Starting phenix.real_space_refine on Tue Apr 29 06:28:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k0x_36780/04_2025/8k0x_36780.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k0x_36780/04_2025/8k0x_36780.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8k0x_36780/04_2025/8k0x_36780.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k0x_36780/04_2025/8k0x_36780.map" model { file = "/net/cci-nas-00/data/ceres_data/8k0x_36780/04_2025/8k0x_36780.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k0x_36780/04_2025/8k0x_36780.cif" } resolution = 3.2 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= 0.005 sd= 0.134 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 52 5.16 5 C 5507 2.51 5 N 1408 2.21 5 O 1480 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 8447 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4214 Classifications: {'peptide': 542} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 523} Chain breaks: 4 Chain: "C" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 19 Unusual residues: {'A8S': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: C Time building chain proxies: 7.60, per 1000 atoms: 0.90 Number of scatterers: 8447 At special positions: 0 Unit cell: (86.9, 100.1, 121, 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 52 16.00 O 1480 8.00 N 1408 7.00 C 5507 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: 2.23 Conformation dependent library (CDL) restraints added in 1.1 seconds 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1988 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 6 sheets defined 55.2% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'A' and resid 106 through 113 removed outlier: 3.575A pdb=" N LEU A 110 " --> pdb=" O GLY A 106 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU A 111 " --> pdb=" O LYS A 107 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASN A 112 " --> pdb=" O SER A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 140 removed outlier: 3.654A pdb=" N LEU A 139 " --> pdb=" O LYS A 136 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LYS A 140 " --> pdb=" O GLN A 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 136 through 140' Processing helix chain 'A' and resid 156 through 169 removed outlier: 3.758A pdb=" N LEU A 167 " --> pdb=" O PHE A 163 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU A 169 " --> pdb=" O ALA A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 189 Processing helix chain 'A' and resid 208 through 219 removed outlier: 3.715A pdb=" N LYS A 213 " --> pdb=" O GLY A 209 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ARG A 214 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA A 218 " --> pdb=" O ARG A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 256 removed outlier: 3.563A pdb=" N ARG A 244 " --> pdb=" O THR A 240 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL A 246 " --> pdb=" O ALA A 242 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA A 253 " --> pdb=" O LEU A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 273 removed outlier: 3.533A pdb=" N GLN A 273 " --> pdb=" O SER A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 303 removed outlier: 3.939A pdb=" N SER A 301 " --> pdb=" O ALA A 297 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL A 302 " --> pdb=" O TYR A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 319 removed outlier: 3.629A pdb=" N LEU A 316 " --> pdb=" O PRO A 312 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU A 317 " --> pdb=" O ALA A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 349 removed outlier: 3.614A pdb=" N THR A 343 " --> pdb=" O GLN A 339 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASP A 346 " --> pdb=" O VAL A 342 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR A 347 " --> pdb=" O THR A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 354 removed outlier: 4.013A pdb=" N VAL A 353 " --> pdb=" O LEU A 349 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LYS A 354 " --> pdb=" O ALA A 350 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 349 through 354' Processing helix chain 'A' and resid 380 through 397 removed outlier: 3.744A pdb=" N ALA A 384 " --> pdb=" O THR A 380 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TRP A 386 " --> pdb=" O CYS A 382 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLN A 389 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE A 392 " --> pdb=" O SER A 388 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU A 393 " --> pdb=" O GLN A 389 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N HIS A 395 " --> pdb=" O CYS A 391 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU A 397 " --> pdb=" O LEU A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 406 Processing helix chain 'A' and resid 407 through 425 removed outlier: 3.813A pdb=" N PHE A 412 " --> pdb=" O LEU A 408 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLN A 413 " --> pdb=" O LEU A 409 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL A 414 " --> pdb=" O ARG A 410 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU A 420 " --> pdb=" O ALA A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 454 removed outlier: 3.723A pdb=" N ARG A 436 " --> pdb=" O ASP A 432 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY A 438 " --> pdb=" O HIS A 434 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N SER A 444 " --> pdb=" O LEU A 440 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY A 448 " --> pdb=" O SER A 444 " (cutoff:3.500A) Proline residue: A 451 - end of helix removed outlier: 3.563A pdb=" N ASN A 454 " --> pdb=" O LEU A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 461 No H-bonds generated for 'chain 'A' and resid 459 through 461' Processing helix chain 'A' and resid 462 through 471 removed outlier: 3.576A pdb=" N THR A 467 " --> pdb=" O ARG A 463 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ARG A 468 " --> pdb=" O ALA A 464 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ALA A 471 " --> pdb=" O THR A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 489 removed outlier: 3.654A pdb=" N TYR A 480 " --> pdb=" O THR A 476 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA A 483 " --> pdb=" O SER A 479 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N HIS A 484 " --> pdb=" O TYR A 480 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU A 486 " --> pdb=" O MET A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 505 removed outlier: 3.812A pdb=" N THR A 501 " --> pdb=" O ALA A 497 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE A 502 " --> pdb=" O SER A 498 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N TRP A 505 " --> pdb=" O THR A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 542 removed outlier: 3.550A pdb=" N THR A 519 " --> pdb=" O PRO A 515 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLY A 532 " --> pdb=" O LEU A 528 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LEU A 533 " --> pdb=" O ALA A 529 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLY A 534 " --> pdb=" O SER A 530 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N MET A 542 " --> pdb=" O GLY A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 561 removed outlier: 3.520A pdb=" N VAL A 553 " --> pdb=" O THR A 549 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL A 559 " --> pdb=" O MET A 555 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR A 561 " --> pdb=" O ALA A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 579 removed outlier: 3.782A pdb=" N LYS A 577 " --> pdb=" O VAL A 574 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N VAL A 579 " --> pdb=" O MET A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 594 removed outlier: 3.866A pdb=" N TYR A 584 " --> pdb=" O SER A 580 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU A 588 " --> pdb=" O TYR A 584 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA A 591 " --> pdb=" O ARG A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 655 removed outlier: 3.782A pdb=" N LEU A 642 " --> pdb=" O SER A 638 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU A 644 " --> pdb=" O GLY A 640 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR A 649 " --> pdb=" O MET A 645 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ARG A 650 " --> pdb=" O PHE A 646 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU A 652 " --> pdb=" O GLY A 648 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 113 removed outlier: 3.574A pdb=" N LEU C 110 " --> pdb=" O GLY C 106 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU C 111 " --> pdb=" O LYS C 107 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASN C 112 " --> pdb=" O SER C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 140 removed outlier: 3.654A pdb=" N LEU C 139 " --> pdb=" O LYS C 136 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS C 140 " --> pdb=" O GLN C 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 136 through 140' Processing helix chain 'C' and resid 156 through 169 removed outlier: 3.758A pdb=" N LEU C 167 " --> pdb=" O PHE C 163 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU C 169 " --> pdb=" O ALA C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 189 Processing helix chain 'C' and resid 208 through 219 removed outlier: 3.716A pdb=" N LYS C 213 " --> pdb=" O GLY C 209 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ARG C 214 " --> pdb=" O GLY C 210 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA C 218 " --> pdb=" O ARG C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 256 removed outlier: 3.563A pdb=" N ARG C 244 " --> pdb=" O THR C 240 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL C 246 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA C 253 " --> pdb=" O LEU C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 273 removed outlier: 3.532A pdb=" N GLN C 273 " --> pdb=" O SER C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 removed outlier: 3.939A pdb=" N SER C 301 " --> pdb=" O ALA C 297 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL C 302 " --> pdb=" O TYR C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 319 removed outlier: 3.628A pdb=" N LEU C 316 " --> pdb=" O PRO C 312 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU C 317 " --> pdb=" O ALA C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 349 removed outlier: 3.614A pdb=" N THR C 343 " --> pdb=" O GLN C 339 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASP C 346 " --> pdb=" O VAL C 342 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR C 347 " --> pdb=" O THR C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 354 removed outlier: 4.012A pdb=" N VAL C 353 " --> pdb=" O LEU C 349 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LYS C 354 " --> pdb=" O ALA C 350 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 349 through 354' Processing helix chain 'C' and resid 380 through 397 removed outlier: 3.745A pdb=" N ALA C 384 " --> pdb=" O THR C 380 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TRP C 386 " --> pdb=" O CYS C 382 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLN C 389 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE C 392 " --> pdb=" O SER C 388 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU C 393 " --> pdb=" O GLN C 389 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N HIS C 395 " --> pdb=" O CYS C 391 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU C 397 " --> pdb=" O LEU C 393 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 406 Processing helix chain 'C' and resid 407 through 425 removed outlier: 3.814A pdb=" N PHE C 412 " --> pdb=" O LEU C 408 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLN C 413 " --> pdb=" O LEU C 409 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL C 414 " --> pdb=" O ARG C 410 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU C 420 " --> pdb=" O ALA C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 454 removed outlier: 3.723A pdb=" N ARG C 436 " --> pdb=" O ASP C 432 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLY C 438 " --> pdb=" O HIS C 434 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N SER C 444 " --> pdb=" O LEU C 440 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY C 448 " --> pdb=" O SER C 444 " (cutoff:3.500A) Proline residue: C 451 - end of helix removed outlier: 3.563A pdb=" N ASN C 454 " --> pdb=" O LEU C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 461 No H-bonds generated for 'chain 'C' and resid 459 through 461' Processing helix chain 'C' and resid 462 through 471 removed outlier: 3.576A pdb=" N THR C 467 " --> pdb=" O ARG C 463 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ARG C 468 " --> pdb=" O ALA C 464 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ALA C 471 " --> pdb=" O THR C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 489 removed outlier: 3.654A pdb=" N TYR C 480 " --> pdb=" O THR C 476 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA C 483 " --> pdb=" O SER C 479 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N HIS C 484 " --> pdb=" O TYR C 480 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU C 486 " --> pdb=" O MET C 482 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 505 removed outlier: 3.813A pdb=" N THR C 501 " --> pdb=" O ALA C 497 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE C 502 " --> pdb=" O SER C 498 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N TRP C 505 " --> pdb=" O THR C 501 " (cutoff:3.500A) Processing helix chain 'C' and resid 513 through 542 removed outlier: 3.550A pdb=" N THR C 519 " --> pdb=" O PRO C 515 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLY C 532 " --> pdb=" O LEU C 528 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LEU C 533 " --> pdb=" O ALA C 529 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLY C 534 " --> pdb=" O SER C 530 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N MET C 542 " --> pdb=" O GLY C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 549 through 561 removed outlier: 3.521A pdb=" N VAL C 553 " --> pdb=" O THR C 549 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL C 559 " --> pdb=" O MET C 555 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR C 561 " --> pdb=" O ALA C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 579 removed outlier: 3.783A pdb=" N LYS C 577 " --> pdb=" O VAL C 574 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL C 579 " --> pdb=" O MET C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 594 removed outlier: 3.867A pdb=" N TYR C 584 " --> pdb=" O SER C 580 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU C 588 " --> pdb=" O TYR C 584 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA C 591 " --> pdb=" O ARG C 587 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 655 removed outlier: 3.782A pdb=" N LEU C 642 " --> pdb=" O SER C 638 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU C 644 " --> pdb=" O GLY C 640 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR C 649 " --> pdb=" O MET C 645 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ARG C 650 " --> pdb=" O PHE C 646 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU C 652 " --> pdb=" O GLY C 648 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 89 through 91 Processing sheet with id=AA2, first strand: chain 'A' and resid 261 through 262 removed outlier: 6.462A pdb=" N MET A 97 " --> pdb=" O THR A 262 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU A 281 " --> pdb=" O LEU A 100 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY A 290 " --> pdb=" O VAL A 278 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N PHE A 288 " --> pdb=" O LEU A 280 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 142 through 145 removed outlier: 6.155A pdb=" N GLY A 143 " --> pdb=" O VAL A 229 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 89 through 91 Processing sheet with id=AA5, first strand: chain 'C' and resid 261 through 262 removed outlier: 6.461A pdb=" N MET C 97 " --> pdb=" O THR C 262 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU C 281 " --> pdb=" O LEU C 100 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY C 290 " --> pdb=" O VAL C 278 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N PHE C 288 " --> pdb=" O LEU C 280 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 142 through 145 removed outlier: 6.154A pdb=" N GLY C 143 " --> pdb=" O VAL C 229 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 294 hydrogen bonds defined for protein. 852 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: 2.16 Time building geometry restraints manager: 2.59 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: 2583 1.34 - 1.45: 1523 1.45 - 1.57: 4433 1.57 - 1.69: 0 1.69 - 1.81: 84 Bond restraints: 8623 Sorted by residual: bond pdb=" C ALA C 350 " pdb=" N PRO C 351 " ideal model delta sigma weight residual 1.339 1.405 -0.066 3.40e-02 8.65e+02 3.79e+00 bond pdb=" C ALA A 350 " pdb=" N PRO A 351 " ideal model delta sigma weight residual 1.339 1.405 -0.066 3.40e-02 8.65e+02 3.72e+00 bond pdb=" C7 A8S C 701 " pdb=" C8 A8S C 701 " ideal model delta sigma weight residual 1.534 1.500 0.034 2.00e-02 2.50e+03 2.81e+00 bond pdb=" CG LEU A 509 " pdb=" CD2 LEU A 509 " ideal model delta sigma weight residual 1.521 1.471 0.050 3.30e-02 9.18e+02 2.28e+00 bond pdb=" CG LEU C 509 " pdb=" CD2 LEU C 509 " ideal model delta sigma weight residual 1.521 1.471 0.050 3.30e-02 9.18e+02 2.27e+00 ... (remaining 8618 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.31: 11229 2.31 - 4.61: 380 4.61 - 6.92: 63 6.92 - 9.23: 19 9.23 - 11.53: 2 Bond angle restraints: 11693 Sorted by residual: angle pdb=" N PHE A 203 " pdb=" CA PHE A 203 " pdb=" C PHE A 203 " ideal model delta sigma weight residual 114.62 107.72 6.90 1.14e+00 7.69e-01 3.67e+01 angle pdb=" N PHE C 203 " pdb=" CA PHE C 203 " pdb=" C PHE C 203 " ideal model delta sigma weight residual 114.62 107.76 6.86 1.14e+00 7.69e-01 3.62e+01 angle pdb=" CA VAL C 514 " pdb=" C VAL C 514 " pdb=" N PRO C 515 " ideal model delta sigma weight residual 118.88 124.60 -5.72 1.54e+00 4.22e-01 1.38e+01 angle pdb=" CA VAL A 514 " pdb=" C VAL A 514 " pdb=" N PRO A 515 " ideal model delta sigma weight residual 118.88 124.56 -5.68 1.54e+00 4.22e-01 1.36e+01 angle pdb=" CA PHE C 203 " pdb=" C PHE C 203 " pdb=" N ILE C 204 " ideal model delta sigma weight residual 119.71 115.40 4.31 1.17e+00 7.31e-01 1.35e+01 ... (remaining 11688 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.07: 4779 15.07 - 30.13: 235 30.13 - 45.20: 58 45.20 - 60.27: 2 60.27 - 75.34: 4 Dihedral angle restraints: 5078 sinusoidal: 1980 harmonic: 3098 Sorted by residual: dihedral pdb=" CA VAL C 45 " pdb=" C VAL C 45 " pdb=" N CYS C 46 " pdb=" CA CYS C 46 " ideal model delta harmonic sigma weight residual 180.00 -157.32 -22.68 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA VAL A 45 " pdb=" C VAL A 45 " pdb=" N CYS A 46 " pdb=" CA CYS A 46 " ideal model delta harmonic sigma weight residual 180.00 -157.40 -22.60 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" CA PRO A 570 " pdb=" C PRO A 570 " pdb=" N SER A 571 " pdb=" CA SER A 571 " ideal model delta harmonic sigma weight residual 180.00 159.70 20.30 0 5.00e+00 4.00e-02 1.65e+01 ... (remaining 5075 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 992 0.058 - 0.115: 323 0.115 - 0.173: 59 0.173 - 0.231: 9 0.231 - 0.289: 8 Chirality restraints: 1391 Sorted by residual: chirality pdb=" CB VAL A 43 " pdb=" CA VAL A 43 " pdb=" CG1 VAL A 43 " pdb=" CG2 VAL A 43 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.08e+00 chirality pdb=" CB VAL C 43 " pdb=" CA VAL C 43 " pdb=" CG1 VAL C 43 " pdb=" CG2 VAL C 43 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CB VAL A 514 " pdb=" CA VAL A 514 " pdb=" CG1 VAL A 514 " pdb=" CG2 VAL A 514 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.72e+00 ... (remaining 1388 not shown) Planarity restraints: 1434 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 459 " -0.035 5.00e-02 4.00e+02 5.19e-02 4.31e+00 pdb=" N PRO A 460 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 460 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 460 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 459 " 0.035 5.00e-02 4.00e+02 5.19e-02 4.31e+00 pdb=" N PRO C 460 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO C 460 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 460 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 311 " -0.031 5.00e-02 4.00e+02 4.65e-02 3.46e+00 pdb=" N PRO A 312 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 312 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 312 " -0.026 5.00e-02 4.00e+02 ... (remaining 1431 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 2585 2.83 - 3.34: 7052 3.34 - 3.86: 12265 3.86 - 4.38: 14638 4.38 - 4.90: 26229 Nonbonded interactions: 62769 Sorted by model distance: nonbonded pdb=" O SER A 282 " pdb=" OG SER A 282 " model vdw 2.307 3.040 nonbonded pdb=" O SER C 282 " pdb=" OG SER C 282 " model vdw 2.307 3.040 nonbonded pdb=" OE1 GLU C 462 " pdb=" OH TYR C 480 " model vdw 2.434 3.040 nonbonded pdb=" OE1 GLU A 462 " pdb=" OH TYR A 480 " model vdw 2.434 3.040 nonbonded pdb=" OE2 GLU A 95 " pdb=" OG1 THR A 277 " model vdw 2.467 3.040 ... (remaining 62764 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'C' and resid 35 through 662) } 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: 0.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 25.050 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 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 : 0.008 0.069 8623 Z= 0.327 Angle : 1.045 11.533 11693 Z= 0.556 Chirality : 0.059 0.289 1391 Planarity : 0.007 0.052 1434 Dihedral : 9.778 75.335 3090 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 1.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % 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: -6.65 (0.16), residues: 1064 helix: -4.74 (0.08), residues: 584 sheet: -3.87 (0.47), residues: 84 loop : -3.63 (0.25), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP C 386 HIS 0.012 0.003 HIS A 427 PHE 0.032 0.004 PHE C 96 TYR 0.024 0.003 TYR A 508 ARG 0.007 0.001 ARG A 214 Details of bonding type rmsd hydrogen bonds : bond 0.35020 ( 294) hydrogen bonds : angle 10.78841 ( 852) covalent geometry : bond 0.00783 ( 8623) covalent geometry : angle 1.04462 (11693) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 0.897 Fit side-chains REVERT: A 289 VAL cc_start: 0.8586 (t) cc_final: 0.8356 (m) REVERT: A 314 ASP cc_start: 0.8014 (t0) cc_final: 0.7654 (m-30) REVERT: C 289 VAL cc_start: 0.8571 (t) cc_final: 0.8337 (m) REVERT: C 314 ASP cc_start: 0.7915 (t0) cc_final: 0.7660 (m-30) outliers start: 0 outliers final: 0 residues processed: 177 average time/residue: 0.3108 time to fit residues: 68.0286 Evaluate side-chains 106 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 2.9990 chunk 81 optimal weight: 0.0980 chunk 45 optimal weight: 0.7980 chunk 27 optimal weight: 0.0370 chunk 55 optimal weight: 6.9990 chunk 43 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 51 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 chunk 98 optimal weight: 2.9990 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 GLN A 461 GLN A 531 GLN C 461 GLN C 531 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.163745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.129142 restraints weight = 9704.907| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 1.71 r_work: 0.3073 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 8623 Z= 0.105 Angle : 0.583 6.802 11693 Z= 0.305 Chirality : 0.041 0.143 1391 Planarity : 0.005 0.036 1434 Dihedral : 5.171 39.624 1196 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 1.74 % Allowed : 6.54 % Favored : 91.72 % 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: -4.72 (0.20), residues: 1064 helix: -3.02 (0.16), residues: 562 sheet: -3.56 (0.51), residues: 82 loop : -2.95 (0.26), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 447 HIS 0.003 0.001 HIS A 219 PHE 0.008 0.001 PHE A 96 TYR 0.010 0.001 TYR A 586 ARG 0.004 0.001 ARG C 117 Details of bonding type rmsd hydrogen bonds : bond 0.04789 ( 294) hydrogen bonds : angle 4.77157 ( 852) covalent geometry : bond 0.00229 ( 8623) covalent geometry : angle 0.58350 (11693) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 125 time to evaluate : 0.957 Fit side-chains REVERT: A 90 MET cc_start: 0.8766 (ptm) cc_final: 0.8462 (ptt) REVERT: A 314 ASP cc_start: 0.8254 (t0) cc_final: 0.7732 (m-30) REVERT: A 491 MET cc_start: 0.8542 (mmp) cc_final: 0.8123 (mmt) REVERT: C 90 MET cc_start: 0.8783 (ptm) cc_final: 0.8488 (ptt) REVERT: C 314 ASP cc_start: 0.8363 (t0) cc_final: 0.7815 (m-30) outliers start: 16 outliers final: 9 residues processed: 133 average time/residue: 0.2845 time to fit residues: 48.6996 Evaluate side-chains 108 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 99 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 569 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 55 optimal weight: 0.0770 chunk 58 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 56 optimal weight: 9.9990 chunk 96 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 overall best weight: 1.5544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.154214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.118389 restraints weight = 9984.377| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 1.75 r_work: 0.2998 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8623 Z= 0.182 Angle : 0.647 7.513 11693 Z= 0.330 Chirality : 0.044 0.190 1391 Planarity : 0.004 0.037 1434 Dihedral : 5.103 37.518 1196 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 2.83 % Allowed : 7.08 % Favored : 90.09 % 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: -3.88 (0.22), residues: 1064 helix: -2.10 (0.19), residues: 566 sheet: -3.53 (0.50), residues: 84 loop : -2.86 (0.27), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 426 HIS 0.007 0.002 HIS A 219 PHE 0.028 0.002 PHE A 502 TYR 0.020 0.002 TYR A 508 ARG 0.004 0.001 ARG C 650 Details of bonding type rmsd hydrogen bonds : bond 0.05695 ( 294) hydrogen bonds : angle 4.38675 ( 852) covalent geometry : bond 0.00447 ( 8623) covalent geometry : angle 0.64684 (11693) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 103 time to evaluate : 0.987 Fit side-chains REVERT: A 90 MET cc_start: 0.8765 (ptm) cc_final: 0.8425 (ptt) REVERT: A 179 LEU cc_start: 0.7747 (OUTLIER) cc_final: 0.7343 (mp) REVERT: A 314 ASP cc_start: 0.8266 (t0) cc_final: 0.7734 (m-30) REVERT: A 408 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8595 (mp) REVERT: C 90 MET cc_start: 0.8779 (ptm) cc_final: 0.8444 (ptt) REVERT: C 314 ASP cc_start: 0.8290 (t0) cc_final: 0.7719 (m-30) outliers start: 26 outliers final: 22 residues processed: 122 average time/residue: 0.2686 time to fit residues: 42.5784 Evaluate side-chains 121 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 97 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 531 GLN Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 531 GLN Chi-restraints excluded: chain C residue 569 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 53 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 64 optimal weight: 0.0370 chunk 98 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 overall best weight: 1.2066 ------------------------------------------------------------------------------- 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 = 0.3649 r_free = 0.3649 target = 0.150231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.113106 restraints weight = 10013.126| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 1.88 r_work: 0.2936 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8623 Z= 0.145 Angle : 0.579 6.763 11693 Z= 0.297 Chirality : 0.042 0.144 1391 Planarity : 0.004 0.038 1434 Dihedral : 4.852 36.334 1196 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 3.59 % Allowed : 7.30 % Favored : 89.11 % 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: -3.30 (0.23), residues: 1064 helix: -1.55 (0.20), residues: 572 sheet: -3.02 (0.52), residues: 84 loop : -2.79 (0.27), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 426 HIS 0.007 0.001 HIS A 219 PHE 0.033 0.002 PHE A 502 TYR 0.011 0.001 TYR C 586 ARG 0.003 0.000 ARG C 158 Details of bonding type rmsd hydrogen bonds : bond 0.04651 ( 294) hydrogen bonds : angle 4.12711 ( 852) covalent geometry : bond 0.00354 ( 8623) covalent geometry : angle 0.57946 (11693) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 100 time to evaluate : 1.345 Fit side-chains REVERT: A 90 MET cc_start: 0.8760 (ptm) cc_final: 0.8452 (ptt) REVERT: A 179 LEU cc_start: 0.7777 (OUTLIER) cc_final: 0.7367 (mp) REVERT: A 314 ASP cc_start: 0.8304 (t0) cc_final: 0.7711 (m-30) REVERT: A 408 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8565 (mp) REVERT: A 531 GLN cc_start: 0.9269 (OUTLIER) cc_final: 0.9005 (tt0) REVERT: C 90 MET cc_start: 0.8771 (ptm) cc_final: 0.8465 (ptt) REVERT: C 179 LEU cc_start: 0.7718 (OUTLIER) cc_final: 0.7290 (mp) REVERT: C 293 ARG cc_start: 0.8556 (ttm110) cc_final: 0.8266 (ttp-110) REVERT: C 314 ASP cc_start: 0.8290 (t0) cc_final: 0.7692 (m-30) REVERT: C 474 MET cc_start: 0.9098 (mtp) cc_final: 0.8850 (mtp) REVERT: C 531 GLN cc_start: 0.9270 (OUTLIER) cc_final: 0.9007 (tt0) outliers start: 33 outliers final: 25 residues processed: 124 average time/residue: 0.2846 time to fit residues: 46.5681 Evaluate side-chains 123 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 93 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 531 GLN Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 531 GLN Chi-restraints excluded: chain C residue 569 VAL Chi-restraints excluded: chain C residue 633 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 62 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 7 optimal weight: 7.9990 chunk 71 optimal weight: 0.3980 chunk 36 optimal weight: 0.8980 chunk 19 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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 = 0.150436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.114704 restraints weight = 9957.632| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 1.75 r_work: 0.2938 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.3208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8623 Z= 0.163 Angle : 0.599 7.034 11693 Z= 0.306 Chirality : 0.043 0.148 1391 Planarity : 0.004 0.040 1434 Dihedral : 4.900 35.945 1196 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 4.14 % Allowed : 7.63 % Favored : 88.24 % 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: -3.02 (0.24), residues: 1064 helix: -1.27 (0.21), residues: 568 sheet: -3.05 (0.52), residues: 80 loop : -2.72 (0.27), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 426 HIS 0.008 0.001 HIS C 219 PHE 0.021 0.002 PHE C 502 TYR 0.013 0.001 TYR C 586 ARG 0.004 0.001 ARG C 431 Details of bonding type rmsd hydrogen bonds : bond 0.04933 ( 294) hydrogen bonds : angle 4.10958 ( 852) covalent geometry : bond 0.00401 ( 8623) covalent geometry : angle 0.59927 (11693) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 91 time to evaluate : 1.070 Fit side-chains REVERT: A 90 MET cc_start: 0.8774 (ptm) cc_final: 0.8480 (ptt) REVERT: A 179 LEU cc_start: 0.7776 (OUTLIER) cc_final: 0.7501 (mp) REVERT: A 285 LYS cc_start: 0.8692 (mppt) cc_final: 0.8403 (mppt) REVERT: A 314 ASP cc_start: 0.8327 (t0) cc_final: 0.7852 (m-30) REVERT: A 408 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8616 (mp) REVERT: A 474 MET cc_start: 0.9123 (mtp) cc_final: 0.8848 (mtp) REVERT: C 90 MET cc_start: 0.8766 (ptm) cc_final: 0.8458 (ptt) REVERT: C 179 LEU cc_start: 0.7731 (OUTLIER) cc_final: 0.7469 (mp) REVERT: C 293 ARG cc_start: 0.8626 (ttm110) cc_final: 0.8371 (ttp-110) REVERT: C 314 ASP cc_start: 0.8341 (t0) cc_final: 0.7846 (m-30) REVERT: C 408 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8572 (mp) REVERT: C 474 MET cc_start: 0.9184 (mtp) cc_final: 0.8916 (mtp) outliers start: 38 outliers final: 27 residues processed: 122 average time/residue: 0.2597 time to fit residues: 42.2787 Evaluate side-chains 118 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 87 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 531 GLN Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 383 ILE Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 531 GLN Chi-restraints excluded: chain C residue 569 VAL Chi-restraints excluded: chain C residue 633 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 20 optimal weight: 2.9990 chunk 91 optimal weight: 0.3980 chunk 77 optimal weight: 5.9990 chunk 79 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 98 optimal weight: 0.0010 chunk 14 optimal weight: 0.5980 chunk 87 optimal weight: 4.9990 chunk 107 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 overall best weight: 0.5586 ------------------------------------------------------------------------------- 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 = 0.3669 r_free = 0.3669 target = 0.152130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.115517 restraints weight = 9896.110| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 1.85 r_work: 0.2979 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.3404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 8623 Z= 0.095 Angle : 0.513 6.849 11693 Z= 0.264 Chirality : 0.040 0.136 1391 Planarity : 0.003 0.040 1434 Dihedral : 4.468 34.426 1196 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 3.49 % Allowed : 8.50 % Favored : 88.02 % 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: -2.49 (0.24), residues: 1064 helix: -0.76 (0.22), residues: 562 sheet: -2.85 (0.53), residues: 80 loop : -2.57 (0.27), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 426 HIS 0.004 0.001 HIS C 219 PHE 0.021 0.001 PHE A 502 TYR 0.007 0.001 TYR C 586 ARG 0.004 0.000 ARG C 158 Details of bonding type rmsd hydrogen bonds : bond 0.03600 ( 294) hydrogen bonds : angle 3.78574 ( 852) covalent geometry : bond 0.00220 ( 8623) covalent geometry : angle 0.51332 (11693) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 94 time to evaluate : 1.190 Fit side-chains REVERT: A 90 MET cc_start: 0.8763 (ptm) cc_final: 0.8474 (ptt) REVERT: A 179 LEU cc_start: 0.7700 (OUTLIER) cc_final: 0.7401 (mp) REVERT: A 314 ASP cc_start: 0.8336 (t0) cc_final: 0.7805 (m-30) REVERT: C 90 MET cc_start: 0.8756 (ptm) cc_final: 0.8452 (ptt) REVERT: C 179 LEU cc_start: 0.7641 (OUTLIER) cc_final: 0.7372 (mp) REVERT: C 293 ARG cc_start: 0.8565 (ttm110) cc_final: 0.8321 (ttp-110) REVERT: C 314 ASP cc_start: 0.8360 (t0) cc_final: 0.7810 (m-30) REVERT: C 317 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8162 (tp) REVERT: C 474 MET cc_start: 0.9094 (mtp) cc_final: 0.8836 (mtp) outliers start: 32 outliers final: 22 residues processed: 119 average time/residue: 0.2908 time to fit residues: 46.6192 Evaluate side-chains 115 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 90 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 569 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 37 optimal weight: 1.9990 chunk 28 optimal weight: 0.0770 chunk 107 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 46 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 95 optimal weight: 0.8980 chunk 77 optimal weight: 5.9990 overall best weight: 0.8740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 531 GLN C 531 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.150931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.114036 restraints weight = 10003.814| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 1.85 r_work: 0.2957 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8623 Z= 0.117 Angle : 0.531 6.847 11693 Z= 0.273 Chirality : 0.041 0.143 1391 Planarity : 0.003 0.040 1434 Dihedral : 4.466 34.797 1196 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 3.49 % Allowed : 9.48 % Favored : 87.04 % 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: -2.33 (0.24), residues: 1064 helix: -0.68 (0.21), residues: 570 sheet: -2.70 (0.54), residues: 80 loop : -2.46 (0.27), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 426 HIS 0.005 0.001 HIS C 219 PHE 0.012 0.001 PHE C 499 TYR 0.010 0.001 TYR C 586 ARG 0.004 0.000 ARG C 158 Details of bonding type rmsd hydrogen bonds : bond 0.04058 ( 294) hydrogen bonds : angle 3.78026 ( 852) covalent geometry : bond 0.00282 ( 8623) covalent geometry : angle 0.53126 (11693) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 97 time to evaluate : 0.912 Fit side-chains REVERT: A 90 MET cc_start: 0.8811 (ptm) cc_final: 0.8532 (ptt) REVERT: A 179 LEU cc_start: 0.7754 (OUTLIER) cc_final: 0.7469 (mp) REVERT: A 314 ASP cc_start: 0.8345 (t0) cc_final: 0.7817 (m-30) REVERT: A 431 ARG cc_start: 0.8541 (ptp-110) cc_final: 0.8185 (mtm-85) REVERT: C 90 MET cc_start: 0.8774 (ptm) cc_final: 0.8468 (ptt) REVERT: C 179 LEU cc_start: 0.7665 (OUTLIER) cc_final: 0.7426 (mp) REVERT: C 293 ARG cc_start: 0.8569 (ttm110) cc_final: 0.8321 (ttp-110) REVERT: C 314 ASP cc_start: 0.8360 (t0) cc_final: 0.7816 (m-30) REVERT: C 317 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.8149 (tp) REVERT: C 474 MET cc_start: 0.9117 (mtp) cc_final: 0.8805 (mtp) outliers start: 32 outliers final: 25 residues processed: 122 average time/residue: 0.2339 time to fit residues: 38.1782 Evaluate side-chains 123 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 95 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 569 VAL Chi-restraints excluded: chain C residue 633 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 30 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 56 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 96 optimal weight: 0.5980 chunk 3 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3705 r_free = 0.3705 target = 0.155521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.119726 restraints weight = 9981.444| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 1.72 r_work: 0.3003 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.3566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8623 Z= 0.105 Angle : 0.511 6.783 11693 Z= 0.263 Chirality : 0.040 0.138 1391 Planarity : 0.003 0.040 1434 Dihedral : 4.346 33.760 1196 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 3.38 % Allowed : 9.91 % Favored : 86.71 % 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 (0.25), residues: 1064 helix: -0.44 (0.22), residues: 564 sheet: -2.65 (0.49), residues: 102 loop : -2.21 (0.29), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 426 HIS 0.005 0.001 HIS C 219 PHE 0.012 0.001 PHE A 499 TYR 0.008 0.001 TYR C 586 ARG 0.004 0.000 ARG C 158 Details of bonding type rmsd hydrogen bonds : bond 0.03737 ( 294) hydrogen bonds : angle 3.67796 ( 852) covalent geometry : bond 0.00252 ( 8623) covalent geometry : angle 0.51078 (11693) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 94 time to evaluate : 1.040 Fit side-chains REVERT: A 90 MET cc_start: 0.8805 (ptm) cc_final: 0.8529 (ptt) REVERT: A 179 LEU cc_start: 0.7696 (OUTLIER) cc_final: 0.7463 (mp) REVERT: A 314 ASP cc_start: 0.8331 (t0) cc_final: 0.7875 (m-30) REVERT: A 431 ARG cc_start: 0.8471 (ptp-110) cc_final: 0.8220 (mtm-85) REVERT: C 90 MET cc_start: 0.8798 (ptm) cc_final: 0.8502 (ptt) REVERT: C 314 ASP cc_start: 0.8257 (t0) cc_final: 0.7802 (m-30) REVERT: C 317 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8214 (tp) outliers start: 31 outliers final: 27 residues processed: 117 average time/residue: 0.2454 time to fit residues: 38.3030 Evaluate side-chains 122 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 93 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 569 VAL Chi-restraints excluded: chain C residue 633 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 42 optimal weight: 0.6980 chunk 50 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 105 optimal weight: 0.0770 chunk 74 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 overall best weight: 0.8742 ------------------------------------------------------------------------------- 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 = 0.3696 r_free = 0.3696 target = 0.154668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.118759 restraints weight = 9963.616| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 1.72 r_work: 0.2991 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.3606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8623 Z= 0.116 Angle : 0.523 6.788 11693 Z= 0.268 Chirality : 0.041 0.137 1391 Planarity : 0.003 0.040 1434 Dihedral : 4.363 32.860 1196 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 3.27 % Allowed : 10.02 % Favored : 86.71 % 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: -1.96 (0.25), residues: 1064 helix: -0.36 (0.22), residues: 564 sheet: -2.84 (0.51), residues: 92 loop : -2.18 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 426 HIS 0.005 0.001 HIS C 219 PHE 0.012 0.001 PHE A 499 TYR 0.010 0.001 TYR A 586 ARG 0.005 0.000 ARG C 158 Details of bonding type rmsd hydrogen bonds : bond 0.03988 ( 294) hydrogen bonds : angle 3.72171 ( 852) covalent geometry : bond 0.00280 ( 8623) covalent geometry : angle 0.52295 (11693) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 98 time to evaluate : 0.983 Fit side-chains REVERT: A 90 MET cc_start: 0.8808 (ptm) cc_final: 0.8531 (ptt) REVERT: A 140 LYS cc_start: 0.7533 (mtmp) cc_final: 0.7315 (ptpp) REVERT: A 314 ASP cc_start: 0.8385 (t0) cc_final: 0.7922 (m-30) REVERT: A 431 ARG cc_start: 0.8498 (ptp-110) cc_final: 0.8256 (mtm-85) REVERT: A 474 MET cc_start: 0.9088 (mtp) cc_final: 0.8792 (mtp) REVERT: C 90 MET cc_start: 0.8803 (ptm) cc_final: 0.8531 (ptt) REVERT: C 314 ASP cc_start: 0.8248 (t0) cc_final: 0.7804 (m-30) REVERT: C 317 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8207 (tp) REVERT: C 474 MET cc_start: 0.9092 (mtp) cc_final: 0.8788 (mtp) outliers start: 30 outliers final: 27 residues processed: 121 average time/residue: 0.2678 time to fit residues: 44.3962 Evaluate side-chains 122 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 94 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 569 VAL Chi-restraints excluded: chain C residue 633 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 47 optimal weight: 0.3980 chunk 27 optimal weight: 10.0000 chunk 6 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 61 optimal weight: 0.0010 chunk 100 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 overall best weight: 1.0390 ------------------------------------------------------------------------------- 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 = 0.3700 r_free = 0.3700 target = 0.153914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.115697 restraints weight = 9704.340| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 1.90 r_work: 0.2901 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.3655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8623 Z= 0.129 Angle : 0.536 6.810 11693 Z= 0.274 Chirality : 0.042 0.141 1391 Planarity : 0.004 0.040 1434 Dihedral : 4.433 32.916 1196 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 3.27 % Allowed : 10.13 % Favored : 86.60 % 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: -1.93 (0.25), residues: 1064 helix: -0.36 (0.22), residues: 566 sheet: -2.78 (0.51), residues: 92 loop : -2.15 (0.29), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 426 HIS 0.006 0.001 HIS A 219 PHE 0.012 0.001 PHE A 499 TYR 0.010 0.001 TYR C 586 ARG 0.004 0.000 ARG C 158 Details of bonding type rmsd hydrogen bonds : bond 0.04167 ( 294) hydrogen bonds : angle 3.77240 ( 852) covalent geometry : bond 0.00316 ( 8623) covalent geometry : angle 0.53627 (11693) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 92 time to evaluate : 0.944 Fit side-chains REVERT: A 90 MET cc_start: 0.8791 (ptm) cc_final: 0.8522 (ptt) REVERT: A 140 LYS cc_start: 0.7455 (mtmp) cc_final: 0.7227 (ptpp) REVERT: A 314 ASP cc_start: 0.8321 (t0) cc_final: 0.7757 (m-30) REVERT: A 431 ARG cc_start: 0.8592 (ptp-110) cc_final: 0.8324 (mtm-85) REVERT: A 474 MET cc_start: 0.9106 (mtp) cc_final: 0.8825 (mtp) REVERT: C 90 MET cc_start: 0.8798 (ptm) cc_final: 0.8529 (ptt) REVERT: C 314 ASP cc_start: 0.8232 (t0) cc_final: 0.7664 (m-30) outliers start: 30 outliers final: 27 residues processed: 116 average time/residue: 0.3220 time to fit residues: 50.9002 Evaluate side-chains 121 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 94 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 383 ILE Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 569 VAL Chi-restraints excluded: chain C residue 633 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 28 optimal weight: 10.0000 chunk 49 optimal weight: 0.0980 chunk 73 optimal weight: 0.9980 chunk 13 optimal weight: 0.0670 chunk 88 optimal weight: 0.7980 chunk 65 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 60 optimal weight: 6.9990 chunk 63 optimal weight: 0.5980 chunk 4 optimal weight: 2.9990 chunk 10 optimal weight: 0.0870 overall best weight: 0.3096 ------------------------------------------------------------------------------- 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 = 0.3604 r_free = 0.3604 target = 0.148616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.108815 restraints weight = 10049.687| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 2.10 r_work: 0.2967 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.3828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 8623 Z= 0.083 Angle : 0.474 6.651 11693 Z= 0.244 Chirality : 0.039 0.129 1391 Planarity : 0.003 0.040 1434 Dihedral : 4.077 33.011 1196 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.72 % Allowed : 11.00 % Favored : 86.27 % 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: -1.45 (0.26), residues: 1064 helix: 0.07 (0.22), residues: 558 sheet: -2.40 (0.52), residues: 102 loop : -1.96 (0.29), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 426 HIS 0.004 0.000 HIS C 219 PHE 0.010 0.001 PHE C 499 TYR 0.006 0.001 TYR C 475 ARG 0.004 0.000 ARG C 158 Details of bonding type rmsd hydrogen bonds : bond 0.03058 ( 294) hydrogen bonds : angle 3.51579 ( 852) covalent geometry : bond 0.00188 ( 8623) covalent geometry : angle 0.47431 (11693) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4991.36 seconds wall clock time: 87 minutes 39.11 seconds (5259.11 seconds total)