Starting phenix.real_space_refine on Fri Aug 22 23:14:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iwj_35768/08_2025/8iwj_35768.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iwj_35768/08_2025/8iwj_35768.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8iwj_35768/08_2025/8iwj_35768.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iwj_35768/08_2025/8iwj_35768.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8iwj_35768/08_2025/8iwj_35768.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iwj_35768/08_2025/8iwj_35768.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.013 sd= 0.141 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 5524 2.51 5 N 1416 2.21 5 O 1492 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8484 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 4242 Classifications: {'peptide': 546} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 527} Chain breaks: 4 Restraints were copied for chains: B Time building chain proxies: 2.99, per 1000 atoms: 0.35 Number of scatterers: 8484 At special positions: 0 Unit cell: (111.1, 69.3, 122.1, 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 1492 8.00 N 1416 7.00 C 5524 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: 0.62 Conformation dependent library (CDL) restraints added in 431.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2004 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 6 sheets defined 57.5% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 106 through 116 removed outlier: 3.579A pdb=" N LEU A 110 " --> pdb=" O GLY A 106 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU A 111 " --> pdb=" O LYS A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 140 removed outlier: 3.762A pdb=" N LYS A 140 " --> pdb=" O LYS A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 169 Processing helix chain 'A' and resid 175 through 180 removed outlier: 3.679A pdb=" N LEU A 179 " --> pdb=" O ARG A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 219 removed outlier: 3.732A pdb=" N SER A 216 " --> pdb=" O ARG A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 255 removed outlier: 3.813A pdb=" N VAL A 246 " --> pdb=" O ALA A 242 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA A 253 " --> pdb=" O LEU A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 275 removed outlier: 3.643A pdb=" N MET A 274 " --> pdb=" O ARG A 270 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE A 275 " --> pdb=" O VAL A 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 270 through 275' Processing helix chain 'A' and resid 295 through 303 removed outlier: 3.615A pdb=" N PHE A 299 " --> pdb=" O ALA A 295 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLU A 300 " --> pdb=" O MET A 296 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N SER A 301 " --> pdb=" O ALA A 297 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL A 302 " --> pdb=" O TYR A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 320 removed outlier: 3.652A pdb=" N LEU A 316 " --> pdb=" O PRO A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 349 removed outlier: 3.722A pdb=" N VAL A 342 " --> pdb=" O ARG A 338 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR A 347 " --> pdb=" O THR A 343 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU A 348 " --> pdb=" O ALA A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 356 removed outlier: 3.516A pdb=" N LYS A 354 " --> pdb=" O ALA A 350 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N THR A 355 " --> pdb=" O PRO A 351 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N CYS A 356 " --> pdb=" O GLN A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 397 removed outlier: 4.210A pdb=" N TRP A 386 " --> pdb=" O CYS A 382 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N HIS A 395 " --> pdb=" O CYS A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 406 removed outlier: 3.516A pdb=" N ARG A 402 " --> pdb=" O LEU A 398 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N HIS A 403 " --> pdb=" O LYS A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 425 removed outlier: 3.512A pdb=" N PHE A 412 " --> pdb=" O LEU A 408 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLN A 413 " --> pdb=" O LEU A 409 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL A 414 " --> pdb=" O ARG A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 454 removed outlier: 3.615A pdb=" N ARG A 436 " --> pdb=" O ASP A 432 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLY A 438 " --> pdb=" O HIS A 434 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N SER A 444 " --> pdb=" O LEU A 440 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY A 448 " --> pdb=" O SER A 444 " (cutoff:3.500A) Proline residue: A 451 - end of helix removed outlier: 3.764A pdb=" N ASN A 454 " --> pdb=" O LEU A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 462 removed outlier: 3.683A pdb=" N GLN A 461 " --> pdb=" O PHE A 457 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLU A 462 " --> pdb=" O THR A 458 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 457 through 462' Processing helix chain 'A' and resid 463 through 472 removed outlier: 3.552A pdb=" N ALA A 471 " --> pdb=" O THR A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 492 removed outlier: 3.617A pdb=" N MET A 482 " --> pdb=" O SER A 478 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA A 483 " --> pdb=" O SER A 479 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N HIS A 484 " --> pdb=" O TYR A 480 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY A 487 " --> pdb=" O ALA A 483 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N SER A 490 " --> pdb=" O LEU A 486 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N MET A 491 " --> pdb=" O GLY A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 504 removed outlier: 3.505A pdb=" N LEU A 500 " --> pdb=" O PRO A 496 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR A 501 " --> pdb=" O ALA A 497 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE A 502 " --> pdb=" O SER A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 542 removed outlier: 3.549A pdb=" N PHE A 516 " --> pdb=" O GLY A 512 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER A 521 " --> pdb=" O LEU A 517 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY A 532 " --> pdb=" O LEU A 528 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU A 533 " --> pdb=" O ALA A 529 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLY A 534 " --> pdb=" O SER A 530 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE A 541 " --> pdb=" O LEU A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 561 Processing helix chain 'A' and resid 575 through 579 removed outlier: 3.687A pdb=" N VAL A 579 " --> pdb=" O MET A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 594 removed outlier: 3.878A pdb=" N TYR A 584 " --> pdb=" O SER A 580 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU A 588 " --> pdb=" O TYR A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 631 removed outlier: 3.944A pdb=" N GLY A 631 " --> pdb=" O GLU A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 658 removed outlier: 3.722A pdb=" N VAL A 639 " --> pdb=" O MET A 635 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N VAL A 641 " --> pdb=" O THR A 637 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR A 649 " --> pdb=" O MET A 645 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG A 650 " --> pdb=" O PHE A 646 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA A 656 " --> pdb=" O LEU A 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 116 removed outlier: 3.579A pdb=" N LEU B 110 " --> pdb=" O GLY B 106 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU B 111 " --> pdb=" O LYS B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 140 removed outlier: 3.762A pdb=" N LYS B 140 " --> pdb=" O LYS B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 169 Processing helix chain 'B' and resid 175 through 180 removed outlier: 3.679A pdb=" N LEU B 179 " --> pdb=" O ARG B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 219 removed outlier: 3.732A pdb=" N SER B 216 " --> pdb=" O ARG B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 255 removed outlier: 3.813A pdb=" N VAL B 246 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA B 253 " --> pdb=" O LEU B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 275 removed outlier: 3.643A pdb=" N MET B 274 " --> pdb=" O ARG B 270 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE B 275 " --> pdb=" O VAL B 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 270 through 275' Processing helix chain 'B' and resid 295 through 303 removed outlier: 3.616A pdb=" N PHE B 299 " --> pdb=" O ALA B 295 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLU B 300 " --> pdb=" O MET B 296 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N SER B 301 " --> pdb=" O ALA B 297 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL B 302 " --> pdb=" O TYR B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 320 removed outlier: 3.652A pdb=" N LEU B 316 " --> pdb=" O PRO B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 349 removed outlier: 3.722A pdb=" N VAL B 342 " --> pdb=" O ARG B 338 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR B 347 " --> pdb=" O THR B 343 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU B 348 " --> pdb=" O ALA B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 356 removed outlier: 3.517A pdb=" N LYS B 354 " --> pdb=" O ALA B 350 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N THR B 355 " --> pdb=" O PRO B 351 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N CYS B 356 " --> pdb=" O GLN B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 397 removed outlier: 4.211A pdb=" N TRP B 386 " --> pdb=" O CYS B 382 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N HIS B 395 " --> pdb=" O CYS B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 406 removed outlier: 3.516A pdb=" N ARG B 402 " --> pdb=" O LEU B 398 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N HIS B 403 " --> pdb=" O LYS B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 425 removed outlier: 3.513A pdb=" N PHE B 412 " --> pdb=" O LEU B 408 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLN B 413 " --> pdb=" O LEU B 409 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL B 414 " --> pdb=" O ARG B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 454 removed outlier: 3.615A pdb=" N ARG B 436 " --> pdb=" O ASP B 432 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLY B 438 " --> pdb=" O HIS B 434 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N SER B 444 " --> pdb=" O LEU B 440 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY B 448 " --> pdb=" O SER B 444 " (cutoff:3.500A) Proline residue: B 451 - end of helix removed outlier: 3.764A pdb=" N ASN B 454 " --> pdb=" O LEU B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 462 removed outlier: 3.682A pdb=" N GLN B 461 " --> pdb=" O PHE B 457 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLU B 462 " --> pdb=" O THR B 458 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 457 through 462' Processing helix chain 'B' and resid 463 through 472 removed outlier: 3.552A pdb=" N ALA B 471 " --> pdb=" O THR B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 492 removed outlier: 3.617A pdb=" N MET B 482 " --> pdb=" O SER B 478 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA B 483 " --> pdb=" O SER B 479 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N HIS B 484 " --> pdb=" O TYR B 480 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY B 487 " --> pdb=" O ALA B 483 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N SER B 490 " --> pdb=" O LEU B 486 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N MET B 491 " --> pdb=" O GLY B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 504 removed outlier: 3.505A pdb=" N LEU B 500 " --> pdb=" O PRO B 496 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR B 501 " --> pdb=" O ALA B 497 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE B 502 " --> pdb=" O SER B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 542 removed outlier: 3.548A pdb=" N PHE B 516 " --> pdb=" O GLY B 512 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER B 521 " --> pdb=" O LEU B 517 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY B 532 " --> pdb=" O LEU B 528 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU B 533 " --> pdb=" O ALA B 529 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLY B 534 " --> pdb=" O SER B 530 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE B 541 " --> pdb=" O LEU B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 561 Processing helix chain 'B' and resid 575 through 579 removed outlier: 3.686A pdb=" N VAL B 579 " --> pdb=" O MET B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 594 removed outlier: 3.879A pdb=" N TYR B 584 " --> pdb=" O SER B 580 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU B 588 " --> pdb=" O TYR B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 631 removed outlier: 3.944A pdb=" N GLY B 631 " --> pdb=" O GLU B 628 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 658 removed outlier: 3.722A pdb=" N VAL B 639 " --> pdb=" O MET B 635 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N VAL B 641 " --> pdb=" O THR B 637 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TYR B 649 " --> pdb=" O MET B 645 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG B 650 " --> pdb=" O PHE B 646 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA B 656 " --> pdb=" O LEU B 652 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 90 through 91 Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 5.443A pdb=" N VAL A 45 " --> pdb=" O GLY A 86 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU A 84 " --> pdb=" O TYR A 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 142 through 145 removed outlier: 6.415A pdb=" N GLY A 143 " --> pdb=" O VAL A 229 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N LEU A 228 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N MET A 97 " --> pdb=" O THR A 262 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL A 278 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N VAL A 289 " --> pdb=" O VAL A 278 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LEU A 280 " --> pdb=" O LEU A 287 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 90 through 91 Processing sheet with id=AA5, first strand: chain 'B' and resid 45 through 47 removed outlier: 5.443A pdb=" N VAL B 45 " --> pdb=" O GLY B 86 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU B 84 " --> pdb=" O TYR B 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 142 through 145 removed outlier: 6.415A pdb=" N GLY B 143 " --> pdb=" O VAL B 229 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N LEU B 228 " --> pdb=" O VAL B 261 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N MET B 97 " --> pdb=" O THR B 262 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL B 278 " --> pdb=" O VAL B 289 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N VAL B 289 " --> pdb=" O VAL B 278 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LEU B 280 " --> pdb=" O LEU B 287 " (cutoff:3.500A) 336 hydrogen bonds defined for protein. 978 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: 1.38 Time building geometry restraints manager: 0.87 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: 2613 1.34 - 1.46: 1750 1.46 - 1.58: 4213 1.58 - 1.70: 0 1.70 - 1.81: 84 Bond restraints: 8660 Sorted by residual: bond pdb=" CB PRO A 451 " pdb=" CG PRO A 451 " ideal model delta sigma weight residual 1.492 1.402 0.090 5.00e-02 4.00e+02 3.24e+00 bond pdb=" CB PRO B 451 " pdb=" CG PRO B 451 " ideal model delta sigma weight residual 1.492 1.402 0.090 5.00e-02 4.00e+02 3.22e+00 bond pdb=" CG LEU B 509 " pdb=" CD2 LEU B 509 " ideal model delta sigma weight residual 1.521 1.462 0.059 3.30e-02 9.18e+02 3.19e+00 bond pdb=" CG LEU A 509 " pdb=" CD2 LEU A 509 " ideal model delta sigma weight residual 1.521 1.462 0.059 3.30e-02 9.18e+02 3.14e+00 bond pdb=" CB VAL A 185 " pdb=" CG1 VAL A 185 " ideal model delta sigma weight residual 1.521 1.463 0.058 3.30e-02 9.18e+02 3.04e+00 ... (remaining 8655 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.63: 11360 2.63 - 5.27: 330 5.27 - 7.90: 38 7.90 - 10.53: 10 10.53 - 13.17: 2 Bond angle restraints: 11740 Sorted by residual: angle pdb=" N VAL B 185 " pdb=" CA VAL B 185 " pdb=" C VAL B 185 " ideal model delta sigma weight residual 112.96 107.28 5.68 1.00e+00 1.00e+00 3.23e+01 angle pdb=" N VAL A 185 " pdb=" CA VAL A 185 " pdb=" C VAL A 185 " ideal model delta sigma weight residual 112.96 107.30 5.66 1.00e+00 1.00e+00 3.21e+01 angle pdb=" N SER A 571 " pdb=" CA SER A 571 " pdb=" C SER A 571 " ideal model delta sigma weight residual 110.80 119.38 -8.58 2.13e+00 2.20e-01 1.62e+01 angle pdb=" N SER B 571 " pdb=" CA SER B 571 " pdb=" C SER B 571 " ideal model delta sigma weight residual 110.80 119.36 -8.56 2.13e+00 2.20e-01 1.61e+01 angle pdb=" CB ARG B 436 " pdb=" CG ARG B 436 " pdb=" CD ARG B 436 " ideal model delta sigma weight residual 111.30 120.24 -8.94 2.30e+00 1.89e-01 1.51e+01 ... (remaining 11735 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.02: 4828 15.02 - 30.03: 211 30.03 - 45.05: 39 45.05 - 60.06: 6 60.06 - 75.08: 6 Dihedral angle restraints: 5090 sinusoidal: 1968 harmonic: 3122 Sorted by residual: dihedral pdb=" CA VAL A 177 " pdb=" C VAL A 177 " pdb=" N LYS A 178 " pdb=" CA LYS A 178 " ideal model delta harmonic sigma weight residual 180.00 155.42 24.58 0 5.00e+00 4.00e-02 2.42e+01 dihedral pdb=" CA VAL B 177 " pdb=" C VAL B 177 " pdb=" N LYS B 178 " pdb=" CA LYS B 178 " ideal model delta harmonic sigma weight residual 180.00 155.43 24.57 0 5.00e+00 4.00e-02 2.41e+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 180.00 155.73 24.27 0 5.00e+00 4.00e-02 2.36e+01 ... (remaining 5087 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 932 0.057 - 0.115: 388 0.115 - 0.172: 62 0.172 - 0.229: 13 0.229 - 0.286: 5 Chirality restraints: 1400 Sorted by residual: chirality pdb=" CB VAL B 177 " pdb=" CA VAL B 177 " pdb=" CG1 VAL B 177 " pdb=" CG2 VAL B 177 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" CB VAL A 177 " pdb=" CA VAL A 177 " pdb=" CG1 VAL A 177 " pdb=" CG2 VAL A 177 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" CB ILE B 630 " pdb=" CA ILE B 630 " pdb=" CG1 ILE B 630 " pdb=" CG2 ILE B 630 " both_signs ideal model delta sigma weight residual False 2.64 2.90 -0.26 2.00e-01 2.50e+01 1.67e+00 ... (remaining 1397 not shown) Planarity restraints: 1440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 450 " 0.040 5.00e-02 4.00e+02 6.01e-02 5.78e+00 pdb=" N PRO A 451 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO A 451 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 451 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 450 " -0.040 5.00e-02 4.00e+02 5.99e-02 5.74e+00 pdb=" N PRO B 451 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO B 451 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 451 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 350 " -0.035 5.00e-02 4.00e+02 5.29e-02 4.48e+00 pdb=" N PRO A 351 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 351 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 351 " -0.030 5.00e-02 4.00e+02 ... (remaining 1437 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 2932 2.87 - 3.38: 7205 3.38 - 3.89: 12546 3.89 - 4.39: 15065 4.39 - 4.90: 26518 Nonbonded interactions: 64266 Sorted by model distance: nonbonded pdb=" O TYR B 298 " pdb=" OG SER B 301 " model vdw 2.363 3.040 nonbonded pdb=" O TYR A 298 " pdb=" OG SER A 301 " model vdw 2.364 3.040 nonbonded pdb=" OG SER A 452 " pdb=" O SER A 530 " model vdw 2.424 3.040 nonbonded pdb=" N GLY A 572 " pdb=" N MET A 573 " model vdw 2.424 2.560 nonbonded pdb=" OG SER B 452 " pdb=" O SER B 530 " model vdw 2.424 3.040 ... (remaining 64261 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.860 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.010 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 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 : 0.010 0.090 8660 Z= 0.420 Angle : 1.062 13.167 11740 Z= 0.560 Chirality : 0.062 0.286 1400 Planarity : 0.007 0.060 1440 Dihedral : 9.688 75.080 3086 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.84 % Favored : 91.98 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -6.16 (0.16), residues: 1072 helix: -4.85 (0.06), residues: 588 sheet: -1.12 (0.62), residues: 62 loop : -3.10 (0.25), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 436 TYR 0.023 0.003 TYR A 526 PHE 0.027 0.004 PHE B 163 TRP 0.024 0.004 TRP B 447 HIS 0.013 0.003 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.01022 ( 8660) covalent geometry : angle 1.06226 (11740) hydrogen bonds : bond 0.36259 ( 336) hydrogen bonds : angle 10.57445 ( 978) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.332 Fit side-chains REVERT: A 224 ASN cc_start: 0.8933 (t0) cc_final: 0.8724 (t0) REVERT: A 474 MET cc_start: 0.8472 (mtp) cc_final: 0.8096 (mtm) REVERT: A 565 TYR cc_start: 0.8624 (m-80) cc_final: 0.8359 (m-80) REVERT: B 224 ASN cc_start: 0.8886 (t0) cc_final: 0.8621 (t0) REVERT: B 565 TYR cc_start: 0.8642 (m-80) cc_final: 0.8330 (m-80) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.6359 time to fit residues: 73.4105 Evaluate side-chains 81 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.4980 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 0.5980 chunk 106 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 ASN A 531 GLN B 130 ASN B 531 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.156053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.113480 restraints weight = 9862.446| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 1.97 r_work: 0.3061 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 8660 Z= 0.106 Angle : 0.579 6.691 11740 Z= 0.302 Chirality : 0.041 0.141 1400 Planarity : 0.005 0.039 1440 Dihedral : 5.418 46.277 1180 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 0.86 % Allowed : 6.59 % Favored : 92.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.19 (0.21), residues: 1072 helix: -2.77 (0.16), residues: 594 sheet: -0.68 (0.65), residues: 62 loop : -2.94 (0.26), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 180 TYR 0.010 0.001 TYR A 586 PHE 0.018 0.001 PHE A 502 TRP 0.012 0.001 TRP A 447 HIS 0.004 0.001 HIS B 219 Details of bonding type rmsd covalent geometry : bond 0.00233 ( 8660) covalent geometry : angle 0.57888 (11740) hydrogen bonds : bond 0.04744 ( 336) hydrogen bonds : angle 4.72877 ( 978) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 0.317 Fit side-chains REVERT: A 224 ASN cc_start: 0.9028 (t0) cc_final: 0.8775 (t0) REVERT: A 565 TYR cc_start: 0.8849 (m-80) cc_final: 0.8562 (m-80) REVERT: B 224 ASN cc_start: 0.9009 (t0) cc_final: 0.8714 (t0) REVERT: B 565 TYR cc_start: 0.8860 (m-80) cc_final: 0.8533 (m-80) outliers start: 8 outliers final: 4 residues processed: 90 average time/residue: 0.5090 time to fit residues: 49.2947 Evaluate side-chains 76 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 72 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 569 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 16 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 83 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 ASN B 130 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.149518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.107222 restraints weight = 9803.898| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 1.98 r_work: 0.2961 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 8660 Z= 0.279 Angle : 0.777 11.474 11740 Z= 0.386 Chirality : 0.049 0.154 1400 Planarity : 0.006 0.080 1440 Dihedral : 5.644 46.206 1180 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 1.73 % Allowed : 7.34 % Favored : 90.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.30 (0.23), residues: 1072 helix: -1.84 (0.19), residues: 602 sheet: -0.37 (0.64), residues: 62 loop : -2.89 (0.27), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 180 TYR 0.017 0.002 TYR A 586 PHE 0.021 0.002 PHE A 96 TRP 0.023 0.003 TRP B 426 HIS 0.007 0.002 HIS B 219 Details of bonding type rmsd covalent geometry : bond 0.00698 ( 8660) covalent geometry : angle 0.77686 (11740) hydrogen bonds : bond 0.07146 ( 336) hydrogen bonds : angle 4.56413 ( 978) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 76 time to evaluate : 0.257 Fit side-chains REVERT: A 90 MET cc_start: 0.9187 (ptm) cc_final: 0.8982 (ppp) REVERT: A 224 ASN cc_start: 0.9017 (t0) cc_final: 0.8697 (t0) REVERT: A 565 TYR cc_start: 0.9001 (m-80) cc_final: 0.8775 (m-80) REVERT: B 224 ASN cc_start: 0.9002 (t0) cc_final: 0.8680 (t0) REVERT: B 565 TYR cc_start: 0.9011 (m-80) cc_final: 0.8758 (m-80) outliers start: 16 outliers final: 13 residues processed: 87 average time/residue: 0.6092 time to fit residues: 56.5806 Evaluate side-chains 87 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 513 ILE Chi-restraints excluded: chain B residue 569 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 68 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 54 optimal weight: 10.0000 chunk 47 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 7 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 ASN B 130 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.149416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.110834 restraints weight = 9983.751| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 2.15 r_work: 0.2845 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2711 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8660 Z= 0.139 Angle : 0.606 9.192 11740 Z= 0.302 Chirality : 0.042 0.135 1400 Planarity : 0.004 0.050 1440 Dihedral : 5.232 43.127 1180 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 1.73 % Allowed : 7.88 % Favored : 90.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.57 (0.24), residues: 1072 helix: -1.16 (0.20), residues: 598 sheet: -0.07 (0.66), residues: 62 loop : -2.71 (0.28), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 180 TYR 0.010 0.001 TYR B 586 PHE 0.015 0.001 PHE B 499 TRP 0.015 0.002 TRP B 426 HIS 0.004 0.001 HIS A 154 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 8660) covalent geometry : angle 0.60596 (11740) hydrogen bonds : bond 0.04975 ( 336) hydrogen bonds : angle 4.12382 ( 978) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 0.341 Fit side-chains REVERT: A 90 MET cc_start: 0.9127 (ptm) cc_final: 0.8926 (ppp) REVERT: A 224 ASN cc_start: 0.8999 (t0) cc_final: 0.8710 (t0) REVERT: A 565 TYR cc_start: 0.9019 (m-80) cc_final: 0.8785 (m-80) REVERT: B 224 ASN cc_start: 0.8995 (t0) cc_final: 0.8696 (t0) REVERT: B 565 TYR cc_start: 0.9020 (m-80) cc_final: 0.8794 (m-80) outliers start: 16 outliers final: 10 residues processed: 92 average time/residue: 0.5754 time to fit residues: 56.6920 Evaluate side-chains 89 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 273 GLN Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 513 ILE Chi-restraints excluded: chain B residue 569 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 103 optimal weight: 2.9990 chunk 63 optimal weight: 0.5980 chunk 23 optimal weight: 9.9990 chunk 40 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 102 optimal weight: 0.3980 chunk 5 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 ASN B 112 ASN B 130 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.145588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.104376 restraints weight = 10027.072| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 2.19 r_work: 0.2851 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8660 Z= 0.128 Angle : 0.575 8.414 11740 Z= 0.288 Chirality : 0.041 0.134 1400 Planarity : 0.004 0.049 1440 Dihedral : 4.991 40.605 1180 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 1.84 % Allowed : 8.42 % Favored : 89.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.13 (0.25), residues: 1072 helix: -0.79 (0.21), residues: 600 sheet: 0.27 (0.68), residues: 62 loop : -2.56 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 180 TYR 0.010 0.001 TYR A 586 PHE 0.015 0.001 PHE A 499 TRP 0.013 0.001 TRP B 426 HIS 0.004 0.001 HIS B 219 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 8660) covalent geometry : angle 0.57532 (11740) hydrogen bonds : bond 0.04702 ( 336) hydrogen bonds : angle 3.94912 ( 978) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 0.335 Fit side-chains REVERT: A 224 ASN cc_start: 0.8977 (t0) cc_final: 0.8671 (t0) REVERT: A 565 TYR cc_start: 0.9024 (m-80) cc_final: 0.8802 (m-80) REVERT: B 90 MET cc_start: 0.9126 (ptm) cc_final: 0.8891 (ppp) REVERT: B 224 ASN cc_start: 0.8971 (t0) cc_final: 0.8663 (t0) REVERT: B 565 TYR cc_start: 0.9039 (m-80) cc_final: 0.8825 (m-80) outliers start: 17 outliers final: 11 residues processed: 94 average time/residue: 0.6157 time to fit residues: 61.7020 Evaluate side-chains 90 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 79 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 513 ILE Chi-restraints excluded: chain B residue 569 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 65 optimal weight: 0.0970 chunk 78 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 19 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 ASN B 130 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.152598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.116714 restraints weight = 9715.000| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 1.64 r_work: 0.2880 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 8660 Z= 0.145 Angle : 0.600 8.323 11740 Z= 0.299 Chirality : 0.042 0.131 1400 Planarity : 0.004 0.050 1440 Dihedral : 5.012 40.701 1180 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 1.84 % Allowed : 8.96 % Favored : 89.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.95 (0.25), residues: 1072 helix: -0.63 (0.21), residues: 598 sheet: 0.44 (0.67), residues: 62 loop : -2.53 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 180 TYR 0.010 0.001 TYR B 586 PHE 0.016 0.001 PHE A 499 TRP 0.014 0.002 TRP B 426 HIS 0.004 0.001 HIS B 219 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 8660) covalent geometry : angle 0.60034 (11740) hydrogen bonds : bond 0.04910 ( 336) hydrogen bonds : angle 3.93811 ( 978) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 76 time to evaluate : 0.351 Fit side-chains REVERT: A 224 ASN cc_start: 0.8983 (t0) cc_final: 0.8703 (t0) REVERT: A 565 TYR cc_start: 0.9004 (m-80) cc_final: 0.8754 (m-80) REVERT: B 90 MET cc_start: 0.9134 (ptm) cc_final: 0.8879 (ppp) REVERT: B 224 ASN cc_start: 0.8975 (t0) cc_final: 0.8688 (t0) REVERT: B 565 TYR cc_start: 0.9005 (m-80) cc_final: 0.8758 (m-80) outliers start: 17 outliers final: 13 residues processed: 87 average time/residue: 0.5504 time to fit residues: 51.5085 Evaluate side-chains 88 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 513 ILE Chi-restraints excluded: chain B residue 569 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 63 optimal weight: 0.7980 chunk 27 optimal weight: 0.0030 chunk 3 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 chunk 75 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 28 optimal weight: 0.0170 chunk 2 optimal weight: 6.9990 chunk 35 optimal weight: 0.8980 chunk 52 optimal weight: 0.7980 chunk 66 optimal weight: 0.5980 overall best weight: 0.4428 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 ASN B 130 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.156643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.118386 restraints weight = 9837.365| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 1.86 r_work: 0.2948 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 8660 Z= 0.084 Angle : 0.511 8.038 11740 Z= 0.254 Chirality : 0.039 0.136 1400 Planarity : 0.003 0.046 1440 Dihedral : 4.587 37.430 1180 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 1.73 % Allowed : 9.29 % Favored : 88.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.52 (0.26), residues: 1072 helix: -0.27 (0.22), residues: 602 sheet: 0.60 (0.67), residues: 62 loop : -2.36 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 180 TYR 0.005 0.001 TYR A 586 PHE 0.016 0.001 PHE B 502 TRP 0.008 0.001 TRP A 426 HIS 0.002 0.000 HIS B 219 Details of bonding type rmsd covalent geometry : bond 0.00183 ( 8660) covalent geometry : angle 0.51096 (11740) hydrogen bonds : bond 0.03370 ( 336) hydrogen bonds : angle 3.65965 ( 978) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 0.341 Fit side-chains REVERT: A 205 ARG cc_start: 0.8065 (tpp-160) cc_final: 0.7681 (tmm160) REVERT: A 224 ASN cc_start: 0.9019 (t0) cc_final: 0.8779 (t0) REVERT: A 565 TYR cc_start: 0.8988 (m-80) cc_final: 0.8731 (m-80) REVERT: A 635 MET cc_start: 0.8321 (OUTLIER) cc_final: 0.8032 (tpt) REVERT: B 90 MET cc_start: 0.9099 (ptm) cc_final: 0.8888 (ppp) REVERT: B 205 ARG cc_start: 0.8080 (tpp-160) cc_final: 0.7691 (tmm160) REVERT: B 224 ASN cc_start: 0.9017 (t0) cc_final: 0.8766 (t0) REVERT: B 565 TYR cc_start: 0.8996 (m-80) cc_final: 0.8746 (m-80) REVERT: B 635 MET cc_start: 0.8308 (OUTLIER) cc_final: 0.8015 (tpt) outliers start: 16 outliers final: 6 residues processed: 90 average time/residue: 0.5431 time to fit residues: 52.5575 Evaluate side-chains 88 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 569 VAL Chi-restraints excluded: chain B residue 635 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 10 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 24 optimal weight: 0.0370 chunk 31 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 overall best weight: 2.4066 ------------------------------------------------------------------------------- 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 = 0.3651 r_free = 0.3651 target = 0.147130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.119655 restraints weight = 9764.331| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.41 r_work: 0.2934 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 8660 Z= 0.229 Angle : 0.686 10.899 11740 Z= 0.339 Chirality : 0.046 0.149 1400 Planarity : 0.005 0.069 1440 Dihedral : 5.160 42.205 1180 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 3.02 % Allowed : 8.75 % Favored : 88.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.84 (0.25), residues: 1072 helix: -0.61 (0.21), residues: 602 sheet: 0.67 (0.67), residues: 62 loop : -2.40 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 436 TYR 0.012 0.002 TYR A 586 PHE 0.021 0.002 PHE B 502 TRP 0.018 0.002 TRP B 426 HIS 0.006 0.001 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00573 ( 8660) covalent geometry : angle 0.68561 (11740) hydrogen bonds : bond 0.05956 ( 336) hydrogen bonds : angle 4.06288 ( 978) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 76 time to evaluate : 0.352 Fit side-chains REVERT: A 224 ASN cc_start: 0.9043 (t0) cc_final: 0.8830 (t0) REVERT: A 565 TYR cc_start: 0.8974 (m-80) cc_final: 0.8728 (m-80) REVERT: B 90 MET cc_start: 0.9120 (ptm) cc_final: 0.8917 (ppp) REVERT: B 224 ASN cc_start: 0.9044 (t0) cc_final: 0.8808 (t0) REVERT: B 565 TYR cc_start: 0.8983 (m-80) cc_final: 0.8731 (m-80) outliers start: 28 outliers final: 17 residues processed: 95 average time/residue: 0.5273 time to fit residues: 53.8875 Evaluate side-chains 91 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 74 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 513 ILE Chi-restraints excluded: chain B residue 569 VAL Chi-restraints excluded: chain B residue 635 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.7980 chunk 28 optimal weight: 0.2980 chunk 49 optimal weight: 0.9980 chunk 96 optimal weight: 0.6980 chunk 26 optimal weight: 7.9990 chunk 29 optimal weight: 3.9990 chunk 95 optimal weight: 0.9990 chunk 7 optimal weight: 0.3980 chunk 17 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 ASN B 130 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.151504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.124693 restraints weight = 9766.362| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.32 r_work: 0.3051 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 8660 Z= 0.095 Angle : 0.536 8.786 11740 Z= 0.266 Chirality : 0.040 0.142 1400 Planarity : 0.003 0.048 1440 Dihedral : 4.734 38.820 1180 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 1.51 % Allowed : 10.37 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.41 (0.26), residues: 1072 helix: -0.22 (0.22), residues: 600 sheet: 0.84 (0.67), residues: 62 loop : -2.27 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 180 TYR 0.006 0.001 TYR A 526 PHE 0.018 0.001 PHE B 502 TRP 0.010 0.001 TRP B 426 HIS 0.003 0.000 HIS B 219 Details of bonding type rmsd covalent geometry : bond 0.00215 ( 8660) covalent geometry : angle 0.53577 (11740) hydrogen bonds : bond 0.03754 ( 336) hydrogen bonds : angle 3.70133 ( 978) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 81 time to evaluate : 0.329 Fit side-chains REVERT: A 565 TYR cc_start: 0.8941 (m-80) cc_final: 0.8678 (m-80) REVERT: B 205 ARG cc_start: 0.8065 (tpp-160) cc_final: 0.7805 (tmm160) REVERT: B 565 TYR cc_start: 0.8928 (m-80) cc_final: 0.8679 (m-80) outliers start: 14 outliers final: 12 residues processed: 90 average time/residue: 0.5694 time to fit residues: 54.7768 Evaluate side-chains 90 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 513 ILE Chi-restraints excluded: chain B residue 569 VAL Chi-restraints excluded: chain B residue 635 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 80 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 62 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 1 optimal weight: 9.9990 chunk 99 optimal weight: 2.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN B 224 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.148357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.119026 restraints weight = 9748.076| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 1.50 r_work: 0.2943 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 8660 Z= 0.244 Angle : 0.719 10.849 11740 Z= 0.354 Chirality : 0.047 0.188 1400 Planarity : 0.005 0.071 1440 Dihedral : 5.203 42.425 1180 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 1.94 % Allowed : 10.91 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.80 (0.25), residues: 1072 helix: -0.59 (0.21), residues: 602 sheet: 0.64 (0.65), residues: 62 loop : -2.34 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 205 TYR 0.013 0.002 TYR B 586 PHE 0.024 0.002 PHE B 502 TRP 0.019 0.002 TRP B 426 HIS 0.006 0.001 HIS A 154 Details of bonding type rmsd covalent geometry : bond 0.00612 ( 8660) covalent geometry : angle 0.71899 (11740) hydrogen bonds : bond 0.06135 ( 336) hydrogen bonds : angle 4.06264 ( 978) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 74 time to evaluate : 0.357 Fit side-chains REVERT: A 205 ARG cc_start: 0.8349 (ttt90) cc_final: 0.8129 (tpp-160) REVERT: A 565 TYR cc_start: 0.8982 (m-80) cc_final: 0.8738 (m-80) REVERT: B 205 ARG cc_start: 0.8128 (tpp-160) cc_final: 0.7710 (tmm160) REVERT: B 565 TYR cc_start: 0.8994 (m-80) cc_final: 0.8745 (m-80) outliers start: 18 outliers final: 13 residues processed: 87 average time/residue: 0.5617 time to fit residues: 52.3522 Evaluate side-chains 84 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 513 ILE Chi-restraints excluded: chain B residue 569 VAL Chi-restraints excluded: chain B residue 635 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 61 optimal weight: 5.9990 chunk 95 optimal weight: 0.7980 chunk 68 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 77 optimal weight: 0.0370 chunk 78 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN B 130 ASN B 224 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.151373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.126166 restraints weight = 9764.721| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 1.23 r_work: 0.3106 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8660 Z= 0.095 Angle : 0.554 9.868 11740 Z= 0.275 Chirality : 0.040 0.187 1400 Planarity : 0.004 0.048 1440 Dihedral : 4.727 38.761 1180 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 2.05 % Allowed : 10.58 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.30 (0.26), residues: 1072 helix: -0.14 (0.22), residues: 600 sheet: 0.83 (0.66), residues: 62 loop : -2.20 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 205 TYR 0.006 0.001 TYR B 526 PHE 0.020 0.001 PHE B 502 TRP 0.009 0.001 TRP A 426 HIS 0.003 0.000 HIS B 219 Details of bonding type rmsd covalent geometry : bond 0.00210 ( 8660) covalent geometry : angle 0.55444 (11740) hydrogen bonds : bond 0.03725 ( 336) hydrogen bonds : angle 3.67861 ( 978) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2822.62 seconds wall clock time: 48 minutes 56.65 seconds (2936.65 seconds total)