Starting phenix.real_space_refine on Tue Sep 24 16:23:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k0x_36780/09_2024/8k0x_36780.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k0x_36780/09_2024/8k0x_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k0x_36780/09_2024/8k0x_36780.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k0x_36780/09_2024/8k0x_36780.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k0x_36780/09_2024/8k0x_36780.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k0x_36780/09_2024/8k0x_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-5461/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: 7.70, per 1000 atoms: 0.91 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: 1.91 Conformation dependent library (CDL) restraints added in 1.0 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: 0.93 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: 2.15 Time building geometry restraints manager: 2.27 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: 1.020 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: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 24.010 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.680 ------------------------------------------------------------------------------- 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= 0.505 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 177 time to evaluate : 0.998 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: 0.3103 time to fit residues: 67.9751 Evaluate side-chains 106 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 1.019 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 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= 0.143 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 *********************** 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 fitting. rotamer outliers: 16 poor density : 125 time to evaluate : 0.922 Fit side-chains REVERT: A 90 MET cc_start: 0.8546 (ptm) cc_final: 0.8200 (ptt) REVERT: A 314 ASP cc_start: 0.7706 (t0) cc_final: 0.7436 (m-30) REVERT: A 491 MET cc_start: 0.8060 (mmp) cc_final: 0.7590 (mmt) REVERT: C 90 MET cc_start: 0.8546 (ptm) cc_final: 0.8208 (ptt) REVERT: C 314 ASP cc_start: 0.7842 (t0) cc_final: 0.7542 (m-30) outliers start: 16 outliers final: 9 residues processed: 133 average time/residue: 0.2668 time to fit residues: 45.6531 Evaluate side-chains 108 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 99 time to evaluate : 0.925 ------------------------------------------------------------------------------- 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 54 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 81 optimal weight: 8.9990 chunk 66 optimal weight: 0.9980 chunk 27 optimal weight: 5.9990 chunk 98 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 97 optimal weight: 0.6980 chunk 33 optimal weight: 4.9990 chunk 78 optimal weight: 5.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 8623 Z= 0.465 Angle : 0.757 8.899 11693 Z= 0.382 Chirality : 0.049 0.220 1391 Planarity : 0.005 0.054 1434 Dihedral : 5.576 38.873 1196 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 3.70 % Allowed : 7.19 % 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: -4.05 (0.22), residues: 1064 helix: -2.31 (0.18), residues: 564 sheet: -3.24 (0.51), residues: 86 loop : -2.91 (0.27), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 426 HIS 0.012 0.002 HIS A 219 PHE 0.029 0.003 PHE A 502 TYR 0.031 0.003 TYR A 508 ARG 0.006 0.001 ARG C 410 *********************** 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 138 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 104 time to evaluate : 0.921 Fit side-chains REVERT: A 90 MET cc_start: 0.8631 (ptm) cc_final: 0.8271 (ptt) REVERT: A 293 ARG cc_start: 0.8026 (ttp-110) cc_final: 0.7817 (ttp-110) REVERT: A 314 ASP cc_start: 0.7746 (t0) cc_final: 0.7528 (m-30) REVERT: A 408 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8597 (mp) REVERT: C 90 MET cc_start: 0.8626 (ptm) cc_final: 0.8274 (ptt) REVERT: C 314 ASP cc_start: 0.7800 (t0) cc_final: 0.7546 (m-30) REVERT: C 408 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8499 (mp) outliers start: 34 outliers final: 24 residues processed: 129 average time/residue: 0.2586 time to fit residues: 43.3752 Evaluate side-chains 121 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 95 time to evaluate : 0.981 ------------------------------------------------------------------------------- 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 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 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 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 633 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 chunk 50 optimal weight: 8.9990 chunk 10 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 98 optimal weight: 0.5980 chunk 104 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 93 optimal weight: 0.8980 chunk 28 optimal weight: 7.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8623 Z= 0.167 Angle : 0.556 6.707 11693 Z= 0.288 Chirality : 0.041 0.140 1391 Planarity : 0.004 0.041 1434 Dihedral : 4.858 36.322 1196 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 2.61 % Allowed : 8.93 % Favored : 88.45 % 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: -3.29 (0.23), residues: 1064 helix: -1.59 (0.20), residues: 572 sheet: -3.02 (0.52), residues: 84 loop : -2.71 (0.27), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 426 HIS 0.005 0.001 HIS A 219 PHE 0.019 0.001 PHE A 502 TYR 0.009 0.001 TYR C 586 ARG 0.003 0.000 ARG C 158 *********************** 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 125 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 101 time to evaluate : 0.881 Fit side-chains REVERT: A 90 MET cc_start: 0.8547 (ptm) cc_final: 0.8183 (ptt) REVERT: A 179 LEU cc_start: 0.7627 (OUTLIER) cc_final: 0.7339 (mp) REVERT: A 314 ASP cc_start: 0.7733 (t0) cc_final: 0.7531 (m-30) REVERT: C 90 MET cc_start: 0.8554 (ptm) cc_final: 0.8211 (ptt) REVERT: C 179 LEU cc_start: 0.7570 (pt) cc_final: 0.7266 (mp) REVERT: C 293 ARG cc_start: 0.7932 (ttm110) cc_final: 0.7695 (ttp-110) REVERT: C 408 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8406 (mp) outliers start: 24 outliers final: 15 residues processed: 119 average time/residue: 0.2698 time to fit residues: 41.7282 Evaluate side-chains 108 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 91 time to evaluate : 0.967 ------------------------------------------------------------------------------- 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 197 THR Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 566 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 43 optimal weight: 0.1980 chunk 89 optimal weight: 3.9990 chunk 72 optimal weight: 0.1980 chunk 0 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.3200 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= 0.209 Angle : 0.567 6.736 11693 Z= 0.290 Chirality : 0.042 0.145 1391 Planarity : 0.004 0.041 1434 Dihedral : 4.792 35.700 1196 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 3.59 % Allowed : 8.71 % Favored : 87.69 % 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: -2.90 (0.24), residues: 1064 helix: -1.22 (0.21), residues: 572 sheet: -2.89 (0.52), residues: 84 loop : -2.61 (0.27), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 426 HIS 0.006 0.001 HIS A 219 PHE 0.027 0.002 PHE A 502 TYR 0.012 0.001 TYR C 586 ARG 0.003 0.000 ARG C 431 *********************** 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 127 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 94 time to evaluate : 0.942 Fit side-chains REVERT: A 90 MET cc_start: 0.8538 (ptm) cc_final: 0.8209 (ptt) REVERT: A 179 LEU cc_start: 0.7637 (OUTLIER) cc_final: 0.7428 (mp) REVERT: A 314 ASP cc_start: 0.7749 (t0) cc_final: 0.7530 (m-30) REVERT: A 408 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8445 (mp) REVERT: A 474 MET cc_start: 0.8951 (mtp) cc_final: 0.8654 (mtp) REVERT: C 90 MET cc_start: 0.8572 (ptm) cc_final: 0.8228 (ptt) REVERT: C 293 ARG cc_start: 0.8025 (ttm110) cc_final: 0.7796 (ttp-110) REVERT: C 408 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8414 (mp) outliers start: 33 outliers final: 22 residues processed: 120 average time/residue: 0.2505 time to fit residues: 39.4509 Evaluate side-chains 115 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 90 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 408 LEU Chi-restraints excluded: chain A residue 450 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 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 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 450 LEU Chi-restraints excluded: chain C residue 514 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 35 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 chunk 25 optimal weight: 0.9990 chunk 104 optimal weight: 6.9990 chunk 86 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 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 : 0.005 0.042 8623 Z= 0.350 Angle : 0.646 7.788 11693 Z= 0.328 Chirality : 0.045 0.155 1391 Planarity : 0.004 0.046 1434 Dihedral : 5.108 35.855 1196 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 3.70 % Allowed : 9.26 % 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: -2.95 (0.24), residues: 1064 helix: -1.30 (0.20), residues: 574 sheet: -2.89 (0.54), residues: 80 loop : -2.58 (0.27), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 426 HIS 0.009 0.001 HIS A 219 PHE 0.014 0.002 PHE C 583 TYR 0.014 0.002 TYR A 586 ARG 0.003 0.001 ARG C 410 *********************** 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 127 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 93 time to evaluate : 0.774 Fit side-chains REVERT: A 90 MET cc_start: 0.8583 (ptm) cc_final: 0.8243 (ptt) REVERT: A 179 LEU cc_start: 0.7594 (OUTLIER) cc_final: 0.7392 (mp) REVERT: A 408 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8495 (mp) REVERT: C 90 MET cc_start: 0.8599 (ptm) cc_final: 0.8254 (ptt) REVERT: C 408 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8470 (mp) outliers start: 34 outliers final: 30 residues processed: 121 average time/residue: 0.2494 time to fit residues: 39.9645 Evaluate side-chains 124 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 91 time to evaluate : 0.912 ------------------------------------------------------------------------------- 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 408 LEU Chi-restraints excluded: chain A residue 450 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 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 128 LEU Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 180 ARG 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 0.4980 chunk 11 optimal weight: 0.9990 chunk 59 optimal weight: 6.9990 chunk 76 optimal weight: 0.0770 chunk 87 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 104 optimal weight: 0.9980 chunk 65 optimal weight: 0.0050 chunk 63 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 64 optimal weight: 0.0670 overall best weight: 0.2890 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.3545 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= 0.114 Angle : 0.500 6.513 11693 Z= 0.258 Chirality : 0.039 0.131 1391 Planarity : 0.003 0.042 1434 Dihedral : 4.429 33.153 1196 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 3.05 % Allowed : 10.68 % 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: -2.29 (0.25), residues: 1064 helix: -0.67 (0.21), residues: 570 sheet: -2.70 (0.56), residues: 80 loop : -2.40 (0.28), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 426 HIS 0.003 0.000 HIS C 219 PHE 0.012 0.001 PHE C 499 TYR 0.005 0.001 TYR A 475 ARG 0.004 0.000 ARG C 158 *********************** 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 126 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 98 time to evaluate : 0.890 Fit side-chains REVERT: A 90 MET cc_start: 0.8540 (ptm) cc_final: 0.8217 (ptt) REVERT: A 474 MET cc_start: 0.8921 (mtp) cc_final: 0.8641 (mtp) REVERT: C 90 MET cc_start: 0.8547 (ptm) cc_final: 0.8236 (ptt) REVERT: C 408 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8325 (mp) outliers start: 28 outliers final: 20 residues processed: 120 average time/residue: 0.2331 time to fit residues: 37.3414 Evaluate side-chains 113 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 92 time to evaluate : 0.822 ------------------------------------------------------------------------------- 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 174 THR Chi-restraints excluded: chain A residue 187 SER 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 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 174 THR Chi-restraints excluded: chain C residue 187 SER 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 569 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.3535 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= 0.217 Angle : 0.566 9.343 11693 Z= 0.286 Chirality : 0.042 0.145 1391 Planarity : 0.004 0.042 1434 Dihedral : 4.637 34.417 1196 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 3.05 % Allowed : 10.89 % Favored : 86.06 % 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: -2.24 (0.25), residues: 1064 helix: -0.64 (0.21), residues: 572 sheet: -2.61 (0.57), residues: 80 loop : -2.37 (0.28), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 426 HIS 0.006 0.001 HIS A 219 PHE 0.013 0.001 PHE A 583 TYR 0.012 0.001 TYR A 586 ARG 0.004 0.000 ARG C 158 *********************** 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 fitting. rotamer outliers: 28 poor density : 97 time to evaluate : 0.982 Fit side-chains REVERT: A 90 MET cc_start: 0.8566 (ptm) cc_final: 0.8245 (ptt) REVERT: A 431 ARG cc_start: 0.8001 (ptp-110) cc_final: 0.7735 (mtm-85) REVERT: C 90 MET cc_start: 0.8590 (ptm) cc_final: 0.8267 (ptt) REVERT: C 408 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8382 (mp) outliers start: 28 outliers final: 24 residues processed: 120 average time/residue: 0.2414 time to fit residues: 38.5326 Evaluate side-chains 120 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 95 time to evaluate : 0.865 ------------------------------------------------------------------------------- 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 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 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 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 90 optimal weight: 3.9990 chunk 97 optimal weight: 0.8980 chunk 99 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 76 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 96 optimal weight: 0.5980 chunk 63 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.3630 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= 0.164 Angle : 0.529 8.300 11693 Z= 0.269 Chirality : 0.041 0.137 1391 Planarity : 0.003 0.042 1434 Dihedral : 4.448 33.366 1196 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 2.94 % Allowed : 11.22 % Favored : 85.84 % 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: -1.96 (0.25), residues: 1064 helix: -0.37 (0.22), residues: 564 sheet: -2.46 (0.58), residues: 80 loop : -2.29 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 426 HIS 0.005 0.001 HIS C 219 PHE 0.013 0.001 PHE A 499 TYR 0.009 0.001 TYR A 586 ARG 0.004 0.000 ARG C 158 *********************** 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 126 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 99 time to evaluate : 0.870 Fit side-chains revert: symmetry clash REVERT: A 90 MET cc_start: 0.8573 (ptm) cc_final: 0.8252 (ptt) REVERT: A 431 ARG cc_start: 0.7968 (ptp-110) cc_final: 0.7730 (mtm-85) REVERT: C 90 MET cc_start: 0.8567 (ptm) cc_final: 0.8247 (ptt) outliers start: 27 outliers final: 26 residues processed: 121 average time/residue: 0.2372 time to fit residues: 38.3595 Evaluate side-chains 121 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 95 time to evaluate : 0.941 ------------------------------------------------------------------------------- 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 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 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 102 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 71 optimal weight: 0.0970 chunk 107 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 52 optimal weight: 0.5980 chunk 68 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3680 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= 0.177 Angle : 0.536 8.208 11693 Z= 0.272 Chirality : 0.041 0.138 1391 Planarity : 0.003 0.042 1434 Dihedral : 4.440 33.023 1196 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 3.05 % Allowed : 11.11 % Favored : 85.84 % 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: -1.84 (0.25), residues: 1064 helix: -0.29 (0.22), residues: 564 sheet: -2.39 (0.58), residues: 80 loop : -2.22 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 426 HIS 0.005 0.001 HIS A 219 PHE 0.013 0.001 PHE C 499 TYR 0.010 0.001 TYR A 586 ARG 0.004 0.000 ARG C 158 ********************** 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 127 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 99 time to evaluate : 0.972 Fit side-chains REVERT: A 90 MET cc_start: 0.8556 (ptm) cc_final: 0.8253 (ptt) REVERT: A 140 LYS cc_start: 0.7632 (mtmp) cc_final: 0.7389 (ptpp) REVERT: A 431 ARG cc_start: 0.7945 (ptp-110) cc_final: 0.7733 (mtm-85) REVERT: A 491 MET cc_start: 0.7902 (mmp) cc_final: 0.7533 (mmt) REVERT: C 90 MET cc_start: 0.8570 (ptm) cc_final: 0.8251 (ptt) REVERT: C 491 MET cc_start: 0.7903 (mmp) cc_final: 0.7536 (mmt) outliers start: 28 outliers final: 27 residues processed: 121 average time/residue: 0.2379 time to fit residues: 38.4224 Evaluate side-chains 128 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 101 time to evaluate : 1.841 ------------------------------------------------------------------------------- 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 128 LEU 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 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 91 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 79 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 88 optimal weight: 0.0970 chunk 10 optimal weight: 0.0670 chunk 15 optimal weight: 0.6980 chunk 75 optimal weight: 4.9990 overall best weight: 0.7518 ------------------------------------------------------------------------------- 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 = 0.3715 r_free = 0.3715 target = 0.155030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.117001 restraints weight = 9566.127| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 1.88 r_work: 0.2922 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.3744 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= 0.160 Angle : 0.520 7.768 11693 Z= 0.265 Chirality : 0.041 0.136 1391 Planarity : 0.003 0.042 1434 Dihedral : 4.349 33.513 1196 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.94 % Allowed : 11.44 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.25), residues: 1064 helix: -0.16 (0.22), residues: 562 sheet: -2.47 (0.52), residues: 102 loop : -2.03 (0.29), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 426 HIS 0.004 0.001 HIS C 219 PHE 0.013 0.001 PHE A 499 TYR 0.009 0.001 TYR A 586 ARG 0.004 0.000 ARG C 158 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1952.20 seconds wall clock time: 35 minutes 17.00 seconds (2117.00 seconds total)