 0.001 TYR A 357 PHE 0.016 0.001 PHE A 500 TRP 0.005 0.001 TRP D 199 HIS 0.005 0.001 HIS B 369 Details of bonding type rmsd covalent geometry : bond 0.00345 (13664) covalent geometry : angle 0.59357 (18496) SS BOND : bond 0.00116 ( 1) SS BOND : angle 0.36510 ( 2) hydrogen bonds : bond 0.03203 ( 303) hydrogen bonds : angle 5.28120 ( 837) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5003.53 seconds wall clock time: 86 minutes 0.46 seconds (5160.46 seconds total)