Starting phenix.real_space_refine on Thu Feb 13 20:15:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6x3f_22021/02_2025/6x3f_22021.cif Found real_map, /net/cci-nas-00/data/ceres_data/6x3f_22021/02_2025/6x3f_22021.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6x3f_22021/02_2025/6x3f_22021.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6x3f_22021/02_2025/6x3f_22021.map" model { file = "/net/cci-nas-00/data/ceres_data/6x3f_22021/02_2025/6x3f_22021.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6x3f_22021/02_2025/6x3f_22021.cif" } resolution = 3.03 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 66 5.16 5 C 6144 2.51 5 N 1488 2.21 5 O 1668 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 9366 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 3115 Classifications: {'peptide': 409} Link IDs: {'PTRANS': 11, 'TRANS': 397} Chain breaks: 2 Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'CHT': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: C, B Time building chain proxies: 6.20, per 1000 atoms: 0.66 Number of scatterers: 9366 At special positions: 0 Unit cell: (115.648, 112.32, 77.376, 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 66 16.00 O 1668 8.00 N 1488 7.00 C 6144 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.57 Conformation dependent library (CDL) restraints added in 1.2 seconds 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2268 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 6 sheets defined 72.9% alpha, 2.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 18 through 40 removed outlier: 3.711A pdb=" N THR A 24 " --> pdb=" O VAL A 20 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU A 30 " --> pdb=" O ALA A 26 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG A 39 " --> pdb=" O GLY A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 81 removed outlier: 3.679A pdb=" N LEU A 59 " --> pdb=" O PRO A 55 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N MET A 60 " --> pdb=" O GLY A 56 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE A 66 " --> pdb=" O MET A 62 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE A 67 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N LEU A 68 " --> pdb=" O LYS A 64 " (cutoff:3.500A) Proline residue: A 69 - end of helix Processing helix chain 'A' and resid 96 through 116 removed outlier: 4.034A pdb=" N THR A 102 " --> pdb=" O TYR A 98 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE A 104 " --> pdb=" O CYS A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 150 removed outlier: 3.982A pdb=" N ASP A 144 " --> pdb=" O ASP A 140 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU A 145 " --> pdb=" O ALA A 141 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ILE A 146 " --> pdb=" O MET A 142 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N PHE A 150 " --> pdb=" O ILE A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 158 Processing helix chain 'A' and resid 211 through 229 removed outlier: 3.699A pdb=" N CYS A 219 " --> pdb=" O LEU A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 247 removed outlier: 3.669A pdb=" N VAL A 237 " --> pdb=" O GLY A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 255 Processing helix chain 'A' and resid 257 through 273 removed outlier: 3.600A pdb=" N PHE A 264 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS A 269 " --> pdb=" O LEU A 265 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLU A 272 " --> pdb=" O GLY A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 282 Processing helix chain 'A' and resid 282 through 296 removed outlier: 3.846A pdb=" N MET A 286 " --> pdb=" O LEU A 282 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N THR A 291 " --> pdb=" O ALA A 287 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA A 294 " --> pdb=" O LEU A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 309 removed outlier: 3.774A pdb=" N VAL A 308 " --> pdb=" O ILE A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 320 removed outlier: 3.670A pdb=" N PHE A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N MET A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 331 removed outlier: 3.846A pdb=" N MET A 329 " --> pdb=" O LEU A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 348 removed outlier: 3.590A pdb=" N GLU A 345 " --> pdb=" O PHE A 341 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLU A 346 " --> pdb=" O ARG A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 359 removed outlier: 3.754A pdb=" N THR A 355 " --> pdb=" O ASP A 351 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N PHE A 357 " --> pdb=" O ARG A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 385 removed outlier: 3.657A pdb=" N ALA A 371 " --> pdb=" O MET A 367 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU A 372 " --> pdb=" O ASP A 368 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ALA A 375 " --> pdb=" O ALA A 371 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N VAL A 376 " --> pdb=" O LEU A 372 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N VAL A 379 " --> pdb=" O ALA A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 408 removed outlier: 3.728A pdb=" N ILE A 395 " --> pdb=" O ILE A 391 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR A 402 " --> pdb=" O SER A 398 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER A 405 " --> pdb=" O ALA A 401 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ILE A 406 " --> pdb=" O THR A 402 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY A 407 " --> pdb=" O SER A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 426 removed outlier: 3.583A pdb=" N THR A 418 " --> pdb=" O ALA A 414 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET A 419 " --> pdb=" O GLY A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 436 removed outlier: 3.876A pdb=" N THR A 434 " --> pdb=" O GLU A 431 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU A 435 " --> pdb=" O ASP A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 458 removed outlier: 4.615A pdb=" N ARG A 445 " --> pdb=" O TRP A 441 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N PHE A 446 " --> pdb=" O LEU A 442 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL A 450 " --> pdb=" O PHE A 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 40 removed outlier: 3.710A pdb=" N THR B 24 " --> pdb=" O VAL B 20 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU B 30 " --> pdb=" O ALA B 26 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG B 39 " --> pdb=" O GLY B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 81 removed outlier: 3.680A pdb=" N LEU B 59 " --> pdb=" O PRO B 55 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N MET B 60 " --> pdb=" O GLY B 56 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE B 66 " --> pdb=" O MET B 62 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE B 67 " --> pdb=" O LEU B 63 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N LEU B 68 " --> pdb=" O LYS B 64 " (cutoff:3.500A) Proline residue: B 69 - end of helix Processing helix chain 'B' and resid 96 through 116 removed outlier: 4.034A pdb=" N THR B 102 " --> pdb=" O TYR B 98 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE B 104 " --> pdb=" O CYS B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 150 removed outlier: 3.982A pdb=" N ASP B 144 " --> pdb=" O ASP B 140 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU B 145 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ILE B 146 " --> pdb=" O MET B 142 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N PHE B 150 " --> pdb=" O ILE B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 158 Processing helix chain 'B' and resid 211 through 229 removed outlier: 3.699A pdb=" N CYS B 219 " --> pdb=" O LEU B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 247 removed outlier: 3.668A pdb=" N VAL B 237 " --> pdb=" O GLY B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 255 Processing helix chain 'B' and resid 257 through 273 removed outlier: 3.600A pdb=" N PHE B 264 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS B 269 " --> pdb=" O LEU B 265 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLU B 272 " --> pdb=" O GLY B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 282 Processing helix chain 'B' and resid 282 through 296 removed outlier: 3.846A pdb=" N MET B 286 " --> pdb=" O LEU B 282 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N THR B 291 " --> pdb=" O ALA B 287 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ALA B 294 " --> pdb=" O LEU B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 309 removed outlier: 3.775A pdb=" N VAL B 308 " --> pdb=" O ILE B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 320 removed outlier: 3.669A pdb=" N PHE B 316 " --> pdb=" O ASN B 312 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N MET B 318 " --> pdb=" O PHE B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 331 removed outlier: 3.846A pdb=" N MET B 329 " --> pdb=" O LEU B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 348 removed outlier: 3.589A pdb=" N GLU B 345 " --> pdb=" O PHE B 341 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU B 346 " --> pdb=" O ARG B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 359 removed outlier: 3.754A pdb=" N THR B 355 " --> pdb=" O ASP B 351 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N PHE B 357 " --> pdb=" O ARG B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 385 removed outlier: 3.657A pdb=" N ALA B 371 " --> pdb=" O MET B 367 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU B 372 " --> pdb=" O ASP B 368 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ALA B 375 " --> pdb=" O ALA B 371 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N VAL B 376 " --> pdb=" O LEU B 372 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N VAL B 379 " --> pdb=" O ALA B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 408 removed outlier: 3.727A pdb=" N ILE B 395 " --> pdb=" O ILE B 391 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR B 402 " --> pdb=" O SER B 398 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER B 405 " --> pdb=" O ALA B 401 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ILE B 406 " --> pdb=" O THR B 402 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY B 407 " --> pdb=" O SER B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 426 removed outlier: 3.584A pdb=" N THR B 418 " --> pdb=" O ALA B 414 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET B 419 " --> pdb=" O GLY B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 436 removed outlier: 3.875A pdb=" N THR B 434 " --> pdb=" O GLU B 431 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU B 435 " --> pdb=" O ASP B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 458 removed outlier: 4.614A pdb=" N ARG B 445 " --> pdb=" O TRP B 441 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N PHE B 446 " --> pdb=" O LEU B 442 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL B 450 " --> pdb=" O PHE B 446 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 40 removed outlier: 3.711A pdb=" N THR C 24 " --> pdb=" O VAL C 20 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU C 30 " --> pdb=" O ALA C 26 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG C 39 " --> pdb=" O GLY C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 81 removed outlier: 3.679A pdb=" N LEU C 59 " --> pdb=" O PRO C 55 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N MET C 60 " --> pdb=" O GLY C 56 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE C 66 " --> pdb=" O MET C 62 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE C 67 " --> pdb=" O LEU C 63 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N LEU C 68 " --> pdb=" O LYS C 64 " (cutoff:3.500A) Proline residue: C 69 - end of helix Processing helix chain 'C' and resid 96 through 116 removed outlier: 4.033A pdb=" N THR C 102 " --> pdb=" O TYR C 98 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE C 104 " --> pdb=" O CYS C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 150 removed outlier: 3.982A pdb=" N ASP C 144 " --> pdb=" O ASP C 140 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU C 145 " --> pdb=" O ALA C 141 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ILE C 146 " --> pdb=" O MET C 142 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N PHE C 150 " --> pdb=" O ILE C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 158 Processing helix chain 'C' and resid 211 through 229 removed outlier: 3.698A pdb=" N CYS C 219 " --> pdb=" O LEU C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 247 removed outlier: 3.669A pdb=" N VAL C 237 " --> pdb=" O GLY C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 255 Processing helix chain 'C' and resid 257 through 273 removed outlier: 3.600A pdb=" N PHE C 264 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS C 269 " --> pdb=" O LEU C 265 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLU C 272 " --> pdb=" O GLY C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 282 Processing helix chain 'C' and resid 282 through 296 removed outlier: 3.845A pdb=" N MET C 286 " --> pdb=" O LEU C 282 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N THR C 291 " --> pdb=" O ALA C 287 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA C 294 " --> pdb=" O LEU C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 309 removed outlier: 3.774A pdb=" N VAL C 308 " --> pdb=" O ILE C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 320 removed outlier: 3.670A pdb=" N PHE C 316 " --> pdb=" O ASN C 312 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N MET C 318 " --> pdb=" O PHE C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 331 removed outlier: 3.845A pdb=" N MET C 329 " --> pdb=" O LEU C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 348 removed outlier: 3.590A pdb=" N GLU C 345 " --> pdb=" O PHE C 341 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU C 346 " --> pdb=" O ARG C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 359 removed outlier: 3.754A pdb=" N THR C 355 " --> pdb=" O ASP C 351 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N PHE C 357 " --> pdb=" O ARG C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 385 removed outlier: 3.657A pdb=" N ALA C 371 " --> pdb=" O MET C 367 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU C 372 " --> pdb=" O ASP C 368 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ALA C 375 " --> pdb=" O ALA C 371 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N VAL C 376 " --> pdb=" O LEU C 372 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N VAL C 379 " --> pdb=" O ALA C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 408 removed outlier: 3.727A pdb=" N ILE C 395 " --> pdb=" O ILE C 391 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR C 402 " --> pdb=" O SER C 398 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER C 405 " --> pdb=" O ALA C 401 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ILE C 406 " --> pdb=" O THR C 402 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY C 407 " --> pdb=" O SER C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 426 removed outlier: 3.582A pdb=" N THR C 418 " --> pdb=" O ALA C 414 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET C 419 " --> pdb=" O GLY C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 436 removed outlier: 3.876A pdb=" N THR C 434 " --> pdb=" O GLU C 431 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU C 435 " --> pdb=" O ASP C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 458 removed outlier: 4.614A pdb=" N ARG C 445 " --> pdb=" O TRP C 441 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N PHE C 446 " --> pdb=" O LEU C 442 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL C 450 " --> pdb=" O PHE C 446 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 160 through 161 Processing sheet with id=AA2, first strand: chain 'A' and resid 164 through 167 Processing sheet with id=AA3, first strand: chain 'B' and resid 160 through 161 Processing sheet with id=AA4, first strand: chain 'B' and resid 164 through 167 Processing sheet with id=AA5, first strand: chain 'C' and resid 160 through 161 Processing sheet with id=AA6, first strand: chain 'C' and resid 164 through 167 517 hydrogen bonds defined for protein. 1497 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: 2.84 Time building geometry restraints manager: 2.94 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: 2847 1.34 - 1.46: 1329 1.46 - 1.57: 5208 1.57 - 1.69: 0 1.69 - 1.81: 117 Bond restraints: 9501 Sorted by residual: bond pdb=" C5 CHT A 601 " pdb=" N1 CHT A 601 " ideal model delta sigma weight residual 1.509 1.456 0.053 2.00e-02 2.50e+03 7.10e+00 bond pdb=" C5 CHT B 601 " pdb=" N1 CHT B 601 " ideal model delta sigma weight residual 1.509 1.456 0.053 2.00e-02 2.50e+03 7.02e+00 bond pdb=" C5 CHT C 601 " pdb=" N1 CHT C 601 " ideal model delta sigma weight residual 1.509 1.456 0.053 2.00e-02 2.50e+03 7.01e+00 bond pdb=" C7 CHT C 601 " pdb=" N1 CHT C 601 " ideal model delta sigma weight residual 1.492 1.451 0.041 2.00e-02 2.50e+03 4.19e+00 bond pdb=" C8 CHT B 601 " pdb=" N1 CHT B 601 " ideal model delta sigma weight residual 1.492 1.451 0.041 2.00e-02 2.50e+03 4.11e+00 ... (remaining 9496 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 12254 1.84 - 3.67: 525 3.67 - 5.51: 73 5.51 - 7.34: 21 7.34 - 9.18: 21 Bond angle restraints: 12894 Sorted by residual: angle pdb=" C VAL C 120 " pdb=" N THR C 121 " pdb=" CA THR C 121 " ideal model delta sigma weight residual 121.70 127.94 -6.24 1.80e+00 3.09e-01 1.20e+01 angle pdb=" C VAL B 120 " pdb=" N THR B 121 " pdb=" CA THR B 121 " ideal model delta sigma weight residual 121.70 127.91 -6.21 1.80e+00 3.09e-01 1.19e+01 angle pdb=" C VAL A 120 " pdb=" N THR A 121 " pdb=" CA THR A 121 " ideal model delta sigma weight residual 121.70 127.91 -6.21 1.80e+00 3.09e-01 1.19e+01 angle pdb=" C ASP B 388 " pdb=" N LEU B 389 " pdb=" CA LEU B 389 " ideal model delta sigma weight residual 121.54 127.45 -5.91 1.91e+00 2.74e-01 9.59e+00 angle pdb=" C ASP A 388 " pdb=" N LEU A 389 " pdb=" CA LEU A 389 " ideal model delta sigma weight residual 121.54 127.44 -5.90 1.91e+00 2.74e-01 9.53e+00 ... (remaining 12889 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 5124 17.91 - 35.83: 429 35.83 - 53.74: 96 53.74 - 71.65: 21 71.65 - 89.56: 6 Dihedral angle restraints: 5676 sinusoidal: 2160 harmonic: 3516 Sorted by residual: dihedral pdb=" CA VAL B 462 " pdb=" C VAL B 462 " pdb=" N GLU B 463 " pdb=" CA GLU B 463 " ideal model delta harmonic sigma weight residual 180.00 160.81 19.19 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA THR A 247 " pdb=" C THR A 247 " pdb=" N MET A 248 " pdb=" CA MET A 248 " ideal model delta harmonic sigma weight residual 180.00 160.82 19.18 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA THR B 247 " pdb=" C THR B 247 " pdb=" N MET B 248 " pdb=" CA MET B 248 " ideal model delta harmonic sigma weight residual 180.00 160.82 19.18 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 5673 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1380 0.071 - 0.143: 210 0.143 - 0.214: 42 0.214 - 0.286: 3 0.286 - 0.357: 3 Chirality restraints: 1638 Sorted by residual: chirality pdb=" CB VAL B 36 " pdb=" CA VAL B 36 " pdb=" CG1 VAL B 36 " pdb=" CG2 VAL B 36 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.36 2.00e-01 2.50e+01 3.19e+00 chirality pdb=" CB VAL C 36 " pdb=" CA VAL C 36 " pdb=" CG1 VAL C 36 " pdb=" CG2 VAL C 36 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.36 2.00e-01 2.50e+01 3.17e+00 chirality pdb=" CB VAL A 36 " pdb=" CA VAL A 36 " pdb=" CG1 VAL A 36 " pdb=" CG2 VAL A 36 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.36 2.00e-01 2.50e+01 3.15e+00 ... (remaining 1635 not shown) Planarity restraints: 1563 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET B 258 " -0.043 5.00e-02 4.00e+02 6.53e-02 6.83e+00 pdb=" N PRO B 259 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO B 259 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 259 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A 258 " 0.043 5.00e-02 4.00e+02 6.53e-02 6.82e+00 pdb=" N PRO A 259 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO A 259 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 259 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET C 258 " 0.043 5.00e-02 4.00e+02 6.53e-02 6.82e+00 pdb=" N PRO C 259 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO C 259 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 259 " 0.037 5.00e-02 4.00e+02 ... (remaining 1560 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 3219 2.86 - 3.37: 8826 3.37 - 3.88: 14813 3.88 - 4.39: 18117 4.39 - 4.90: 31053 Nonbonded interactions: 76028 Sorted by model distance: nonbonded pdb=" OH TYR B 98 " pdb=" OD1 ASP B 455 " model vdw 2.351 3.040 nonbonded pdb=" OH TYR A 98 " pdb=" OD1 ASP A 455 " model vdw 2.351 3.040 nonbonded pdb=" OH TYR C 98 " pdb=" OD1 ASP C 455 " model vdw 2.352 3.040 nonbonded pdb=" OH TYR C 373 " pdb=" OD1 ASP C 440 " model vdw 2.369 3.040 nonbonded pdb=" OH TYR A 373 " pdb=" OD1 ASP A 440 " model vdw 2.369 3.040 ... (remaining 76023 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } 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: 1.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 24.790 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 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 : 0.006 0.055 9501 Z= 0.385 Angle : 0.934 9.177 12894 Z= 0.489 Chirality : 0.058 0.357 1638 Planarity : 0.008 0.065 1563 Dihedral : 14.719 89.564 3408 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 0.00 % Allowed : 13.51 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.78 (0.13), residues: 1209 helix: -4.59 (0.07), residues: 933 sheet: -3.31 (0.65), residues: 54 loop : -2.49 (0.33), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 441 HIS 0.001 0.001 HIS C 41 PHE 0.011 0.002 PHE C 159 TYR 0.012 0.002 TYR C 162 ARG 0.005 0.001 ARG A 353 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 1.085 Fit side-chains REVERT: A 149 MET cc_start: 0.8776 (mtt) cc_final: 0.8543 (mtp) REVERT: A 163 LYS cc_start: 0.8467 (tttm) cc_final: 0.8119 (tptp) REVERT: B 149 MET cc_start: 0.8755 (mtt) cc_final: 0.8534 (mtp) REVERT: B 163 LYS cc_start: 0.8481 (tttm) cc_final: 0.8244 (tmtt) REVERT: B 280 ARG cc_start: 0.6785 (ttt180) cc_final: 0.6295 (ttp-110) REVERT: B 306 PHE cc_start: 0.7504 (t80) cc_final: 0.7286 (t80) REVERT: B 307 ILE cc_start: 0.8214 (mm) cc_final: 0.8013 (mt) REVERT: C 149 MET cc_start: 0.8729 (mtt) cc_final: 0.8483 (mtp) REVERT: C 280 ARG cc_start: 0.6844 (ttt180) cc_final: 0.6472 (ttp-110) REVERT: C 307 ILE cc_start: 0.8236 (mm) cc_final: 0.7984 (mt) REVERT: C 342 ARG cc_start: 0.7488 (ttp80) cc_final: 0.7013 (ttp-170) REVERT: C 445 ARG cc_start: 0.7729 (mpt180) cc_final: 0.7518 (mpt180) outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 0.2483 time to fit residues: 57.9285 Evaluate side-chains 143 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 70 optimal weight: 4.9990 chunk 108 optimal weight: 0.1980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 ASN A 385 ASN A 413 GLN B 347 ASN B 385 ASN B 413 GLN C 347 ASN C 385 ASN C 413 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.146007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.102135 restraints weight = 10046.308| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 1.91 r_work: 0.2943 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2798 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9501 Z= 0.217 Angle : 0.594 6.576 12894 Z= 0.311 Chirality : 0.041 0.142 1638 Planarity : 0.006 0.042 1563 Dihedral : 5.351 19.903 1293 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.92 % Allowed : 15.16 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.49 (0.19), residues: 1209 helix: -2.71 (0.13), residues: 948 sheet: -3.12 (0.65), residues: 54 loop : -2.76 (0.35), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 441 HIS 0.001 0.000 HIS B 41 PHE 0.022 0.002 PHE A 306 TYR 0.006 0.001 TYR A 285 ARG 0.006 0.001 ARG A 353 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 155 time to evaluate : 1.062 Fit side-chains REVERT: A 163 LYS cc_start: 0.8740 (tttm) cc_final: 0.8387 (tmtt) REVERT: A 228 LYS cc_start: 0.7609 (mtpt) cc_final: 0.7368 (mttp) REVERT: A 262 ILE cc_start: 0.8006 (tt) cc_final: 0.7490 (pt) REVERT: B 149 MET cc_start: 0.9003 (mtt) cc_final: 0.8797 (mtp) REVERT: B 228 LYS cc_start: 0.7832 (mtpt) cc_final: 0.7584 (mttp) REVERT: B 280 ARG cc_start: 0.7026 (ttt180) cc_final: 0.6199 (ttp-110) REVERT: B 325 LEU cc_start: 0.6644 (tt) cc_final: 0.5763 (mp) REVERT: C 21 LEU cc_start: 0.6966 (OUTLIER) cc_final: 0.6706 (tp) REVERT: C 149 MET cc_start: 0.9020 (mtt) cc_final: 0.8807 (mtp) REVERT: C 228 LYS cc_start: 0.7858 (mtpt) cc_final: 0.7620 (mttp) REVERT: C 280 ARG cc_start: 0.7037 (ttt180) cc_final: 0.6294 (ttp-110) REVERT: C 298 ILE cc_start: 0.8571 (mm) cc_final: 0.8309 (mp) REVERT: C 325 LEU cc_start: 0.6656 (tt) cc_final: 0.5980 (mp) REVERT: C 342 ARG cc_start: 0.7011 (ttp80) cc_final: 0.6638 (ttp-170) outliers start: 30 outliers final: 17 residues processed: 175 average time/residue: 0.2451 time to fit residues: 57.6406 Evaluate side-chains 159 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 141 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 304 ILE Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 461 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 8 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 92 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 104 optimal weight: 0.9990 chunk 68 optimal weight: 10.0000 chunk 109 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 51 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.147918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.103207 restraints weight = 10125.271| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 2.00 r_work: 0.2936 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9501 Z= 0.164 Angle : 0.534 8.172 12894 Z= 0.274 Chirality : 0.039 0.127 1638 Planarity : 0.004 0.031 1563 Dihedral : 4.814 16.828 1293 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.04 % Allowed : 16.91 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.77 (0.23), residues: 1209 helix: -1.44 (0.16), residues: 957 sheet: -2.68 (0.69), residues: 54 loop : -2.46 (0.38), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 441 HIS 0.001 0.000 HIS B 41 PHE 0.020 0.001 PHE B 306 TYR 0.008 0.001 TYR C 285 ARG 0.008 0.001 ARG B 353 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 141 time to evaluate : 0.978 Fit side-chains REVERT: A 228 LYS cc_start: 0.7506 (mtpt) cc_final: 0.7290 (mttm) REVERT: A 260 LEU cc_start: 0.8025 (tp) cc_final: 0.7786 (tp) REVERT: B 41 HIS cc_start: 0.7237 (t70) cc_final: 0.6831 (m-70) REVERT: B 228 LYS cc_start: 0.7582 (mtpt) cc_final: 0.7184 (mttt) REVERT: B 280 ARG cc_start: 0.6946 (ttt180) cc_final: 0.6149 (ttp-110) REVERT: B 342 ARG cc_start: 0.6910 (ttp80) cc_final: 0.6612 (ttp80) REVERT: C 21 LEU cc_start: 0.6885 (OUTLIER) cc_final: 0.6608 (tp) REVERT: C 41 HIS cc_start: 0.7087 (t70) cc_final: 0.6597 (m-70) REVERT: C 149 MET cc_start: 0.8907 (mtt) cc_final: 0.8686 (mtp) REVERT: C 325 LEU cc_start: 0.6299 (tt) cc_final: 0.5660 (mp) REVERT: C 342 ARG cc_start: 0.7026 (ttp80) cc_final: 0.6689 (ttp-170) outliers start: 21 outliers final: 14 residues processed: 155 average time/residue: 0.2263 time to fit residues: 49.1975 Evaluate side-chains 152 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 137 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 304 ILE Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 461 ILE Chi-restraints excluded: chain C residue 462 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 69 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 96 optimal weight: 0.9990 chunk 118 optimal weight: 5.9990 chunk 95 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 36 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 chunk 67 optimal weight: 10.0000 chunk 31 optimal weight: 0.6980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 312 ASN C 312 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.145532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.100995 restraints weight = 10042.065| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 1.95 r_work: 0.2906 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9501 Z= 0.228 Angle : 0.545 8.207 12894 Z= 0.277 Chirality : 0.040 0.121 1638 Planarity : 0.004 0.028 1563 Dihedral : 4.739 16.725 1293 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.94 % Allowed : 18.27 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.24), residues: 1209 helix: -0.92 (0.17), residues: 945 sheet: -2.60 (0.69), residues: 54 loop : -2.13 (0.38), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 19 HIS 0.002 0.001 HIS B 41 PHE 0.017 0.002 PHE C 306 TYR 0.007 0.001 TYR B 285 ARG 0.007 0.000 ARG B 353 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 142 time to evaluate : 1.057 Fit side-chains REVERT: A 41 HIS cc_start: 0.6905 (t70) cc_final: 0.6620 (m-70) REVERT: A 228 LYS cc_start: 0.7523 (mtpt) cc_final: 0.7287 (mttp) REVERT: A 262 ILE cc_start: 0.7721 (tt) cc_final: 0.7287 (tt) REVERT: B 41 HIS cc_start: 0.7361 (t70) cc_final: 0.7058 (m-70) REVERT: B 228 LYS cc_start: 0.7630 (mtpt) cc_final: 0.7252 (mttt) REVERT: B 262 ILE cc_start: 0.7793 (tt) cc_final: 0.7519 (tt) REVERT: B 342 ARG cc_start: 0.6935 (ttp80) cc_final: 0.6610 (ttp80) REVERT: B 353 ARG cc_start: 0.5328 (mtm-85) cc_final: 0.5037 (mtm-85) REVERT: C 21 LEU cc_start: 0.6950 (OUTLIER) cc_final: 0.6668 (tp) REVERT: C 41 HIS cc_start: 0.7033 (t70) cc_final: 0.6731 (m-70) REVERT: C 149 MET cc_start: 0.8892 (mtt) cc_final: 0.8686 (mtp) REVERT: C 342 ARG cc_start: 0.6975 (ttp80) cc_final: 0.6474 (ttp-170) outliers start: 20 outliers final: 13 residues processed: 156 average time/residue: 0.2065 time to fit residues: 45.9427 Evaluate side-chains 148 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 134 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 411 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 33 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 116 optimal weight: 0.6980 chunk 38 optimal weight: 5.9990 chunk 34 optimal weight: 0.8980 chunk 55 optimal weight: 0.5980 chunk 87 optimal weight: 5.9990 chunk 79 optimal weight: 6.9990 chunk 59 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.147942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.102647 restraints weight = 9982.290| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 1.94 r_work: 0.2926 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9501 Z= 0.161 Angle : 0.503 7.138 12894 Z= 0.257 Chirality : 0.039 0.119 1638 Planarity : 0.003 0.027 1563 Dihedral : 4.492 17.272 1293 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.65 % Allowed : 19.24 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.25), residues: 1209 helix: -0.61 (0.17), residues: 960 sheet: -2.38 (0.72), residues: 54 loop : -1.92 (0.40), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 441 HIS 0.001 0.000 HIS B 41 PHE 0.011 0.001 PHE C 306 TYR 0.005 0.001 TYR B 285 ARG 0.005 0.000 ARG B 353 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 133 time to evaluate : 1.007 Fit side-chains REVERT: A 228 LYS cc_start: 0.7564 (mtpt) cc_final: 0.7174 (mttt) REVERT: A 262 ILE cc_start: 0.7794 (tt) cc_final: 0.7362 (tt) REVERT: B 228 LYS cc_start: 0.7617 (mtpt) cc_final: 0.7252 (mttt) REVERT: B 307 ILE cc_start: 0.7921 (mm) cc_final: 0.7688 (mt) REVERT: C 21 LEU cc_start: 0.6945 (OUTLIER) cc_final: 0.6639 (tp) REVERT: C 149 MET cc_start: 0.8904 (mtt) cc_final: 0.8703 (mtp) REVERT: C 342 ARG cc_start: 0.6971 (ttp80) cc_final: 0.6466 (ttp-170) outliers start: 17 outliers final: 12 residues processed: 147 average time/residue: 0.1940 time to fit residues: 41.7732 Evaluate side-chains 146 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 133 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 461 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 96 optimal weight: 0.8980 chunk 10 optimal weight: 0.1980 chunk 117 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 chunk 39 optimal weight: 0.1980 chunk 114 optimal weight: 0.8980 chunk 90 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 chunk 59 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 HIS C 41 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.149559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.104666 restraints weight = 9909.515| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 1.99 r_work: 0.2939 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9501 Z= 0.140 Angle : 0.486 6.390 12894 Z= 0.249 Chirality : 0.039 0.117 1638 Planarity : 0.003 0.025 1563 Dihedral : 4.297 18.095 1293 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.55 % Allowed : 19.83 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.25), residues: 1209 helix: -0.29 (0.18), residues: 960 sheet: -2.28 (0.74), residues: 54 loop : -1.69 (0.41), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 441 HIS 0.001 0.000 HIS C 296 PHE 0.010 0.001 PHE B 306 TYR 0.006 0.001 TYR C 285 ARG 0.003 0.000 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 133 time to evaluate : 1.213 Fit side-chains REVERT: A 228 LYS cc_start: 0.7556 (mtpt) cc_final: 0.7163 (mtmt) REVERT: A 262 ILE cc_start: 0.7828 (tt) cc_final: 0.7377 (tt) REVERT: A 286 MET cc_start: 0.8292 (mtm) cc_final: 0.8087 (mtt) REVERT: B 228 LYS cc_start: 0.7587 (mtpt) cc_final: 0.7235 (mttt) REVERT: B 307 ILE cc_start: 0.7968 (mm) cc_final: 0.7758 (mt) REVERT: B 353 ARG cc_start: 0.5852 (mtm180) cc_final: 0.5043 (mtm-85) REVERT: C 21 LEU cc_start: 0.6876 (OUTLIER) cc_final: 0.6585 (tp) outliers start: 16 outliers final: 14 residues processed: 145 average time/residue: 0.1910 time to fit residues: 40.7713 Evaluate side-chains 146 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 131 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 411 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 115 optimal weight: 0.0870 chunk 39 optimal weight: 2.9990 chunk 14 optimal weight: 0.0470 chunk 83 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 52 optimal weight: 0.4980 chunk 104 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 110 optimal weight: 0.2980 chunk 68 optimal weight: 8.9990 overall best weight: 0.3256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.152295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.106658 restraints weight = 10033.395| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 1.96 r_work: 0.2971 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9501 Z= 0.116 Angle : 0.467 5.952 12894 Z= 0.239 Chirality : 0.038 0.114 1638 Planarity : 0.003 0.025 1563 Dihedral : 4.078 17.983 1293 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.04 % Allowed : 19.73 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.26), residues: 1209 helix: 0.01 (0.18), residues: 978 sheet: -2.21 (0.76), residues: 54 loop : -1.57 (0.44), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP C 441 HIS 0.001 0.000 HIS C 41 PHE 0.009 0.001 PHE B 306 TYR 0.007 0.001 TYR C 285 ARG 0.005 0.000 ARG C 342 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 139 time to evaluate : 1.083 Fit side-chains REVERT: A 228 LYS cc_start: 0.7475 (mtpt) cc_final: 0.7088 (mtmt) REVERT: A 262 ILE cc_start: 0.7732 (tt) cc_final: 0.7279 (tt) REVERT: A 286 MET cc_start: 0.8271 (mtm) cc_final: 0.8053 (mtt) REVERT: A 367 MET cc_start: 0.6983 (mtm) cc_final: 0.6762 (mtm) REVERT: B 228 LYS cc_start: 0.7456 (mtpt) cc_final: 0.7111 (mtmt) REVERT: B 353 ARG cc_start: 0.5819 (mtm180) cc_final: 0.5034 (mtm-85) outliers start: 21 outliers final: 17 residues processed: 156 average time/residue: 0.1872 time to fit residues: 43.3494 Evaluate side-chains 151 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 134 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 411 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 69 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 106 optimal weight: 8.9990 chunk 18 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 86 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 chunk 43 optimal weight: 0.7980 chunk 116 optimal weight: 0.0060 chunk 42 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 overall best weight: 1.3602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.146416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.099661 restraints weight = 10159.777| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 1.87 r_work: 0.2918 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9501 Z= 0.236 Angle : 0.533 7.168 12894 Z= 0.266 Chirality : 0.041 0.128 1638 Planarity : 0.003 0.025 1563 Dihedral : 4.384 21.417 1293 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.94 % Allowed : 20.41 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.25), residues: 1209 helix: -0.04 (0.18), residues: 963 sheet: -2.22 (0.74), residues: 54 loop : -1.31 (0.42), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 19 HIS 0.001 0.000 HIS A 41 PHE 0.014 0.002 PHE C 240 TYR 0.007 0.001 TYR C 305 ARG 0.005 0.000 ARG C 342 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 134 time to evaluate : 0.984 Fit side-chains REVERT: A 262 ILE cc_start: 0.7841 (tt) cc_final: 0.7376 (tt) REVERT: B 163 LYS cc_start: 0.8608 (tttm) cc_final: 0.8404 (tptp) REVERT: B 228 LYS cc_start: 0.7609 (mtpt) cc_final: 0.7261 (mtmt) REVERT: B 353 ARG cc_start: 0.5947 (mtm180) cc_final: 0.5100 (mtm-85) REVERT: C 21 LEU cc_start: 0.7030 (OUTLIER) cc_final: 0.6734 (tp) REVERT: C 41 HIS cc_start: 0.7849 (m90) cc_final: 0.7632 (m90) outliers start: 20 outliers final: 17 residues processed: 150 average time/residue: 0.1907 time to fit residues: 41.8146 Evaluate side-chains 152 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 134 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 411 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 100 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 70 optimal weight: 0.6980 chunk 7 optimal weight: 0.5980 chunk 27 optimal weight: 0.3980 chunk 114 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.149025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.103963 restraints weight = 9991.373| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 1.95 r_work: 0.2913 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2766 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9501 Z= 0.152 Angle : 0.491 6.984 12894 Z= 0.248 Chirality : 0.039 0.118 1638 Planarity : 0.003 0.027 1563 Dihedral : 4.193 20.972 1293 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.04 % Allowed : 19.92 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.26), residues: 1209 helix: 0.11 (0.18), residues: 981 sheet: -2.20 (0.74), residues: 54 loop : -1.56 (0.45), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 441 HIS 0.001 0.000 HIS C 41 PHE 0.009 0.001 PHE C 240 TYR 0.006 0.001 TYR C 285 ARG 0.006 0.000 ARG C 342 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 135 time to evaluate : 1.006 Fit side-chains REVERT: A 163 LYS cc_start: 0.8744 (tttm) cc_final: 0.8501 (tptp) REVERT: A 262 ILE cc_start: 0.7703 (tt) cc_final: 0.7250 (tt) REVERT: A 286 MET cc_start: 0.8310 (mtm) cc_final: 0.8090 (mtt) REVERT: B 228 LYS cc_start: 0.7506 (mtpt) cc_final: 0.7135 (mtmt) REVERT: B 353 ARG cc_start: 0.5837 (mtm180) cc_final: 0.5020 (mtm-85) REVERT: B 432 ASP cc_start: 0.8644 (OUTLIER) cc_final: 0.8279 (m-30) REVERT: C 21 LEU cc_start: 0.6815 (OUTLIER) cc_final: 0.6531 (tp) REVERT: C 41 HIS cc_start: 0.7871 (m90) cc_final: 0.7657 (m90) outliers start: 21 outliers final: 18 residues processed: 151 average time/residue: 0.1932 time to fit residues: 42.8192 Evaluate side-chains 154 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 134 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 411 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 12 optimal weight: 0.5980 chunk 21 optimal weight: 3.9990 chunk 69 optimal weight: 0.0570 chunk 20 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 45 optimal weight: 0.5980 chunk 108 optimal weight: 10.0000 chunk 83 optimal weight: 0.0870 chunk 56 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 overall best weight: 0.3876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.152168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.107957 restraints weight = 10084.420| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 2.01 r_work: 0.2953 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9501 Z= 0.123 Angle : 0.477 7.173 12894 Z= 0.241 Chirality : 0.038 0.116 1638 Planarity : 0.003 0.024 1563 Dihedral : 3.994 19.645 1293 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.65 % Allowed : 20.41 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.26), residues: 1209 helix: 0.39 (0.18), residues: 981 sheet: -2.20 (0.75), residues: 54 loop : -1.51 (0.45), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 441 HIS 0.001 0.000 HIS C 41 PHE 0.009 0.001 PHE B 306 TYR 0.006 0.001 TYR C 285 ARG 0.006 0.000 ARG C 342 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 137 time to evaluate : 1.096 Fit side-chains REVERT: A 163 LYS cc_start: 0.8797 (tttm) cc_final: 0.8553 (tptp) REVERT: A 262 ILE cc_start: 0.7777 (tt) cc_final: 0.7324 (tt) REVERT: A 286 MET cc_start: 0.8288 (mtm) cc_final: 0.8064 (mtt) REVERT: B 228 LYS cc_start: 0.7471 (mtpt) cc_final: 0.7155 (mtmt) REVERT: B 329 MET cc_start: 0.5488 (mmm) cc_final: 0.5275 (mmm) REVERT: B 353 ARG cc_start: 0.5888 (mtm180) cc_final: 0.5042 (mtm-85) REVERT: B 432 ASP cc_start: 0.8616 (OUTLIER) cc_final: 0.8284 (m-30) outliers start: 17 outliers final: 16 residues processed: 151 average time/residue: 0.1897 time to fit residues: 42.1385 Evaluate side-chains 146 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 129 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 411 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 54 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 chunk 113 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 63 optimal weight: 0.0980 chunk 110 optimal weight: 7.9990 chunk 86 optimal weight: 3.9990 chunk 90 optimal weight: 0.2980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.149683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.104337 restraints weight = 9954.278| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 1.98 r_work: 0.2916 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9501 Z= 0.169 Angle : 0.506 7.576 12894 Z= 0.254 Chirality : 0.039 0.117 1638 Planarity : 0.003 0.025 1563 Dihedral : 4.085 20.517 1293 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.75 % Allowed : 20.51 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.26), residues: 1209 helix: 0.36 (0.18), residues: 984 sheet: -2.15 (0.75), residues: 54 loop : -1.44 (0.46), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 441 HIS 0.001 0.000 HIS C 296 PHE 0.011 0.001 PHE A 240 TYR 0.005 0.001 TYR C 305 ARG 0.006 0.000 ARG C 342 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5060.04 seconds wall clock time: 90 minutes 17.79 seconds (5417.79 seconds total)