Starting phenix.real_space_refine on Wed Sep 25 02:37:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x2l_22011/09_2024/6x2l_22011.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x2l_22011/09_2024/6x2l_22011.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x2l_22011/09_2024/6x2l_22011.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x2l_22011/09_2024/6x2l_22011.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x2l_22011/09_2024/6x2l_22011.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x2l_22011/09_2024/6x2l_22011.cif" } resolution = 2.85 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 69 5.16 5 C 6159 2.51 5 N 1491 2.21 5 O 1677 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 9396 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3132 Classifications: {'peptide': 411} Link IDs: {'PTRANS': 11, 'TRANS': 399} Chain breaks: 2 Restraints were copied for chains: C, B Time building chain proxies: 5.68, per 1000 atoms: 0.60 Number of scatterers: 9396 At special positions: 0 Unit cell: (113.984, 109.824, 82.368, 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 69 16.00 O 1677 8.00 N 1491 7.00 C 6159 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: 2.25 Conformation dependent library (CDL) restraints added in 1.2 seconds 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2280 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 6 sheets defined 81.3% alpha, 1.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid 21 through 40 removed outlier: 3.613A pdb=" N ALA A 27 " --> pdb=" O SER A 23 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARG A 39 " --> pdb=" O GLY A 35 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU A 40 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 53 removed outlier: 3.739A pdb=" N ALA A 53 " --> pdb=" O LYS A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 86 removed outlier: 3.580A pdb=" N LEU A 59 " --> pdb=" O PRO A 55 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS A 64 " --> pdb=" O MET A 60 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE A 66 " --> pdb=" O MET A 62 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE A 67 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N LEU A 68 " --> pdb=" O LYS A 64 " (cutoff:3.500A) Proline residue: A 69 - end of helix removed outlier: 3.761A pdb=" N SER A 84 " --> pdb=" O ALA A 80 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL A 86 " --> pdb=" O LEU A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 117 removed outlier: 3.565A pdb=" N VAL A 95 " --> pdb=" O GLY A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 150 removed outlier: 3.554A pdb=" N MET A 142 " --> pdb=" O THR A 138 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE A 146 " --> pdb=" O MET A 142 " (cutoff:3.500A) removed outlier: 3.531A 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 230 removed outlier: 3.517A pdb=" N GLY A 227 " --> pdb=" O GLY A 223 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLY A 230 " --> pdb=" O ILE A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 273 Proline residue: A 259 - end of helix removed outlier: 3.631A pdb=" N PHE A 264 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS A 269 " --> pdb=" O LEU A 265 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU A 272 " --> pdb=" O GLY A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 299 removed outlier: 3.679A pdb=" N THR A 291 " --> pdb=" O ALA A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 309 removed outlier: 3.623A pdb=" N VAL A 308 " --> pdb=" O ILE A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 319 removed outlier: 3.608A pdb=" N PHE A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 330 removed outlier: 3.548A pdb=" N THR A 326 " --> pdb=" O GLN A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 349 removed outlier: 4.158A pdb=" N ARG A 342 " --> pdb=" O PRO A 338 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ASN A 347 " --> pdb=" O CYS A 343 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLN A 349 " --> pdb=" O GLU A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 363 removed outlier: 4.179A pdb=" N PHE A 357 " --> pdb=" O ARG A 353 " (cutoff:3.500A) Proline residue: A 360 - end of helix Processing helix chain 'A' and resid 367 through 385 removed outlier: 3.595A pdb=" N VAL A 379 " --> pdb=" O ALA A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 401 removed outlier: 3.696A pdb=" N THR A 396 " --> pdb=" O GLY A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 406 removed outlier: 3.527A pdb=" N SER A 405 " --> pdb=" O THR A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 427 removed outlier: 3.592A pdb=" N MET A 419 " --> pdb=" O GLY A 415 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL A 426 " --> pdb=" O VAL A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 431 No H-bonds generated for 'chain 'A' and resid 429 through 431' Processing helix chain 'A' and resid 432 through 438 removed outlier: 3.995A pdb=" N ILE A 436 " --> pdb=" O ASP A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 466 removed outlier: 3.594A pdb=" N LEU A 443 " --> pdb=" O VAL A 439 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ARG A 445 " --> pdb=" O TRP A 441 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N PHE A 446 " --> pdb=" O LEU A 442 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N MET A 449 " --> pdb=" O ARG A 445 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASP A 455 " --> pdb=" O ASN A 451 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR A 459 " --> pdb=" O ASP A 455 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLY A 460 " --> pdb=" O ALA A 456 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS A 464 " --> pdb=" O GLY A 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 40 removed outlier: 3.613A pdb=" N ALA B 27 " --> pdb=" O SER B 23 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARG B 39 " --> pdb=" O GLY B 35 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU B 40 " --> pdb=" O VAL B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 53 removed outlier: 3.739A pdb=" N ALA B 53 " --> pdb=" O LYS B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 86 removed outlier: 3.580A pdb=" N LEU B 59 " --> pdb=" O PRO B 55 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS B 64 " --> pdb=" O MET B 60 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE B 66 " --> pdb=" O MET B 62 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE B 67 " --> pdb=" O LEU B 63 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N LEU B 68 " --> pdb=" O LYS B 64 " (cutoff:3.500A) Proline residue: B 69 - end of helix removed outlier: 3.761A pdb=" N SER B 84 " --> pdb=" O ALA B 80 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL B 86 " --> pdb=" O LEU B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 117 removed outlier: 3.565A pdb=" N VAL B 95 " --> pdb=" O GLY B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 150 removed outlier: 3.554A pdb=" N MET B 142 " --> pdb=" O THR B 138 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE B 146 " --> pdb=" O MET B 142 " (cutoff:3.500A) removed outlier: 3.531A 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 230 removed outlier: 3.518A pdb=" N GLY B 227 " --> pdb=" O GLY B 223 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLY B 230 " --> pdb=" O ILE B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 273 Proline residue: B 259 - end of helix removed outlier: 3.631A pdb=" N PHE B 264 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS B 269 " --> pdb=" O LEU B 265 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU B 272 " --> pdb=" O GLY B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 299 removed outlier: 3.679A pdb=" N THR B 291 " --> pdb=" O ALA B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 309 removed outlier: 3.624A pdb=" N VAL B 308 " --> pdb=" O ILE B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 319 removed outlier: 3.608A pdb=" N PHE B 316 " --> pdb=" O ASN B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 330 removed outlier: 3.549A pdb=" N THR B 326 " --> pdb=" O GLN B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 349 removed outlier: 4.158A pdb=" N ARG B 342 " --> pdb=" O PRO B 338 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ASN B 347 " --> pdb=" O CYS B 343 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN B 349 " --> pdb=" O GLU B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 363 removed outlier: 4.179A pdb=" N PHE B 357 " --> pdb=" O ARG B 353 " (cutoff:3.500A) Proline residue: B 360 - end of helix Processing helix chain 'B' and resid 367 through 385 removed outlier: 3.595A pdb=" N VAL B 379 " --> pdb=" O ALA B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 401 removed outlier: 3.696A pdb=" N THR B 396 " --> pdb=" O GLY B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 406 removed outlier: 3.528A pdb=" N SER B 405 " --> pdb=" O THR B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 427 removed outlier: 3.592A pdb=" N MET B 419 " --> pdb=" O GLY B 415 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL B 426 " --> pdb=" O VAL B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 431 No H-bonds generated for 'chain 'B' and resid 429 through 431' Processing helix chain 'B' and resid 432 through 438 removed outlier: 3.994A pdb=" N ILE B 436 " --> pdb=" O ASP B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 466 removed outlier: 3.595A pdb=" N LEU B 443 " --> pdb=" O VAL B 439 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ARG B 445 " --> pdb=" O TRP B 441 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N PHE B 446 " --> pdb=" O LEU B 442 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N MET B 449 " --> pdb=" O ARG B 445 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASP B 455 " --> pdb=" O ASN B 451 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR B 459 " --> pdb=" O ASP B 455 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLY B 460 " --> pdb=" O ALA B 456 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS B 464 " --> pdb=" O GLY B 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 40 removed outlier: 3.613A pdb=" N ALA C 27 " --> pdb=" O SER C 23 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARG C 39 " --> pdb=" O GLY C 35 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU C 40 " --> pdb=" O VAL C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 53 removed outlier: 3.739A pdb=" N ALA C 53 " --> pdb=" O LYS C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 86 removed outlier: 3.579A pdb=" N LEU C 59 " --> pdb=" O PRO C 55 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS C 64 " --> pdb=" O MET C 60 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE C 66 " --> pdb=" O MET C 62 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE C 67 " --> pdb=" O LEU C 63 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N LEU C 68 " --> pdb=" O LYS C 64 " (cutoff:3.500A) Proline residue: C 69 - end of helix removed outlier: 3.762A pdb=" N SER C 84 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL C 86 " --> pdb=" O LEU C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 117 removed outlier: 3.565A pdb=" N VAL C 95 " --> pdb=" O GLY C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 150 removed outlier: 3.555A pdb=" N MET C 142 " --> pdb=" O THR C 138 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE C 146 " --> pdb=" O MET C 142 " (cutoff:3.500A) removed outlier: 3.531A 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 230 removed outlier: 3.518A pdb=" N GLY C 227 " --> pdb=" O GLY C 223 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLY C 230 " --> pdb=" O ILE C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 273 Proline residue: C 259 - end of helix removed outlier: 3.631A pdb=" N PHE C 264 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS C 269 " --> pdb=" O LEU C 265 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU C 272 " --> pdb=" O GLY C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 299 removed outlier: 3.678A pdb=" N THR C 291 " --> pdb=" O ALA C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 309 removed outlier: 3.622A pdb=" N VAL C 308 " --> pdb=" O ILE C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 319 removed outlier: 3.608A pdb=" N PHE C 316 " --> pdb=" O ASN C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 330 removed outlier: 3.548A pdb=" N THR C 326 " --> pdb=" O GLN C 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 349 removed outlier: 4.158A pdb=" N ARG C 342 " --> pdb=" O PRO C 338 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ASN C 347 " --> pdb=" O CYS C 343 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLN C 349 " --> pdb=" O GLU C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 363 removed outlier: 4.179A pdb=" N PHE C 357 " --> pdb=" O ARG C 353 " (cutoff:3.500A) Proline residue: C 360 - end of helix Processing helix chain 'C' and resid 367 through 385 removed outlier: 3.595A pdb=" N VAL C 379 " --> pdb=" O ALA C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 401 removed outlier: 3.696A pdb=" N THR C 396 " --> pdb=" O GLY C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 406 removed outlier: 3.527A pdb=" N SER C 405 " --> pdb=" O THR C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 427 removed outlier: 3.592A pdb=" N MET C 419 " --> pdb=" O GLY C 415 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL C 426 " --> pdb=" O VAL C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 432 removed outlier: 3.589A pdb=" N ASP C 432 " --> pdb=" O PRO C 429 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 429 through 432' Processing helix chain 'C' and resid 433 through 438 Processing helix chain 'C' and resid 439 through 466 removed outlier: 3.594A pdb=" N LEU C 443 " --> pdb=" O VAL C 439 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ARG C 445 " --> pdb=" O TRP C 441 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N PHE C 446 " --> pdb=" O LEU C 442 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N MET C 449 " --> pdb=" O ARG C 445 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP C 455 " --> pdb=" O ASN C 451 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR C 459 " --> pdb=" O ASP C 455 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLY C 460 " --> pdb=" O ALA C 456 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS C 464 " --> pdb=" O GLY C 460 " (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 167 624 hydrogen bonds defined for protein. 1836 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: 2.53 Time building geometry restraints manager: 2.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1670 1.32 - 1.45: 2168 1.45 - 1.57: 5573 1.57 - 1.70: 0 1.70 - 1.82: 123 Bond restraints: 9534 Sorted by residual: bond pdb=" C MET C 419 " pdb=" O MET C 419 " ideal model delta sigma weight residual 1.237 1.200 0.037 1.19e-02 7.06e+03 9.55e+00 bond pdb=" C MET A 419 " pdb=" O MET A 419 " ideal model delta sigma weight residual 1.237 1.200 0.036 1.19e-02 7.06e+03 9.28e+00 bond pdb=" C MET B 419 " pdb=" O MET B 419 " ideal model delta sigma weight residual 1.237 1.201 0.036 1.19e-02 7.06e+03 9.09e+00 bond pdb=" N LEU B 372 " pdb=" CA LEU B 372 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.23e-02 6.61e+03 5.41e+00 bond pdb=" N LEU A 372 " pdb=" CA LEU A 372 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.23e-02 6.61e+03 5.20e+00 ... (remaining 9529 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 12242 1.89 - 3.77: 591 3.77 - 5.66: 73 5.66 - 7.55: 18 7.55 - 9.44: 12 Bond angle restraints: 12936 Sorted by residual: angle pdb=" C ASP C 388 " pdb=" N LEU C 389 " pdb=" CA LEU C 389 " ideal model delta sigma weight residual 121.54 128.88 -7.34 1.91e+00 2.74e-01 1.48e+01 angle pdb=" C ASP A 388 " pdb=" N LEU A 389 " pdb=" CA LEU A 389 " ideal model delta sigma weight residual 121.54 128.87 -7.33 1.91e+00 2.74e-01 1.47e+01 angle pdb=" C ASP B 388 " pdb=" N LEU B 389 " pdb=" CA LEU B 389 " ideal model delta sigma weight residual 121.54 128.84 -7.30 1.91e+00 2.74e-01 1.46e+01 angle pdb=" CB MET C 473 " pdb=" CG MET C 473 " pdb=" SD MET C 473 " ideal model delta sigma weight residual 112.70 103.26 9.44 3.00e+00 1.11e-01 9.89e+00 angle pdb=" CB MET A 473 " pdb=" CG MET A 473 " pdb=" SD MET A 473 " ideal model delta sigma weight residual 112.70 103.30 9.40 3.00e+00 1.11e-01 9.82e+00 ... (remaining 12931 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.78: 5150 16.78 - 33.56: 430 33.56 - 50.35: 96 50.35 - 67.13: 21 67.13 - 83.91: 9 Dihedral angle restraints: 5706 sinusoidal: 2172 harmonic: 3534 Sorted by residual: dihedral pdb=" CA LEU A 384 " pdb=" C LEU A 384 " pdb=" N ASN A 385 " pdb=" CA ASN A 385 " ideal model delta harmonic sigma weight residual 180.00 160.52 19.48 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA LEU C 384 " pdb=" C LEU C 384 " pdb=" N ASN C 385 " pdb=" CA ASN C 385 " ideal model delta harmonic sigma weight residual 180.00 160.53 19.47 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA LEU B 384 " pdb=" C LEU B 384 " pdb=" N ASN B 385 " pdb=" CA ASN B 385 " ideal model delta harmonic sigma weight residual 180.00 160.54 19.46 0 5.00e+00 4.00e-02 1.52e+01 ... (remaining 5703 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 847 0.039 - 0.077: 565 0.077 - 0.116: 154 0.116 - 0.154: 59 0.154 - 0.193: 19 Chirality restraints: 1644 Sorted by residual: chirality pdb=" CB VAL C 433 " pdb=" CA VAL C 433 " pdb=" CG1 VAL C 433 " pdb=" CG2 VAL C 433 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 9.28e-01 chirality pdb=" CB VAL B 433 " pdb=" CA VAL B 433 " pdb=" CG1 VAL B 433 " pdb=" CG2 VAL B 433 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 9.04e-01 chirality pdb=" CB VAL A 433 " pdb=" CA VAL A 433 " pdb=" CG1 VAL A 433 " pdb=" CG2 VAL A 433 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 8.92e-01 ... (remaining 1641 not shown) Planarity restraints: 1572 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 301 " -0.049 5.00e-02 4.00e+02 7.26e-02 8.43e+00 pdb=" N PRO C 302 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO C 302 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 302 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 301 " -0.049 5.00e-02 4.00e+02 7.25e-02 8.40e+00 pdb=" N PRO B 302 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO B 302 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 302 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 301 " -0.049 5.00e-02 4.00e+02 7.25e-02 8.40e+00 pdb=" N PRO A 302 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO A 302 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 302 " -0.041 5.00e-02 4.00e+02 ... (remaining 1569 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 60 2.64 - 3.21: 8450 3.21 - 3.77: 14468 3.77 - 4.34: 20729 4.34 - 4.90: 33676 Nonbonded interactions: 77383 Sorted by model distance: nonbonded pdb=" N GLN B 413 " pdb=" OE1 GLN B 413 " model vdw 2.078 3.120 nonbonded pdb=" N GLN A 413 " pdb=" OE1 GLN A 413 " model vdw 2.079 3.120 nonbonded pdb=" N GLN C 413 " pdb=" OE1 GLN C 413 " model vdw 2.079 3.120 nonbonded pdb=" O SER A 331 " pdb=" OG SER A 331 " model vdw 2.339 3.040 nonbonded pdb=" O SER B 331 " pdb=" OG SER B 331 " model vdw 2.339 3.040 ... (remaining 77378 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 'B' selection = chain 'C' } 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: 1.750 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: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 22.810 Find NCS groups from input model: 0.260 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:11.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.075 9534 Z= 0.585 Angle : 0.960 9.435 12936 Z= 0.513 Chirality : 0.056 0.193 1644 Planarity : 0.007 0.073 1572 Dihedral : 13.682 83.912 3426 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % 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: -6.46 (0.14), residues: 1215 helix: -4.23 (0.07), residues: 975 sheet: -2.87 (0.80), residues: 54 loop : -2.72 (0.35), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 276 HIS 0.003 0.001 HIS B 41 PHE 0.021 0.003 PHE B 341 TYR 0.020 0.003 TYR C 373 ARG 0.006 0.001 ARG B 353 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 200 time to evaluate : 1.125 Fit side-chains REVERT: A 93 ARG cc_start: 0.8160 (mtt180) cc_final: 0.7933 (mtm-85) REVERT: A 200 TYR cc_start: 0.8079 (m-80) cc_final: 0.7821 (m-80) REVERT: A 322 GLN cc_start: 0.8018 (tp40) cc_final: 0.7739 (mm-40) REVERT: A 352 LYS cc_start: 0.8364 (tmtm) cc_final: 0.7721 (mtmt) REVERT: A 393 GLN cc_start: 0.8605 (mt0) cc_final: 0.8184 (mt0) REVERT: B 200 TYR cc_start: 0.8220 (m-80) cc_final: 0.7731 (m-10) REVERT: B 248 MET cc_start: 0.8289 (tpp) cc_final: 0.8083 (tpt) REVERT: B 280 ARG cc_start: 0.8040 (ttp80) cc_final: 0.7807 (tmm160) REVERT: C 200 TYR cc_start: 0.8208 (m-80) cc_final: 0.7746 (m-10) REVERT: C 248 MET cc_start: 0.8260 (tpp) cc_final: 0.8023 (mmt) REVERT: C 316 PHE cc_start: 0.8052 (t80) cc_final: 0.7805 (t80) REVERT: C 322 GLN cc_start: 0.8040 (tp40) cc_final: 0.7667 (mm110) outliers start: 0 outliers final: 2 residues processed: 200 average time/residue: 1.2476 time to fit residues: 266.2401 Evaluate side-chains 148 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 146 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain C residue 461 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 0.8980 chunk 93 optimal weight: 0.6980 chunk 51 optimal weight: 9.9990 chunk 31 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 96 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 71 optimal weight: 0.0170 chunk 111 optimal weight: 0.9990 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN B 85 ASN C 85 ASN C 156 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9534 Z= 0.167 Angle : 0.559 8.084 12936 Z= 0.292 Chirality : 0.038 0.130 1644 Planarity : 0.005 0.037 1572 Dihedral : 4.546 18.591 1297 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.74 % Allowed : 10.34 % Favored : 87.92 % 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: -2.96 (0.20), residues: 1215 helix: -1.59 (0.14), residues: 960 sheet: -3.04 (0.69), residues: 54 loop : -2.34 (0.38), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 441 HIS 0.001 0.000 HIS B 296 PHE 0.015 0.002 PHE B 218 TYR 0.010 0.001 TYR B 373 ARG 0.005 0.000 ARG A 353 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 178 time to evaluate : 0.969 Fit side-chains REVERT: A 248 MET cc_start: 0.8080 (OUTLIER) cc_final: 0.7691 (mmt) REVERT: A 322 GLN cc_start: 0.7879 (tp40) cc_final: 0.7546 (mm-40) REVERT: A 329 MET cc_start: 0.6349 (mmm) cc_final: 0.5961 (mtt) REVERT: B 200 TYR cc_start: 0.8047 (m-80) cc_final: 0.7640 (m-10) REVERT: B 473 MET cc_start: 0.7120 (ttt) cc_final: 0.6831 (mtp) REVERT: C 248 MET cc_start: 0.8057 (tpp) cc_final: 0.7627 (mmt) REVERT: C 280 ARG cc_start: 0.7788 (OUTLIER) cc_final: 0.7092 (ttm170) REVERT: C 322 GLN cc_start: 0.7820 (tp40) cc_final: 0.7439 (mm-40) outliers start: 18 outliers final: 6 residues processed: 188 average time/residue: 1.0002 time to fit residues: 203.3898 Evaluate side-chains 149 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 141 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 248 MET Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain C residue 205 MET Chi-restraints excluded: chain C residue 280 ARG Chi-restraints excluded: chain C residue 373 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 62 optimal weight: 0.9980 chunk 34 optimal weight: 9.9990 chunk 92 optimal weight: 4.9990 chunk 76 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 111 optimal weight: 1.9990 chunk 120 optimal weight: 0.8980 chunk 99 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS A 156 GLN B 85 ASN B 312 ASN B 393 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9534 Z= 0.213 Angle : 0.539 7.001 12936 Z= 0.277 Chirality : 0.039 0.126 1644 Planarity : 0.004 0.032 1572 Dihedral : 4.157 18.000 1293 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.00 % Allowed : 13.72 % Favored : 83.29 % 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: -1.11 (0.23), residues: 1215 helix: -0.17 (0.16), residues: 963 sheet: -2.54 (0.71), residues: 54 loop : -2.38 (0.39), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 19 HIS 0.001 0.000 HIS C 296 PHE 0.015 0.002 PHE C 218 TYR 0.007 0.001 TYR B 257 ARG 0.004 0.000 ARG A 353 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 160 time to evaluate : 1.079 Fit side-chains REVERT: A 248 MET cc_start: 0.8113 (OUTLIER) cc_final: 0.7772 (mmp) REVERT: A 276 TRP cc_start: 0.7250 (m100) cc_final: 0.7040 (m-90) REVERT: A 393 GLN cc_start: 0.8510 (mt0) cc_final: 0.8139 (mt0) REVERT: B 75 MET cc_start: 0.8569 (mmm) cc_final: 0.8267 (tpp) REVERT: B 200 TYR cc_start: 0.8076 (m-80) cc_final: 0.7687 (m-10) REVERT: B 473 MET cc_start: 0.7116 (ttt) cc_final: 0.6843 (mtp) REVERT: C 248 MET cc_start: 0.8067 (tpp) cc_final: 0.7600 (mmt) REVERT: C 280 ARG cc_start: 0.7783 (OUTLIER) cc_final: 0.7093 (ttm170) REVERT: C 322 GLN cc_start: 0.7857 (tp40) cc_final: 0.7471 (mm-40) REVERT: C 393 GLN cc_start: 0.8592 (mt0) cc_final: 0.8390 (mt0) outliers start: 31 outliers final: 13 residues processed: 175 average time/residue: 1.2955 time to fit residues: 243.1275 Evaluate side-chains 160 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 145 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 248 MET Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 373 TYR Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 205 MET Chi-restraints excluded: chain C residue 280 ARG Chi-restraints excluded: chain C residue 388 ASP Chi-restraints excluded: chain C residue 411 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 110 optimal weight: 9.9990 chunk 84 optimal weight: 9.9990 chunk 58 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 75 optimal weight: 4.9990 chunk 112 optimal weight: 4.9990 chunk 118 optimal weight: 0.6980 chunk 106 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 99 optimal weight: 0.7980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN B 85 ASN C 85 ASN C 312 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9534 Z= 0.188 Angle : 0.509 6.494 12936 Z= 0.261 Chirality : 0.038 0.125 1644 Planarity : 0.004 0.034 1572 Dihedral : 3.975 17.930 1293 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.80 % Allowed : 15.36 % Favored : 81.84 % 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: -0.06 (0.24), residues: 1215 helix: 0.60 (0.17), residues: 951 sheet: -2.35 (0.71), residues: 54 loop : -1.97 (0.38), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 19 HIS 0.000 0.000 HIS A 296 PHE 0.015 0.001 PHE C 316 TYR 0.007 0.001 TYR C 373 ARG 0.003 0.000 ARG A 353 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 155 time to evaluate : 1.060 Fit side-chains REVERT: A 220 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8670 (tp) REVERT: A 248 MET cc_start: 0.8096 (OUTLIER) cc_final: 0.7766 (mmp) REVERT: A 276 TRP cc_start: 0.7232 (m100) cc_final: 0.7030 (m-90) REVERT: A 393 GLN cc_start: 0.8504 (mt0) cc_final: 0.8126 (mt0) REVERT: B 200 TYR cc_start: 0.8113 (m-80) cc_final: 0.7736 (m-10) REVERT: B 303 LEU cc_start: 0.8335 (tp) cc_final: 0.7954 (tt) REVERT: B 473 MET cc_start: 0.7111 (ttt) cc_final: 0.6839 (mtp) REVERT: C 248 MET cc_start: 0.8033 (tpp) cc_final: 0.7594 (mmt) REVERT: C 280 ARG cc_start: 0.7798 (OUTLIER) cc_final: 0.7125 (ttm170) REVERT: C 322 GLN cc_start: 0.7832 (tp40) cc_final: 0.7434 (mm-40) REVERT: C 342 ARG cc_start: 0.7537 (ppt170) cc_final: 0.7317 (ppt90) REVERT: C 463 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7446 (tm-30) outliers start: 29 outliers final: 12 residues processed: 170 average time/residue: 1.1340 time to fit residues: 207.0059 Evaluate side-chains 153 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 137 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 248 MET Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 373 TYR Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 205 MET Chi-restraints excluded: chain C residue 280 ARG Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 463 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 67 optimal weight: 10.0000 chunk 1 optimal weight: 4.9990 chunk 88 optimal weight: 0.4980 chunk 49 optimal weight: 0.6980 chunk 101 optimal weight: 1.9990 chunk 82 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 60 optimal weight: 0.5980 chunk 106 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 40 optimal weight: 7.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN B 85 ASN B 393 GLN C 85 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9534 Z= 0.164 Angle : 0.496 5.894 12936 Z= 0.254 Chirality : 0.038 0.124 1644 Planarity : 0.003 0.030 1572 Dihedral : 3.815 18.269 1293 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.29 % Allowed : 15.75 % Favored : 80.97 % 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: 0.58 (0.25), residues: 1215 helix: 1.03 (0.17), residues: 963 sheet: -2.08 (0.75), residues: 54 loop : -1.81 (0.40), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 19 HIS 0.000 0.000 HIS A 296 PHE 0.013 0.001 PHE A 218 TYR 0.008 0.001 TYR C 373 ARG 0.003 0.000 ARG A 353 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 157 time to evaluate : 1.079 Fit side-chains REVERT: A 220 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8672 (tp) REVERT: A 248 MET cc_start: 0.8081 (OUTLIER) cc_final: 0.7754 (mmp) REVERT: A 342 ARG cc_start: 0.7734 (ppt90) cc_final: 0.7508 (ppt90) REVERT: A 393 GLN cc_start: 0.8484 (mt0) cc_final: 0.8084 (mt0) REVERT: A 463 GLU cc_start: 0.7528 (tm-30) cc_final: 0.7251 (tt0) REVERT: B 75 MET cc_start: 0.8490 (mmm) cc_final: 0.8203 (tpp) REVERT: B 200 TYR cc_start: 0.8102 (m-80) cc_final: 0.7723 (m-10) REVERT: B 303 LEU cc_start: 0.8359 (tp) cc_final: 0.8009 (tt) REVERT: B 320 MET cc_start: 0.7703 (OUTLIER) cc_final: 0.7443 (mmt) REVERT: B 473 MET cc_start: 0.7122 (ttt) cc_final: 0.6849 (mtp) REVERT: C 248 MET cc_start: 0.8034 (tpp) cc_final: 0.7566 (mmt) REVERT: C 303 LEU cc_start: 0.8337 (tp) cc_final: 0.8018 (tt) REVERT: C 322 GLN cc_start: 0.7797 (tp40) cc_final: 0.7404 (mm-40) REVERT: C 342 ARG cc_start: 0.7547 (ppt170) cc_final: 0.7328 (ppt90) REVERT: C 463 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.7450 (tm-30) outliers start: 34 outliers final: 15 residues processed: 171 average time/residue: 1.1323 time to fit residues: 208.2407 Evaluate side-chains 166 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 147 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 248 MET Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 320 MET Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 463 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 107 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 119 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN B 85 ASN B 393 GLN C 85 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9534 Z= 0.211 Angle : 0.521 5.778 12936 Z= 0.265 Chirality : 0.039 0.125 1644 Planarity : 0.003 0.031 1572 Dihedral : 3.862 18.253 1293 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.67 % Allowed : 16.23 % Favored : 80.10 % 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: 0.84 (0.25), residues: 1215 helix: 1.17 (0.17), residues: 969 sheet: -1.86 (0.77), residues: 54 loop : -1.61 (0.41), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 276 HIS 0.001 0.000 HIS C 296 PHE 0.014 0.001 PHE A 218 TYR 0.009 0.001 TYR C 373 ARG 0.002 0.000 ARG A 353 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 151 time to evaluate : 1.057 Fit side-chains REVERT: A 220 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8681 (tp) REVERT: A 248 MET cc_start: 0.8113 (OUTLIER) cc_final: 0.7852 (mmp) REVERT: A 393 GLN cc_start: 0.8501 (mt0) cc_final: 0.8101 (mt0) REVERT: B 75 MET cc_start: 0.8495 (mmm) cc_final: 0.8205 (tpp) REVERT: B 200 TYR cc_start: 0.8114 (m-80) cc_final: 0.7720 (m-10) REVERT: B 320 MET cc_start: 0.7744 (OUTLIER) cc_final: 0.7494 (mmt) REVERT: B 473 MET cc_start: 0.7133 (ttt) cc_final: 0.6842 (mtp) REVERT: C 248 MET cc_start: 0.8064 (tpp) cc_final: 0.7598 (mmt) REVERT: C 303 LEU cc_start: 0.8338 (tp) cc_final: 0.8006 (tt) REVERT: C 320 MET cc_start: 0.7687 (OUTLIER) cc_final: 0.7451 (mmt) REVERT: C 322 GLN cc_start: 0.7778 (tp40) cc_final: 0.7428 (mm-40) REVERT: C 342 ARG cc_start: 0.7548 (ppt170) cc_final: 0.7301 (ppt90) REVERT: C 463 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.7440 (tm-30) outliers start: 38 outliers final: 19 residues processed: 167 average time/residue: 1.0873 time to fit residues: 195.3155 Evaluate side-chains 169 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 145 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 248 MET Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 320 MET Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 286 MET Chi-restraints excluded: chain C residue 320 MET Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 463 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 13 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 chunk 86 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 118 optimal weight: 0.4980 chunk 74 optimal weight: 0.0270 chunk 72 optimal weight: 0.7980 chunk 54 optimal weight: 0.0370 chunk 73 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 overall best weight: 0.4316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN B 85 ASN C 85 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.3271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9534 Z= 0.133 Angle : 0.479 5.543 12936 Z= 0.245 Chirality : 0.037 0.123 1644 Planarity : 0.003 0.026 1572 Dihedral : 3.661 17.758 1293 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.71 % Allowed : 17.49 % Favored : 79.81 % 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: 1.36 (0.25), residues: 1215 helix: 1.60 (0.17), residues: 960 sheet: -1.83 (0.78), residues: 54 loop : -1.64 (0.40), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 276 HIS 0.001 0.000 HIS C 41 PHE 0.011 0.001 PHE A 218 TYR 0.012 0.001 TYR C 373 ARG 0.002 0.000 ARG A 353 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 160 time to evaluate : 1.070 Fit side-chains REVERT: A 248 MET cc_start: 0.8028 (tpt) cc_final: 0.7756 (mmp) REVERT: A 393 GLN cc_start: 0.8484 (mt0) cc_final: 0.8082 (mt0) REVERT: A 463 GLU cc_start: 0.7461 (tm-30) cc_final: 0.7214 (tt0) REVERT: B 75 MET cc_start: 0.8484 (mmm) cc_final: 0.8210 (tpp) REVERT: B 200 TYR cc_start: 0.8049 (m-80) cc_final: 0.7688 (m-10) REVERT: B 303 LEU cc_start: 0.8420 (tp) cc_final: 0.8069 (tt) REVERT: B 320 MET cc_start: 0.7713 (OUTLIER) cc_final: 0.7449 (mmt) REVERT: B 463 GLU cc_start: 0.7521 (tt0) cc_final: 0.7291 (tm-30) REVERT: B 473 MET cc_start: 0.7136 (ttt) cc_final: 0.6849 (mtp) REVERT: C 248 MET cc_start: 0.8033 (tpp) cc_final: 0.7769 (mmt) REVERT: C 303 LEU cc_start: 0.8319 (tp) cc_final: 0.8017 (tt) REVERT: C 322 GLN cc_start: 0.7708 (tp40) cc_final: 0.7372 (mm-40) REVERT: C 342 ARG cc_start: 0.7538 (ppt170) cc_final: 0.7297 (ppt90) outliers start: 28 outliers final: 13 residues processed: 170 average time/residue: 1.1149 time to fit residues: 203.7035 Evaluate side-chains 161 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 147 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 320 MET Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 411 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 70 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 75 optimal weight: 9.9990 chunk 80 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 11 optimal weight: 0.0070 chunk 93 optimal weight: 0.6980 chunk 107 optimal weight: 1.9990 chunk 113 optimal weight: 0.8980 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.3302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9534 Z= 0.160 Angle : 0.503 6.515 12936 Z= 0.255 Chirality : 0.038 0.122 1644 Planarity : 0.003 0.026 1572 Dihedral : 3.672 17.886 1293 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.51 % Allowed : 18.36 % Favored : 79.13 % 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: 1.51 (0.25), residues: 1215 helix: 1.70 (0.17), residues: 960 sheet: -1.73 (0.77), residues: 54 loop : -1.58 (0.40), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 276 HIS 0.001 0.000 HIS C 296 PHE 0.019 0.001 PHE C 316 TYR 0.013 0.001 TYR C 373 ARG 0.002 0.000 ARG A 353 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 156 time to evaluate : 1.157 Fit side-chains REVERT: A 248 MET cc_start: 0.8058 (tpt) cc_final: 0.7814 (mmp) REVERT: A 393 GLN cc_start: 0.8504 (mt0) cc_final: 0.8099 (mt0) REVERT: A 463 GLU cc_start: 0.7486 (tm-30) cc_final: 0.7272 (tt0) REVERT: B 75 MET cc_start: 0.8496 (mmm) cc_final: 0.8213 (tpp) REVERT: B 142 MET cc_start: 0.8357 (mmm) cc_final: 0.8074 (mmm) REVERT: B 200 TYR cc_start: 0.8041 (m-80) cc_final: 0.7687 (m-10) REVERT: B 303 LEU cc_start: 0.8433 (tp) cc_final: 0.8082 (tt) REVERT: B 320 MET cc_start: 0.7712 (OUTLIER) cc_final: 0.7460 (mmt) REVERT: B 463 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.7340 (tm-30) REVERT: B 473 MET cc_start: 0.7139 (ttt) cc_final: 0.6841 (mtp) REVERT: C 248 MET cc_start: 0.8100 (tpp) cc_final: 0.7811 (mmt) REVERT: C 303 LEU cc_start: 0.8331 (tp) cc_final: 0.8014 (tt) REVERT: C 322 GLN cc_start: 0.7664 (tp40) cc_final: 0.7295 (mm-40) REVERT: C 342 ARG cc_start: 0.7540 (ppt170) cc_final: 0.7290 (ppt90) outliers start: 26 outliers final: 16 residues processed: 168 average time/residue: 1.1140 time to fit residues: 201.5770 Evaluate side-chains 167 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 149 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 320 MET Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 463 GLU Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 205 MET Chi-restraints excluded: chain C residue 274 GLU Chi-restraints excluded: chain C residue 411 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 4.9990 chunk 110 optimal weight: 0.7980 chunk 113 optimal weight: 0.8980 chunk 66 optimal weight: 6.9990 chunk 48 optimal weight: 5.9990 chunk 86 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 99 optimal weight: 0.7980 chunk 104 optimal weight: 0.9980 chunk 72 optimal weight: 0.7980 chunk 116 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN B 85 ASN C 85 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9534 Z= 0.181 Angle : 0.521 6.296 12936 Z= 0.265 Chirality : 0.038 0.128 1644 Planarity : 0.003 0.026 1572 Dihedral : 3.723 17.564 1293 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.71 % Allowed : 19.13 % Favored : 78.16 % 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: 1.52 (0.25), residues: 1215 helix: 1.66 (0.17), residues: 969 sheet: -1.70 (0.77), residues: 54 loop : -1.47 (0.41), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 276 HIS 0.001 0.000 HIS C 296 PHE 0.018 0.001 PHE C 316 TYR 0.015 0.001 TYR C 373 ARG 0.002 0.000 ARG A 353 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 149 time to evaluate : 1.073 Fit side-chains REVERT: A 248 MET cc_start: 0.8073 (tpt) cc_final: 0.7814 (mmp) REVERT: A 393 GLN cc_start: 0.8500 (mt0) cc_final: 0.8089 (mt0) REVERT: B 75 MET cc_start: 0.8510 (mmm) cc_final: 0.8235 (tpp) REVERT: B 142 MET cc_start: 0.8368 (mmm) cc_final: 0.8067 (mmm) REVERT: B 200 TYR cc_start: 0.8040 (m-80) cc_final: 0.7685 (m-10) REVERT: B 303 LEU cc_start: 0.8407 (tp) cc_final: 0.8066 (tt) REVERT: B 320 MET cc_start: 0.7774 (OUTLIER) cc_final: 0.7511 (mmt) REVERT: B 463 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.7319 (tm-30) REVERT: B 473 MET cc_start: 0.7132 (ttt) cc_final: 0.6807 (mtp) REVERT: C 248 MET cc_start: 0.8098 (tpp) cc_final: 0.7789 (mmt) REVERT: C 303 LEU cc_start: 0.8319 (tp) cc_final: 0.7993 (tt) REVERT: C 316 PHE cc_start: 0.8134 (t80) cc_final: 0.7898 (t80) REVERT: C 322 GLN cc_start: 0.7659 (tp40) cc_final: 0.7349 (mm-40) REVERT: C 342 ARG cc_start: 0.7545 (ppt170) cc_final: 0.7294 (ppt90) REVERT: C 463 GLU cc_start: 0.7717 (tp30) cc_final: 0.7352 (tm-30) outliers start: 28 outliers final: 20 residues processed: 162 average time/residue: 1.0293 time to fit residues: 180.2645 Evaluate side-chains 168 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 146 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 320 MET Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 463 GLU Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 205 MET Chi-restraints excluded: chain C residue 274 GLU Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 434 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 71 optimal weight: 7.9990 chunk 55 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 122 optimal weight: 5.9990 chunk 112 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 75 optimal weight: 0.9990 chunk 59 optimal weight: 0.6980 chunk 77 optimal weight: 0.9990 chunk 103 optimal weight: 7.9990 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 85 ASN B 85 ASN C 85 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.3357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9534 Z= 0.183 Angle : 0.521 6.271 12936 Z= 0.265 Chirality : 0.038 0.133 1644 Planarity : 0.003 0.037 1572 Dihedral : 3.737 17.288 1293 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.61 % Allowed : 19.32 % Favored : 78.07 % 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: 1.55 (0.25), residues: 1215 helix: 1.68 (0.18), residues: 969 sheet: -1.67 (0.77), residues: 54 loop : -1.45 (0.41), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 276 HIS 0.001 0.000 HIS C 41 PHE 0.017 0.001 PHE C 316 TYR 0.015 0.001 TYR C 373 ARG 0.002 0.000 ARG C 61 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 148 time to evaluate : 1.058 Fit side-chains REVERT: A 248 MET cc_start: 0.8073 (OUTLIER) cc_final: 0.7811 (mmp) REVERT: A 393 GLN cc_start: 0.8497 (mt0) cc_final: 0.8073 (mt0) REVERT: B 75 MET cc_start: 0.8515 (mmm) cc_final: 0.8235 (tpp) REVERT: B 142 MET cc_start: 0.8365 (mmm) cc_final: 0.8054 (mmm) REVERT: B 200 TYR cc_start: 0.8050 (m-80) cc_final: 0.7700 (m-10) REVERT: B 320 MET cc_start: 0.7799 (OUTLIER) cc_final: 0.7557 (mmt) REVERT: B 342 ARG cc_start: 0.7617 (ppt170) cc_final: 0.7317 (ppt90) REVERT: B 463 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.7297 (tm-30) REVERT: B 473 MET cc_start: 0.7152 (ttt) cc_final: 0.6844 (mtp) REVERT: C 248 MET cc_start: 0.8097 (tpp) cc_final: 0.7808 (mmt) REVERT: C 303 LEU cc_start: 0.8322 (tp) cc_final: 0.8001 (tt) REVERT: C 322 GLN cc_start: 0.7687 (tp40) cc_final: 0.7387 (mm-40) REVERT: C 342 ARG cc_start: 0.7525 (ppt170) cc_final: 0.7273 (ppt90) REVERT: C 463 GLU cc_start: 0.7725 (tp30) cc_final: 0.7327 (tm-30) outliers start: 27 outliers final: 21 residues processed: 161 average time/residue: 1.1105 time to fit residues: 192.8169 Evaluate side-chains 173 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 149 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 248 MET Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 320 MET Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 463 GLU Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 205 MET Chi-restraints excluded: chain C residue 274 GLU Chi-restraints excluded: chain C residue 286 MET Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 434 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 29 optimal weight: 5.9990 chunk 89 optimal weight: 0.0670 chunk 14 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 40 optimal weight: 20.0000 chunk 100 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 85 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN B 85 ASN C 85 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.139782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.098620 restraints weight = 11196.934| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 1.91 r_work: 0.2902 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.3483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9534 Z= 0.158 Angle : 0.516 9.460 12936 Z= 0.261 Chirality : 0.038 0.125 1644 Planarity : 0.003 0.035 1572 Dihedral : 3.678 16.662 1293 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.71 % Allowed : 19.71 % Favored : 77.58 % 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: 1.74 (0.26), residues: 1215 helix: 1.82 (0.18), residues: 966 sheet: -1.66 (0.77), residues: 54 loop : -1.36 (0.41), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 276 HIS 0.001 0.000 HIS C 41 PHE 0.012 0.001 PHE A 218 TYR 0.014 0.001 TYR C 373 ARG 0.002 0.000 ARG A 353 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3834.15 seconds wall clock time: 67 minutes 23.69 seconds (4043.69 seconds total)