Starting phenix.real_space_refine on Tue Nov 18 06:57:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6p47_20245/11_2025/6p47_20245.cif Found real_map, /net/cci-nas-00/data/ceres_data/6p47_20245/11_2025/6p47_20245.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6p47_20245/11_2025/6p47_20245.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6p47_20245/11_2025/6p47_20245.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6p47_20245/11_2025/6p47_20245.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6p47_20245/11_2025/6p47_20245.map" } resolution = 3.9 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= 0.000 sd= 0.003 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 82 5.16 5 C 7872 2.51 5 N 1928 2.21 5 O 2090 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11972 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 5986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 725, 5986 Classifications: {'peptide': 725} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 31, 'TRANS': 693} Chain breaks: 8 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Restraints were copied for chains: B Time building chain proxies: 5.28, per 1000 atoms: 0.44 Number of scatterers: 11972 At special positions: 0 Unit cell: (83.661, 119.667, 116.49, 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 82 16.00 O 2090 8.00 N 1928 7.00 C 7872 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 338 " - pdb=" SG CYS A 365 " distance=2.01 Simple disulfide: pdb=" SG CYS A 349 " - pdb=" SG CYS A 807 " distance=2.03 Simple disulfide: pdb=" SG CYS A 596 " - pdb=" SG CYS A 601 " distance=2.03 Simple disulfide: pdb=" SG CYS B 338 " - pdb=" SG CYS B 365 " distance=2.01 Simple disulfide: pdb=" SG CYS B 349 " - pdb=" SG CYS B 807 " distance=2.03 Simple disulfide: pdb=" SG CYS B 596 " - pdb=" SG CYS B 601 " distance=2.03 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: 1.14 Conformation dependent library (CDL) restraints added in 565.5 milliseconds 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2764 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 4 sheets defined 59.2% alpha, 1.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 90 through 109 removed outlier: 3.503A pdb=" N GLU A 102 " --> pdb=" O ARG A 98 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N SER A 103 " --> pdb=" O GLN A 99 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ASN A 104 " --> pdb=" O ALA A 100 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU A 105 " --> pdb=" O TYR A 101 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N HIS A 108 " --> pdb=" O ASN A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 140 removed outlier: 3.991A pdb=" N TYR A 138 " --> pdb=" O VAL A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 219 removed outlier: 3.635A pdb=" N ILE A 212 " --> pdb=" O THR A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 239 Processing helix chain 'A' and resid 264 through 272 removed outlier: 3.814A pdb=" N LEU A 269 " --> pdb=" O GLU A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 292 removed outlier: 3.739A pdb=" N ILE A 288 " --> pdb=" O PRO A 284 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG A 289 " --> pdb=" O LEU A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 327 removed outlier: 4.014A pdb=" N GLN A 308 " --> pdb=" O GLY A 304 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL A 316 " --> pdb=" O LEU A 312 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY A 317 " --> pdb=" O ALA A 313 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR A 323 " --> pdb=" O ALA A 319 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ASP A 327 " --> pdb=" O TYR A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 363 removed outlier: 3.690A pdb=" N ILE A 363 " --> pdb=" O ARG A 360 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 360 through 363' Processing helix chain 'A' and resid 364 through 376 removed outlier: 4.432A pdb=" N LYS A 370 " --> pdb=" O GLU A 366 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ILE A 373 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N PHE A 374 " --> pdb=" O LYS A 370 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N SER A 376 " --> pdb=" O CYS A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 401 removed outlier: 3.528A pdb=" N VAL A 388 " --> pdb=" O VAL A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 408 Processing helix chain 'A' and resid 446 through 462 removed outlier: 3.730A pdb=" N SER A 458 " --> pdb=" O THR A 454 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N VAL A 460 " --> pdb=" O CYS A 456 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE A 461 " --> pdb=" O ALA A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 486 removed outlier: 4.131A pdb=" N ILE A 467 " --> pdb=" O TRP A 463 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE A 468 " --> pdb=" O ILE A 464 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE A 472 " --> pdb=" O ILE A 468 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR A 477 " --> pdb=" O GLY A 473 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER A 480 " --> pdb=" O VAL A 476 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE A 483 " --> pdb=" O LEU A 479 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N VAL A 484 " --> pdb=" O SER A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 537 removed outlier: 3.631A pdb=" N MET A 507 " --> pdb=" O LEU A 503 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N THR A 509 " --> pdb=" O PRO A 505 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE A 516 " --> pdb=" O THR A 512 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SER A 517 " --> pdb=" O ALA A 513 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS A 530 " --> pdb=" O THR A 526 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL A 531 " --> pdb=" O ILE A 527 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE A 535 " --> pdb=" O VAL A 531 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN A 537 " --> pdb=" O ILE A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 572 removed outlier: 3.537A pdb=" N TYR A 547 " --> pdb=" O THR A 543 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLU A 548 " --> pdb=" O GLN A 544 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N MET A 553 " --> pdb=" O ASN A 549 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS A 554 " --> pdb=" O SER A 550 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU A 557 " --> pdb=" O MET A 553 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N PHE A 558 " --> pdb=" O LYS A 554 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER A 565 " --> pdb=" O VAL A 561 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N SER A 566 " --> pdb=" O ASN A 562 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N CYS A 567 " --> pdb=" O TYR A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 637 removed outlier: 3.756A pdb=" N GLN A 608 " --> pdb=" O GLU A 604 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLN A 623 " --> pdb=" O TRP A 619 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLU A 624 " --> pdb=" O ASN A 620 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU A 626 " --> pdb=" O ILE A 622 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LEU A 627 " --> pdb=" O GLN A 623 " (cutoff:3.500A) Proline residue: A 628 - end of helix removed outlier: 3.826A pdb=" N MET A 631 " --> pdb=" O LEU A 627 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY A 635 " --> pdb=" O MET A 631 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ARG A 636 " --> pdb=" O ASN A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 655 removed outlier: 3.564A pdb=" N TYR A 654 " --> pdb=" O GLU A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 680 removed outlier: 3.766A pdb=" N MET A 671 " --> pdb=" O GLU A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 709 removed outlier: 3.506A pdb=" N VAL A 694 " --> pdb=" O LEU A 690 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LEU A 698 " --> pdb=" O VAL A 694 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ARG A 701 " --> pdb=" O ILE A 697 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASP A 703 " --> pdb=" O GLU A 699 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ALA A 704 " --> pdb=" O ILE A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 747 removed outlier: 3.715A pdb=" N LEU A 735 " --> pdb=" O GLY A 731 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N VAL A 738 " --> pdb=" O ILE A 734 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA A 741 " --> pdb=" O VAL A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 760 removed outlier: 3.512A pdb=" N PHE A 760 " --> pdb=" O TYR A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 825 through 857 removed outlier: 3.591A pdb=" N TRP A 829 " --> pdb=" O ASN A 825 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA A 834 " --> pdb=" O HIS A 830 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE A 840 " --> pdb=" O LEU A 836 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 868 Processing helix chain 'A' and resid 868 through 880 removed outlier: 3.701A pdb=" N LEU A 874 " --> pdb=" O ARG A 870 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLN A 876 " --> pdb=" O LYS A 872 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS A 877 " --> pdb=" O TYR A 873 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N HIS A 880 " --> pdb=" O GLN A 876 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 109 removed outlier: 3.502A pdb=" N GLU B 102 " --> pdb=" O ARG B 98 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N SER B 103 " --> pdb=" O GLN B 99 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ASN B 104 " --> pdb=" O ALA B 100 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU B 105 " --> pdb=" O TYR B 101 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N HIS B 108 " --> pdb=" O ASN B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 140 removed outlier: 3.992A pdb=" N TYR B 138 " --> pdb=" O VAL B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 219 removed outlier: 3.635A pdb=" N ILE B 212 " --> pdb=" O THR B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 239 Processing helix chain 'B' and resid 264 through 272 removed outlier: 3.813A pdb=" N LEU B 269 " --> pdb=" O GLU B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 292 removed outlier: 3.740A pdb=" N ILE B 288 " --> pdb=" O PRO B 284 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG B 289 " --> pdb=" O LEU B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 327 removed outlier: 4.014A pdb=" N GLN B 308 " --> pdb=" O GLY B 304 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL B 316 " --> pdb=" O LEU B 312 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY B 317 " --> pdb=" O ALA B 313 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR B 323 " --> pdb=" O ALA B 319 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ASP B 327 " --> pdb=" O TYR B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 363 removed outlier: 3.690A pdb=" N ILE B 363 " --> pdb=" O ARG B 360 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 360 through 363' Processing helix chain 'B' and resid 364 through 376 removed outlier: 4.431A pdb=" N LYS B 370 " --> pdb=" O GLU B 366 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ILE B 373 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N PHE B 374 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N SER B 376 " --> pdb=" O CYS B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 401 removed outlier: 3.527A pdb=" N VAL B 388 " --> pdb=" O VAL B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 408 Processing helix chain 'B' and resid 446 through 462 removed outlier: 3.730A pdb=" N SER B 458 " --> pdb=" O THR B 454 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N VAL B 460 " --> pdb=" O CYS B 456 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE B 461 " --> pdb=" O ALA B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 486 removed outlier: 4.131A pdb=" N ILE B 467 " --> pdb=" O TRP B 463 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE B 468 " --> pdb=" O ILE B 464 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE B 472 " --> pdb=" O ILE B 468 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TYR B 477 " --> pdb=" O GLY B 473 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER B 480 " --> pdb=" O VAL B 476 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE B 483 " --> pdb=" O LEU B 479 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N VAL B 484 " --> pdb=" O SER B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 537 removed outlier: 3.632A pdb=" N MET B 507 " --> pdb=" O LEU B 503 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N THR B 509 " --> pdb=" O PRO B 505 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE B 516 " --> pdb=" O THR B 512 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER B 517 " --> pdb=" O ALA B 513 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS B 530 " --> pdb=" O THR B 526 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL B 531 " --> pdb=" O ILE B 527 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE B 535 " --> pdb=" O VAL B 531 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN B 537 " --> pdb=" O ILE B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 572 removed outlier: 3.537A pdb=" N TYR B 547 " --> pdb=" O THR B 543 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLU B 548 " --> pdb=" O GLN B 544 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N MET B 553 " --> pdb=" O ASN B 549 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS B 554 " --> pdb=" O SER B 550 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU B 557 " --> pdb=" O MET B 553 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N PHE B 558 " --> pdb=" O LYS B 554 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N SER B 565 " --> pdb=" O VAL B 561 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N SER B 566 " --> pdb=" O ASN B 562 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N CYS B 567 " --> pdb=" O TYR B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 637 removed outlier: 3.755A pdb=" N GLN B 608 " --> pdb=" O GLU B 604 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLN B 623 " --> pdb=" O TRP B 619 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLU B 624 " --> pdb=" O ASN B 620 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU B 626 " --> pdb=" O ILE B 622 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LEU B 627 " --> pdb=" O GLN B 623 " (cutoff:3.500A) Proline residue: B 628 - end of helix removed outlier: 3.826A pdb=" N MET B 631 " --> pdb=" O LEU B 627 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY B 635 " --> pdb=" O MET B 631 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ARG B 636 " --> pdb=" O ASN B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 651 through 655 removed outlier: 3.564A pdb=" N TYR B 654 " --> pdb=" O GLU B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 680 removed outlier: 3.766A pdb=" N MET B 671 " --> pdb=" O GLU B 667 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 709 removed outlier: 3.507A pdb=" N VAL B 694 " --> pdb=" O LEU B 690 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LEU B 698 " --> pdb=" O VAL B 694 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ARG B 701 " --> pdb=" O ILE B 697 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASP B 703 " --> pdb=" O GLU B 699 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ALA B 704 " --> pdb=" O ILE B 700 " (cutoff:3.500A) Processing helix chain 'B' and resid 725 through 747 removed outlier: 3.715A pdb=" N LEU B 735 " --> pdb=" O GLY B 731 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N VAL B 738 " --> pdb=" O ILE B 734 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA B 741 " --> pdb=" O VAL B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 750 through 760 removed outlier: 3.513A pdb=" N PHE B 760 " --> pdb=" O TYR B 756 " (cutoff:3.500A) Processing helix chain 'B' and resid 825 through 857 removed outlier: 3.591A pdb=" N TRP B 829 " --> pdb=" O ASN B 825 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA B 834 " --> pdb=" O HIS B 830 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE B 840 " --> pdb=" O LEU B 836 " (cutoff:3.500A) Processing helix chain 'B' and resid 863 through 868 Processing helix chain 'B' and resid 868 through 880 removed outlier: 3.701A pdb=" N LEU B 874 " --> pdb=" O ARG B 870 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLN B 876 " --> pdb=" O LYS B 872 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS B 877 " --> pdb=" O TYR B 873 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N HIS B 880 " --> pdb=" O GLN B 876 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 125 through 127 Processing sheet with id=AA2, first strand: chain 'A' and resid 145 through 146 removed outlier: 3.786A pdb=" N LEU A 146 " --> pdb=" O SER A 190 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N SER A 190 " --> pdb=" O LEU A 146 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 125 through 127 Processing sheet with id=AA4, first strand: chain 'B' and resid 145 through 146 removed outlier: 3.786A pdb=" N LEU B 146 " --> pdb=" O SER B 190 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N SER B 190 " --> pdb=" O LEU B 146 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 524 hydrogen bonds defined for protein. 1566 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: 1.77 Time building geometry restraints manager: 1.40 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: 3515 1.34 - 1.46: 2910 1.46 - 1.58: 5749 1.58 - 1.70: 0 1.70 - 1.82: 124 Bond restraints: 12298 Sorted by residual: bond pdb=" C LEU B 627 " pdb=" N PRO B 628 " ideal model delta sigma weight residual 1.336 1.369 -0.034 9.80e-03 1.04e+04 1.17e+01 bond pdb=" C LEU A 627 " pdb=" N PRO A 628 " ideal model delta sigma weight residual 1.336 1.369 -0.033 9.80e-03 1.04e+04 1.12e+01 bond pdb=" N PRO A 421 " pdb=" CD PRO A 421 " ideal model delta sigma weight residual 1.473 1.513 -0.040 1.40e-02 5.10e+03 8.01e+00 bond pdb=" N PRO B 421 " pdb=" CD PRO B 421 " ideal model delta sigma weight residual 1.473 1.513 -0.040 1.40e-02 5.10e+03 7.96e+00 bond pdb=" N PRO B 340 " pdb=" CA PRO B 340 " ideal model delta sigma weight residual 1.469 1.487 -0.018 7.40e-03 1.83e+04 6.08e+00 ... (remaining 12293 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 15572 2.12 - 4.25: 860 4.25 - 6.37: 147 6.37 - 8.49: 61 8.49 - 10.61: 24 Bond angle restraints: 16664 Sorted by residual: angle pdb=" CA PRO A 340 " pdb=" C PRO A 340 " pdb=" N ASP A 341 " ideal model delta sigma weight residual 116.20 109.36 6.84 8.00e-01 1.56e+00 7.31e+01 angle pdb=" CA PRO B 340 " pdb=" C PRO B 340 " pdb=" N ASP B 341 " ideal model delta sigma weight residual 116.20 109.37 6.83 8.00e-01 1.56e+00 7.29e+01 angle pdb=" N LEU B 503 " pdb=" CA LEU B 503 " pdb=" C LEU B 503 " ideal model delta sigma weight residual 111.36 119.69 -8.33 1.09e+00 8.42e-01 5.84e+01 angle pdb=" N LYS A 862 " pdb=" CA LYS A 862 " pdb=" CB LYS A 862 " ideal model delta sigma weight residual 110.90 100.75 10.15 1.33e+00 5.65e-01 5.83e+01 angle pdb=" N LEU A 503 " pdb=" CA LEU A 503 " pdb=" C LEU A 503 " ideal model delta sigma weight residual 111.36 119.68 -8.32 1.09e+00 8.42e-01 5.83e+01 ... (remaining 16659 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.23: 6170 17.23 - 34.46: 824 34.46 - 51.69: 156 51.69 - 68.92: 72 68.92 - 86.15: 18 Dihedral angle restraints: 7240 sinusoidal: 2950 harmonic: 4290 Sorted by residual: dihedral pdb=" CB CYS B 349 " pdb=" SG CYS B 349 " pdb=" SG CYS B 807 " pdb=" CB CYS B 807 " ideal model delta sinusoidal sigma weight residual -86.00 -146.80 60.80 1 1.00e+01 1.00e-02 4.92e+01 dihedral pdb=" CB CYS A 349 " pdb=" SG CYS A 349 " pdb=" SG CYS A 807 " pdb=" CB CYS A 807 " ideal model delta sinusoidal sigma weight residual -86.00 -146.80 60.80 1 1.00e+01 1.00e-02 4.92e+01 dihedral pdb=" CA LEU B 123 " pdb=" C LEU B 123 " pdb=" N VAL B 124 " pdb=" CA VAL B 124 " ideal model delta harmonic sigma weight residual -180.00 -151.43 -28.57 0 5.00e+00 4.00e-02 3.27e+01 ... (remaining 7237 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 1457 0.077 - 0.155: 282 0.155 - 0.232: 58 0.232 - 0.310: 9 0.310 - 0.387: 10 Chirality restraints: 1816 Sorted by residual: chirality pdb=" CA THR B 504 " pdb=" N THR B 504 " pdb=" C THR B 504 " pdb=" CB THR B 504 " both_signs ideal model delta sigma weight residual False 2.53 2.14 0.39 2.00e-01 2.50e+01 3.75e+00 chirality pdb=" CA THR A 504 " pdb=" N THR A 504 " pdb=" C THR A 504 " pdb=" CB THR A 504 " both_signs ideal model delta sigma weight residual False 2.53 2.14 0.39 2.00e-01 2.50e+01 3.72e+00 chirality pdb=" CA ASP B 353 " pdb=" N ASP B 353 " pdb=" C ASP B 353 " pdb=" CB ASP B 353 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.38e+00 ... (remaining 1813 not shown) Planarity restraints: 2066 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 420 " 0.068 5.00e-02 4.00e+02 1.02e-01 1.68e+01 pdb=" N PRO A 421 " -0.177 5.00e-02 4.00e+02 pdb=" CA PRO A 421 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO A 421 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 420 " 0.068 5.00e-02 4.00e+02 1.02e-01 1.67e+01 pdb=" N PRO B 421 " -0.177 5.00e-02 4.00e+02 pdb=" CA PRO B 421 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO B 421 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PRO B 340 " 0.015 2.00e-02 2.50e+03 3.11e-02 9.67e+00 pdb=" C PRO B 340 " -0.054 2.00e-02 2.50e+03 pdb=" O PRO B 340 " 0.021 2.00e-02 2.50e+03 pdb=" N ASP B 341 " 0.018 2.00e-02 2.50e+03 ... (remaining 2063 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 3054 2.77 - 3.31: 11735 3.31 - 3.84: 20391 3.84 - 4.37: 23821 4.37 - 4.90: 37772 Nonbonded interactions: 96773 Sorted by model distance: nonbonded pdb=" O ILE A 743 " pdb=" OG1 THR A 747 " model vdw 2.243 3.040 nonbonded pdb=" O ILE B 743 " pdb=" OG1 THR B 747 " model vdw 2.244 3.040 nonbonded pdb=" O GLN B 506 " pdb=" OG SER B 510 " model vdw 2.271 3.040 nonbonded pdb=" O GLN A 506 " pdb=" OG SER A 510 " model vdw 2.271 3.040 nonbonded pdb=" O VAL A 476 " pdb=" OG SER A 480 " model vdw 2.280 3.040 ... (remaining 96768 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 group one per residue 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: 1.140 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.090 Find NCS groups from input model: 0.100 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: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 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 : 0.007 0.057 12304 Z= 0.347 Angle : 1.211 10.613 16676 Z= 0.705 Chirality : 0.072 0.387 1816 Planarity : 0.009 0.102 2066 Dihedral : 17.018 86.147 4458 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.57 % Allowed : 8.77 % Favored : 90.66 % Rotamer: Outliers : 3.68 % Allowed : 11.50 % Favored : 84.82 % Cbeta Deviations : 0.14 % 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 are not related in a simple way. whole: -5.94 (0.15), residues: 1414 helix: -4.01 (0.10), residues: 732 sheet: -4.06 (0.44), residues: 54 loop : -3.74 (0.20), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 420 TYR 0.034 0.002 TYR A 306 PHE 0.021 0.002 PHE B 231 TRP 0.024 0.002 TRP B 397 HIS 0.005 0.001 HIS A 830 Details of bonding type rmsd covalent geometry : bond 0.00717 (12298) covalent geometry : angle 1.20984 (16664) SS BOND : bond 0.00986 ( 6) SS BOND : angle 2.08683 ( 12) hydrogen bonds : bond 0.30479 ( 524) hydrogen bonds : angle 10.25683 ( 1566) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 350 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 MET cc_start: 0.3007 (tmm) cc_final: 0.2506 (ttp) REVERT: A 403 GLU cc_start: 0.7830 (pt0) cc_final: 0.7386 (pt0) REVERT: A 428 ASN cc_start: 0.8229 (p0) cc_final: 0.7771 (p0) REVERT: A 463 TRP cc_start: 0.6533 (t-100) cc_final: 0.5998 (t-100) REVERT: A 558 PHE cc_start: 0.8407 (t80) cc_final: 0.7963 (t80) REVERT: A 612 ILE cc_start: 0.9048 (mt) cc_final: 0.7725 (mt) REVERT: A 621 ASN cc_start: 0.8224 (m-40) cc_final: 0.8015 (m110) REVERT: A 667 GLU cc_start: 0.7407 (mp0) cc_final: 0.7132 (mp0) REVERT: A 685 PHE cc_start: 0.8305 (t80) cc_final: 0.8094 (t80) REVERT: A 867 LYS cc_start: 0.8332 (mmtm) cc_final: 0.8100 (mmtp) REVERT: A 870 ARG cc_start: 0.7280 (ttt180) cc_final: 0.7039 (mpt180) REVERT: B 386 MET cc_start: 0.8021 (mmp) cc_final: 0.7818 (mmt) REVERT: B 463 TRP cc_start: 0.7271 (t-100) cc_final: 0.6877 (t-100) REVERT: B 467 ILE cc_start: 0.8558 (mp) cc_final: 0.8279 (mp) REVERT: B 558 PHE cc_start: 0.8037 (t80) cc_final: 0.7632 (t80) REVERT: B 616 LYS cc_start: 0.9221 (tptt) cc_final: 0.8705 (tptp) REVERT: B 685 PHE cc_start: 0.8448 (t80) cc_final: 0.8187 (t80) REVERT: B 867 LYS cc_start: 0.8806 (mmtm) cc_final: 0.8484 (mmmm) outliers start: 48 outliers final: 14 residues processed: 384 average time/residue: 0.1113 time to fit residues: 60.6296 Evaluate side-chains 276 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 262 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 759 SER Chi-restraints excluded: chain A residue 865 LYS Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 480 SER Chi-restraints excluded: chain B residue 684 SER Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 865 LYS Chi-restraints excluded: chain B residue 875 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 ASN A 143 HIS ** A 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 415 GLN A 740 ASN B 56 ASN B 143 HIS B 234 ASN ** B 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 621 ASN B 740 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.105000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.088445 restraints weight = 38589.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.089699 restraints weight = 25691.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.089980 restraints weight = 19639.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.090408 restraints weight = 17878.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.090383 restraints weight = 16938.458| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 12304 Z= 0.174 Angle : 0.798 9.005 16676 Z= 0.429 Chirality : 0.046 0.181 1816 Planarity : 0.007 0.061 2066 Dihedral : 7.890 83.868 1620 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.91 % Favored : 90.81 % Rotamer: Outliers : 2.53 % Allowed : 19.56 % Favored : 77.91 % 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 are not related in a simple way. whole: -4.29 (0.18), residues: 1414 helix: -2.17 (0.15), residues: 800 sheet: -3.68 (0.55), residues: 44 loop : -3.72 (0.21), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 70 TYR 0.019 0.002 TYR B 242 PHE 0.022 0.002 PHE A 385 TRP 0.026 0.002 TRP B 397 HIS 0.003 0.001 HIS A 275 Details of bonding type rmsd covalent geometry : bond 0.00366 (12298) covalent geometry : angle 0.79684 (16664) SS BOND : bond 0.00411 ( 6) SS BOND : angle 1.51844 ( 12) hydrogen bonds : bond 0.06690 ( 524) hydrogen bonds : angle 5.90660 ( 1566) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 307 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 395 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7895 (tp30) REVERT: A 415 GLN cc_start: 0.7529 (mp-120) cc_final: 0.7284 (mp10) REVERT: A 428 ASN cc_start: 0.8163 (p0) cc_final: 0.7748 (p0) REVERT: A 463 TRP cc_start: 0.6430 (t-100) cc_final: 0.6053 (t-100) REVERT: A 542 ARG cc_start: 0.8011 (mmm-85) cc_final: 0.7152 (mmm-85) REVERT: A 558 PHE cc_start: 0.8386 (t80) cc_final: 0.8122 (t80) REVERT: A 678 VAL cc_start: 0.9033 (m) cc_final: 0.8644 (p) REVERT: A 685 PHE cc_start: 0.8493 (t80) cc_final: 0.8143 (t80) REVERT: A 697 ILE cc_start: 0.9361 (pt) cc_final: 0.9035 (mt) REVERT: A 867 LYS cc_start: 0.8030 (mmtm) cc_final: 0.7570 (mmmt) REVERT: A 870 ARG cc_start: 0.7104 (ttt180) cc_final: 0.6885 (tmt170) REVERT: B 294 GLU cc_start: 0.8159 (tp30) cc_final: 0.7799 (tp30) REVERT: B 332 THR cc_start: 0.7441 (OUTLIER) cc_final: 0.7198 (t) REVERT: B 396 PHE cc_start: 0.8316 (OUTLIER) cc_final: 0.7766 (m-80) REVERT: B 420 ARG cc_start: 0.7293 (mtt90) cc_final: 0.6954 (mmt90) REVERT: B 463 TRP cc_start: 0.7238 (t-100) cc_final: 0.6803 (t-100) REVERT: B 467 ILE cc_start: 0.8619 (mp) cc_final: 0.8201 (mp) REVERT: B 509 THR cc_start: 0.7749 (m) cc_final: 0.7433 (m) REVERT: B 556 PHE cc_start: 0.8406 (t80) cc_final: 0.8138 (t80) REVERT: B 558 PHE cc_start: 0.7848 (t80) cc_final: 0.7566 (t80) REVERT: B 612 ILE cc_start: 0.8984 (mt) cc_final: 0.8190 (mt) REVERT: B 685 PHE cc_start: 0.8510 (t80) cc_final: 0.8237 (t80) REVERT: B 687 LEU cc_start: 0.9234 (OUTLIER) cc_final: 0.8864 (mm) REVERT: B 859 ASP cc_start: 0.7730 (m-30) cc_final: 0.7455 (m-30) REVERT: B 867 LYS cc_start: 0.8549 (mmtm) cc_final: 0.8150 (mmmt) outliers start: 33 outliers final: 20 residues processed: 324 average time/residue: 0.0987 time to fit residues: 46.6620 Evaluate side-chains 286 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 262 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 PHE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 750 MET Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 759 SER Chi-restraints excluded: chain A residue 851 PHE Chi-restraints excluded: chain B residue 47 PHE Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 396 PHE Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 703 ASP Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 750 MET Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 851 PHE Chi-restraints excluded: chain B residue 875 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 111 optimal weight: 6.9990 chunk 10 optimal weight: 8.9990 chunk 53 optimal weight: 2.9990 chunk 74 optimal weight: 8.9990 chunk 70 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 115 optimal weight: 0.6980 chunk 41 optimal weight: 7.9990 chunk 21 optimal weight: 1.9990 chunk 82 optimal weight: 0.0470 chunk 14 optimal weight: 9.9990 overall best weight: 0.9484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 HIS B 249 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.103826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.086287 restraints weight = 37969.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.088292 restraints weight = 23111.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.089589 restraints weight = 16413.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.090478 restraints weight = 13133.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.090972 restraints weight = 11334.398| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 12304 Z= 0.155 Angle : 0.758 9.350 16676 Z= 0.401 Chirality : 0.045 0.171 1816 Planarity : 0.006 0.055 2066 Dihedral : 7.044 86.406 1607 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.34 % Favored : 90.38 % Rotamer: Outliers : 3.22 % Allowed : 21.17 % Favored : 75.61 % 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 are not related in a simple way. whole: -3.58 (0.19), residues: 1414 helix: -1.48 (0.16), residues: 804 sheet: -3.31 (0.58), residues: 44 loop : -3.62 (0.22), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 252 TYR 0.014 0.001 TYR B 306 PHE 0.024 0.002 PHE A 681 TRP 0.020 0.001 TRP A 397 HIS 0.002 0.000 HIS A 830 Details of bonding type rmsd covalent geometry : bond 0.00334 (12298) covalent geometry : angle 0.75744 (16664) SS BOND : bond 0.00446 ( 6) SS BOND : angle 1.47392 ( 12) hydrogen bonds : bond 0.05625 ( 524) hydrogen bonds : angle 5.41366 ( 1566) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 291 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 LEU cc_start: 0.6210 (OUTLIER) cc_final: 0.5911 (mm) REVERT: A 192 MET cc_start: 0.2581 (mpp) cc_final: 0.2263 (ttp) REVERT: A 395 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.8175 (tp30) REVERT: A 398 LYS cc_start: 0.9214 (mtmm) cc_final: 0.8918 (mtmm) REVERT: A 403 GLU cc_start: 0.8315 (pt0) cc_final: 0.7944 (pt0) REVERT: A 415 GLN cc_start: 0.7400 (mp-120) cc_final: 0.6964 (mp10) REVERT: A 428 ASN cc_start: 0.8316 (p0) cc_final: 0.7989 (p0) REVERT: A 463 TRP cc_start: 0.6798 (t-100) cc_final: 0.6487 (t-100) REVERT: A 503 LEU cc_start: 0.9087 (pt) cc_final: 0.8877 (mm) REVERT: A 558 PHE cc_start: 0.8361 (t80) cc_final: 0.8047 (t80) REVERT: A 678 VAL cc_start: 0.9062 (m) cc_final: 0.8783 (p) REVERT: A 685 PHE cc_start: 0.8701 (t80) cc_final: 0.8348 (t80) REVERT: A 697 ILE cc_start: 0.9443 (pt) cc_final: 0.9148 (mt) REVERT: A 870 ARG cc_start: 0.7124 (ttt180) cc_final: 0.6827 (tmt170) REVERT: B 123 LEU cc_start: 0.6383 (OUTLIER) cc_final: 0.5815 (mm) REVERT: B 332 THR cc_start: 0.7555 (OUTLIER) cc_final: 0.7328 (t) REVERT: B 396 PHE cc_start: 0.8627 (OUTLIER) cc_final: 0.8009 (m-80) REVERT: B 415 GLN cc_start: 0.7786 (mp10) cc_final: 0.7334 (mp10) REVERT: B 420 ARG cc_start: 0.7791 (mtt90) cc_final: 0.7473 (mmt90) REVERT: B 463 TRP cc_start: 0.7418 (t-100) cc_final: 0.6866 (t-100) REVERT: B 678 VAL cc_start: 0.9188 (m) cc_final: 0.8840 (p) REVERT: B 685 PHE cc_start: 0.8563 (t80) cc_final: 0.8192 (t80) REVERT: B 773 MET cc_start: 0.8466 (mtp) cc_final: 0.8219 (mtm) REVERT: B 851 PHE cc_start: 0.8623 (OUTLIER) cc_final: 0.7531 (m-80) REVERT: B 867 LYS cc_start: 0.8318 (mmtm) cc_final: 0.8088 (mmtm) outliers start: 42 outliers final: 19 residues processed: 318 average time/residue: 0.0988 time to fit residues: 46.6251 Evaluate side-chains 284 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 259 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 PHE Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 750 MET Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 851 PHE Chi-restraints excluded: chain B residue 47 PHE Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 396 PHE Chi-restraints excluded: chain B residue 477 TYR Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 703 ASP Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 851 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 85 optimal weight: 7.9990 chunk 59 optimal weight: 1.9990 chunk 143 optimal weight: 10.0000 chunk 30 optimal weight: 1.9990 chunk 35 optimal weight: 7.9990 chunk 87 optimal weight: 8.9990 chunk 55 optimal weight: 0.4980 chunk 117 optimal weight: 6.9990 chunk 120 optimal weight: 1.9990 chunk 124 optimal weight: 0.3980 chunk 49 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 414 GLN B 655 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.103322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.086120 restraints weight = 37690.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.088020 restraints weight = 22450.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.089230 restraints weight = 16167.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 17)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.089991 restraints weight = 12962.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.090462 restraints weight = 11301.680| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 12304 Z= 0.159 Angle : 0.749 9.206 16676 Z= 0.391 Chirality : 0.045 0.187 1816 Planarity : 0.005 0.050 2066 Dihedral : 6.662 89.037 1601 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.34 % Favored : 90.38 % Rotamer: Outliers : 3.60 % Allowed : 23.31 % Favored : 73.08 % 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 are not related in a simple way. whole: -3.06 (0.21), residues: 1414 helix: -1.00 (0.17), residues: 792 sheet: -2.88 (0.68), residues: 44 loop : -3.46 (0.23), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 191 TYR 0.020 0.001 TYR B 580 PHE 0.046 0.002 PHE A 485 TRP 0.017 0.001 TRP A 397 HIS 0.003 0.001 HIS A 830 Details of bonding type rmsd covalent geometry : bond 0.00351 (12298) covalent geometry : angle 0.74864 (16664) SS BOND : bond 0.00356 ( 6) SS BOND : angle 1.19905 ( 12) hydrogen bonds : bond 0.05132 ( 524) hydrogen bonds : angle 5.19407 ( 1566) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 272 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 LEU cc_start: 0.6244 (OUTLIER) cc_final: 0.5993 (mm) REVERT: A 395 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.8151 (tp30) REVERT: A 398 LYS cc_start: 0.9227 (mtmm) cc_final: 0.8950 (mtmm) REVERT: A 403 GLU cc_start: 0.8223 (pt0) cc_final: 0.7750 (pt0) REVERT: A 407 GLU cc_start: 0.8879 (mt-10) cc_final: 0.8672 (mm-30) REVERT: A 415 GLN cc_start: 0.7363 (mp-120) cc_final: 0.7022 (mp10) REVERT: A 428 ASN cc_start: 0.8293 (p0) cc_final: 0.7980 (p0) REVERT: A 463 TRP cc_start: 0.6898 (t-100) cc_final: 0.6346 (t-100) REVERT: A 535 ILE cc_start: 0.9152 (tp) cc_final: 0.8817 (tp) REVERT: A 558 PHE cc_start: 0.8392 (t80) cc_final: 0.8173 (t80) REVERT: A 685 PHE cc_start: 0.8789 (t80) cc_final: 0.8278 (t80) REVERT: A 697 ILE cc_start: 0.9415 (pt) cc_final: 0.9196 (mt) REVERT: A 703 ASP cc_start: 0.8505 (OUTLIER) cc_final: 0.8241 (p0) REVERT: A 870 ARG cc_start: 0.7166 (ttt180) cc_final: 0.6853 (tmt170) REVERT: B 123 LEU cc_start: 0.6591 (OUTLIER) cc_final: 0.6039 (mm) REVERT: B 294 GLU cc_start: 0.8276 (tp30) cc_final: 0.8045 (tp30) REVERT: B 396 PHE cc_start: 0.8643 (t80) cc_final: 0.8049 (m-80) REVERT: B 415 GLN cc_start: 0.7939 (mp10) cc_final: 0.7610 (mp10) REVERT: B 420 ARG cc_start: 0.7864 (mtt90) cc_final: 0.7570 (mmt90) REVERT: B 463 TRP cc_start: 0.7370 (t-100) cc_final: 0.6955 (t-100) REVERT: B 468 ILE cc_start: 0.9257 (tt) cc_final: 0.9029 (mt) REVERT: B 657 GLN cc_start: 0.8741 (tp40) cc_final: 0.8500 (tp-100) REVERT: B 678 VAL cc_start: 0.9186 (m) cc_final: 0.8945 (p) REVERT: B 685 PHE cc_start: 0.8514 (t80) cc_final: 0.8179 (t80) REVERT: B 706 LYS cc_start: 0.9184 (OUTLIER) cc_final: 0.8975 (ttpt) REVERT: B 851 PHE cc_start: 0.8571 (OUTLIER) cc_final: 0.7790 (m-80) outliers start: 47 outliers final: 26 residues processed: 303 average time/residue: 0.0950 time to fit residues: 43.2351 Evaluate side-chains 287 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 255 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 PHE Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 703 ASP Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 750 MET Chi-restraints excluded: chain A residue 851 PHE Chi-restraints excluded: chain B residue 47 PHE Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 477 TYR Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 703 ASP Chi-restraints excluded: chain B residue 706 LYS Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 851 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 63 optimal weight: 6.9990 chunk 43 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 102 optimal weight: 0.6980 chunk 119 optimal weight: 10.0000 chunk 55 optimal weight: 2.9990 chunk 120 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 GLN B 674 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.103024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.085658 restraints weight = 38081.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.087525 restraints weight = 22314.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.088785 restraints weight = 15860.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.089557 restraints weight = 12702.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.090189 restraints weight = 11052.622| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.3612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 12304 Z= 0.163 Angle : 0.758 9.032 16676 Z= 0.392 Chirality : 0.045 0.231 1816 Planarity : 0.005 0.049 2066 Dihedral : 6.425 91.247 1597 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.97 % Favored : 89.75 % Rotamer: Outliers : 3.91 % Allowed : 24.92 % Favored : 71.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.93 (0.21), residues: 1414 helix: -0.85 (0.18), residues: 808 sheet: -2.81 (0.66), residues: 44 loop : -3.56 (0.22), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 191 TYR 0.022 0.001 TYR A 242 PHE 0.027 0.002 PHE A 681 TRP 0.018 0.001 TRP B 359 HIS 0.003 0.001 HIS A 830 Details of bonding type rmsd covalent geometry : bond 0.00363 (12298) covalent geometry : angle 0.75746 (16664) SS BOND : bond 0.00368 ( 6) SS BOND : angle 1.21575 ( 12) hydrogen bonds : bond 0.04974 ( 524) hydrogen bonds : angle 5.09221 ( 1566) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 275 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 GLU cc_start: 0.8381 (tp30) cc_final: 0.7557 (tp30) REVERT: A 395 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.8314 (tp30) REVERT: A 403 GLU cc_start: 0.8295 (pt0) cc_final: 0.7790 (pt0) REVERT: A 428 ASN cc_start: 0.8186 (p0) cc_final: 0.7865 (p0) REVERT: A 463 TRP cc_start: 0.7021 (t-100) cc_final: 0.6426 (t-100) REVERT: A 535 ILE cc_start: 0.9204 (tp) cc_final: 0.8926 (tp) REVERT: A 558 PHE cc_start: 0.8393 (t80) cc_final: 0.8111 (t80) REVERT: A 631 MET cc_start: 0.8258 (mpp) cc_final: 0.7950 (mpp) REVERT: A 685 PHE cc_start: 0.8841 (t80) cc_final: 0.8272 (t80) REVERT: A 870 ARG cc_start: 0.7189 (ttt180) cc_final: 0.6858 (tmt170) REVERT: B 123 LEU cc_start: 0.6581 (OUTLIER) cc_final: 0.6163 (mm) REVERT: B 396 PHE cc_start: 0.8704 (t80) cc_final: 0.8136 (m-80) REVERT: B 415 GLN cc_start: 0.8103 (mp10) cc_final: 0.7768 (mp10) REVERT: B 463 TRP cc_start: 0.7413 (t-100) cc_final: 0.6971 (t-100) REVERT: B 657 GLN cc_start: 0.8822 (tp40) cc_final: 0.8562 (tp-100) REVERT: B 678 VAL cc_start: 0.9230 (m) cc_final: 0.8984 (p) REVERT: B 685 PHE cc_start: 0.8540 (t80) cc_final: 0.8147 (t80) REVERT: B 851 PHE cc_start: 0.8573 (OUTLIER) cc_final: 0.7798 (m-80) outliers start: 51 outliers final: 29 residues processed: 308 average time/residue: 0.0895 time to fit residues: 42.1200 Evaluate side-chains 280 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 248 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 851 PHE Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 477 TYR Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 703 ASP Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 851 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 9 optimal weight: 0.5980 chunk 14 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 113 optimal weight: 0.1980 chunk 4 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 53 optimal weight: 0.9990 chunk 114 optimal weight: 4.9990 chunk 78 optimal weight: 8.9990 chunk 2 optimal weight: 4.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 844 HIS B 674 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.103856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.088155 restraints weight = 37143.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.089777 restraints weight = 24172.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.090276 restraints weight = 16599.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.090379 restraints weight = 15563.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.090669 restraints weight = 14807.833| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.3843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 12304 Z= 0.166 Angle : 0.779 10.454 16676 Z= 0.400 Chirality : 0.046 0.314 1816 Planarity : 0.005 0.052 2066 Dihedral : 6.376 92.138 1597 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.69 % Favored : 90.03 % Rotamer: Outliers : 3.99 % Allowed : 26.46 % Favored : 69.56 % 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 are not related in a simple way. whole: -2.76 (0.21), residues: 1414 helix: -0.69 (0.18), residues: 806 sheet: -2.64 (0.67), residues: 44 loop : -3.52 (0.22), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 420 TYR 0.016 0.001 TYR B 580 PHE 0.046 0.002 PHE A 485 TRP 0.019 0.001 TRP B 359 HIS 0.003 0.001 HIS A 830 Details of bonding type rmsd covalent geometry : bond 0.00373 (12298) covalent geometry : angle 0.77906 (16664) SS BOND : bond 0.00341 ( 6) SS BOND : angle 1.11342 ( 12) hydrogen bonds : bond 0.04995 ( 524) hydrogen bonds : angle 5.10905 ( 1566) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 271 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 GLU cc_start: 0.8034 (tp30) cc_final: 0.7295 (tp30) REVERT: A 403 GLU cc_start: 0.8008 (pt0) cc_final: 0.7764 (pt0) REVERT: A 428 ASN cc_start: 0.7965 (p0) cc_final: 0.7616 (p0) REVERT: A 463 TRP cc_start: 0.6929 (t-100) cc_final: 0.6627 (t-100) REVERT: A 558 PHE cc_start: 0.8398 (t80) cc_final: 0.7915 (t80) REVERT: A 685 PHE cc_start: 0.8724 (t80) cc_final: 0.8241 (t80) REVERT: A 773 MET cc_start: 0.8562 (mtm) cc_final: 0.7879 (mpp) REVERT: A 870 ARG cc_start: 0.7234 (ttt180) cc_final: 0.6969 (tmt170) REVERT: B 123 LEU cc_start: 0.6885 (OUTLIER) cc_final: 0.6359 (mm) REVERT: B 294 GLU cc_start: 0.8112 (tp30) cc_final: 0.7904 (tp30) REVERT: B 396 PHE cc_start: 0.8520 (OUTLIER) cc_final: 0.7962 (m-80) REVERT: B 415 GLN cc_start: 0.8129 (mp10) cc_final: 0.7757 (mp10) REVERT: B 463 TRP cc_start: 0.7168 (t-100) cc_final: 0.6803 (t-100) REVERT: B 657 GLN cc_start: 0.8631 (tp40) cc_final: 0.8424 (tp-100) REVERT: B 678 VAL cc_start: 0.9208 (m) cc_final: 0.8966 (p) REVERT: B 685 PHE cc_start: 0.8437 (t80) cc_final: 0.8093 (t80) REVERT: B 851 PHE cc_start: 0.8464 (OUTLIER) cc_final: 0.7859 (m-80) outliers start: 52 outliers final: 36 residues processed: 299 average time/residue: 0.0933 time to fit residues: 42.8291 Evaluate side-chains 291 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 252 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 703 ASP Chi-restraints excluded: chain A residue 706 LYS Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 851 PHE Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 396 PHE Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 477 TYR Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 703 ASP Chi-restraints excluded: chain B residue 706 LYS Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 765 TYR Chi-restraints excluded: chain B residue 851 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 96 optimal weight: 6.9990 chunk 103 optimal weight: 2.9990 chunk 127 optimal weight: 0.9980 chunk 101 optimal weight: 5.9990 chunk 57 optimal weight: 0.0870 chunk 100 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 28 optimal weight: 0.6980 chunk 10 optimal weight: 0.0050 chunk 42 optimal weight: 6.9990 overall best weight: 0.5172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 674 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.105781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.089691 restraints weight = 36897.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.091496 restraints weight = 23220.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.092616 restraints weight = 16941.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.093402 restraints weight = 13814.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.093961 restraints weight = 12030.974| |-----------------------------------------------------------------------------| r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.4070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 12304 Z= 0.147 Angle : 0.781 10.814 16676 Z= 0.398 Chirality : 0.046 0.267 1816 Planarity : 0.005 0.052 2066 Dihedral : 5.809 31.743 1594 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.62 % Favored : 90.10 % Rotamer: Outliers : 3.60 % Allowed : 27.91 % Favored : 68.48 % 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 are not related in a simple way. whole: -2.71 (0.21), residues: 1414 helix: -0.68 (0.18), residues: 804 sheet: -2.33 (0.71), residues: 44 loop : -3.46 (0.23), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 420 TYR 0.027 0.001 TYR B 580 PHE 0.024 0.002 PHE A 485 TRP 0.039 0.001 TRP A 273 HIS 0.003 0.000 HIS A 830 Details of bonding type rmsd covalent geometry : bond 0.00325 (12298) covalent geometry : angle 0.78042 (16664) SS BOND : bond 0.00242 ( 6) SS BOND : angle 1.03959 ( 12) hydrogen bonds : bond 0.04876 ( 524) hydrogen bonds : angle 5.11893 ( 1566) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 286 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 133 GLU cc_start: 0.7984 (tp30) cc_final: 0.7353 (tp30) REVERT: A 403 GLU cc_start: 0.7781 (pt0) cc_final: 0.6917 (pt0) REVERT: A 415 GLN cc_start: 0.6906 (mp10) cc_final: 0.6652 (mp10) REVERT: A 428 ASN cc_start: 0.8008 (p0) cc_final: 0.7680 (p0) REVERT: A 463 TRP cc_start: 0.6754 (t-100) cc_final: 0.6199 (t-100) REVERT: A 539 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7656 (pm20) REVERT: A 558 PHE cc_start: 0.8358 (t80) cc_final: 0.7980 (t80) REVERT: A 685 PHE cc_start: 0.8635 (t80) cc_final: 0.8189 (t80) REVERT: A 851 PHE cc_start: 0.8413 (OUTLIER) cc_final: 0.8102 (m-80) REVERT: B 123 LEU cc_start: 0.6701 (OUTLIER) cc_final: 0.6238 (mm) REVERT: B 396 PHE cc_start: 0.8448 (t80) cc_final: 0.7854 (m-80) REVERT: B 463 TRP cc_start: 0.6992 (t-100) cc_final: 0.6674 (t-100) REVERT: B 616 LYS cc_start: 0.9230 (tptt) cc_final: 0.8998 (tptp) REVERT: B 678 VAL cc_start: 0.9174 (m) cc_final: 0.8966 (p) REVERT: B 685 PHE cc_start: 0.8555 (t80) cc_final: 0.8173 (t80) REVERT: B 851 PHE cc_start: 0.8376 (OUTLIER) cc_final: 0.7838 (m-80) outliers start: 47 outliers final: 23 residues processed: 315 average time/residue: 0.0951 time to fit residues: 45.5708 Evaluate side-chains 291 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 264 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain A residue 706 LYS Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 851 PHE Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 674 GLN Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 703 ASP Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 851 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 95 optimal weight: 4.9990 chunk 72 optimal weight: 9.9990 chunk 143 optimal weight: 3.9990 chunk 117 optimal weight: 4.9990 chunk 101 optimal weight: 0.8980 chunk 41 optimal weight: 8.9990 chunk 37 optimal weight: 20.0000 chunk 26 optimal weight: 2.9990 chunk 116 optimal weight: 0.9980 chunk 4 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 415 GLN A 655 HIS A 830 HIS B 674 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.102817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.086745 restraints weight = 37091.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.088395 restraints weight = 24596.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.089443 restraints weight = 18617.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.090151 restraints weight = 15437.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.090574 restraints weight = 13665.308| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.4288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 12304 Z= 0.193 Angle : 0.817 10.906 16676 Z= 0.421 Chirality : 0.048 0.241 1816 Planarity : 0.005 0.050 2066 Dihedral : 5.796 34.992 1594 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 16.93 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.83 % Favored : 89.89 % Rotamer: Outliers : 3.45 % Allowed : 28.37 % Favored : 68.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.61 (0.21), residues: 1414 helix: -0.52 (0.18), residues: 806 sheet: -2.59 (0.66), residues: 44 loop : -3.55 (0.22), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 235 TYR 0.013 0.001 TYR A 580 PHE 0.055 0.002 PHE A 485 TRP 0.051 0.002 TRP A 273 HIS 0.002 0.001 HIS A 830 Details of bonding type rmsd covalent geometry : bond 0.00434 (12298) covalent geometry : angle 0.81648 (16664) SS BOND : bond 0.00336 ( 6) SS BOND : angle 1.09446 ( 12) hydrogen bonds : bond 0.04967 ( 524) hydrogen bonds : angle 5.22805 ( 1566) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 263 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 ASP cc_start: 0.8741 (m-30) cc_final: 0.8401 (m-30) REVERT: A 133 GLU cc_start: 0.8221 (tp30) cc_final: 0.7623 (tp30) REVERT: A 428 ASN cc_start: 0.8077 (p0) cc_final: 0.7653 (p0) REVERT: A 463 TRP cc_start: 0.7101 (t-100) cc_final: 0.6677 (t-100) REVERT: A 507 MET cc_start: 0.7992 (ppp) cc_final: 0.7791 (ppp) REVERT: A 553 MET cc_start: 0.8035 (tpt) cc_final: 0.7069 (tpp) REVERT: A 558 PHE cc_start: 0.8425 (t80) cc_final: 0.7925 (t80) REVERT: A 685 PHE cc_start: 0.8727 (t80) cc_final: 0.8116 (t80) REVERT: A 773 MET cc_start: 0.8529 (mtm) cc_final: 0.7807 (mpp) REVERT: A 851 PHE cc_start: 0.8551 (OUTLIER) cc_final: 0.8089 (m-80) REVERT: B 123 LEU cc_start: 0.6827 (OUTLIER) cc_final: 0.6354 (mm) REVERT: B 235 ARG cc_start: 0.8112 (mmm160) cc_final: 0.7149 (ttm-80) REVERT: B 294 GLU cc_start: 0.8146 (tp30) cc_final: 0.7926 (tp30) REVERT: B 396 PHE cc_start: 0.8738 (t80) cc_final: 0.8145 (m-80) REVERT: B 463 TRP cc_start: 0.7242 (t-100) cc_final: 0.6885 (t-100) REVERT: B 678 VAL cc_start: 0.9240 (m) cc_final: 0.9030 (p) REVERT: B 685 PHE cc_start: 0.8708 (t80) cc_final: 0.8091 (t80) REVERT: B 851 PHE cc_start: 0.8497 (OUTLIER) cc_final: 0.7835 (m-80) outliers start: 45 outliers final: 29 residues processed: 290 average time/residue: 0.0916 time to fit residues: 40.6612 Evaluate side-chains 283 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 251 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 706 LYS Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 765 TYR Chi-restraints excluded: chain A residue 851 PHE Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 407 GLU Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 765 TYR Chi-restraints excluded: chain B residue 851 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 15 optimal weight: 6.9990 chunk 41 optimal weight: 0.7980 chunk 94 optimal weight: 0.6980 chunk 68 optimal weight: 0.8980 chunk 131 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 92 optimal weight: 2.9990 chunk 132 optimal weight: 0.6980 chunk 86 optimal weight: 0.9980 chunk 125 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 830 HIS B 275 HIS B 330 ASN B 674 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.105258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.089730 restraints weight = 36852.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.091342 restraints weight = 23773.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.092404 restraints weight = 17721.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.093104 restraints weight = 14599.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.093395 restraints weight = 12901.898| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.4459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 12304 Z= 0.152 Angle : 0.832 11.573 16676 Z= 0.420 Chirality : 0.047 0.334 1816 Planarity : 0.005 0.050 2066 Dihedral : 5.753 34.014 1594 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.34 % Favored : 90.38 % Rotamer: Outliers : 2.84 % Allowed : 29.68 % Favored : 67.48 % 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 are not related in a simple way. whole: -2.55 (0.21), residues: 1414 helix: -0.50 (0.18), residues: 808 sheet: -2.29 (0.72), residues: 44 loop : -3.51 (0.22), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 420 TYR 0.014 0.001 TYR A 323 PHE 0.053 0.002 PHE A 485 TRP 0.034 0.001 TRP A 273 HIS 0.003 0.000 HIS A 143 Details of bonding type rmsd covalent geometry : bond 0.00345 (12298) covalent geometry : angle 0.83196 (16664) SS BOND : bond 0.00248 ( 6) SS BOND : angle 0.97973 ( 12) hydrogen bonds : bond 0.04749 ( 524) hydrogen bonds : angle 5.21209 ( 1566) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 279 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 ASP cc_start: 0.8619 (m-30) cc_final: 0.8274 (m-30) REVERT: A 133 GLU cc_start: 0.8179 (tp30) cc_final: 0.7574 (tp30) REVERT: A 415 GLN cc_start: 0.6988 (mp10) cc_final: 0.6356 (pm20) REVERT: A 428 ASN cc_start: 0.8141 (p0) cc_final: 0.7777 (p0) REVERT: A 463 TRP cc_start: 0.6984 (t-100) cc_final: 0.6767 (t-100) REVERT: A 553 MET cc_start: 0.7915 (tpt) cc_final: 0.7007 (tpp) REVERT: A 558 PHE cc_start: 0.8382 (t80) cc_final: 0.7859 (t80) REVERT: A 621 ASN cc_start: 0.8194 (m-40) cc_final: 0.7974 (m-40) REVERT: A 685 PHE cc_start: 0.8727 (t80) cc_final: 0.8137 (t80) REVERT: A 773 MET cc_start: 0.8424 (mtm) cc_final: 0.7727 (mpp) REVERT: A 851 PHE cc_start: 0.8497 (OUTLIER) cc_final: 0.8106 (m-80) REVERT: B 123 LEU cc_start: 0.6794 (OUTLIER) cc_final: 0.6311 (mm) REVERT: B 133 GLU cc_start: 0.8153 (tp30) cc_final: 0.7515 (tp30) REVERT: B 235 ARG cc_start: 0.7985 (mmm160) cc_final: 0.7234 (ttm-80) REVERT: B 396 PHE cc_start: 0.8572 (t80) cc_final: 0.8003 (m-80) REVERT: B 463 TRP cc_start: 0.7129 (t-100) cc_final: 0.6780 (t-100) REVERT: B 685 PHE cc_start: 0.8632 (t80) cc_final: 0.8382 (t80) REVERT: B 687 LEU cc_start: 0.9188 (OUTLIER) cc_final: 0.8918 (mm) REVERT: B 697 ILE cc_start: 0.9452 (pt) cc_final: 0.9174 (mm) REVERT: B 851 PHE cc_start: 0.8447 (OUTLIER) cc_final: 0.7827 (m-80) outliers start: 37 outliers final: 24 residues processed: 303 average time/residue: 0.0922 time to fit residues: 42.8136 Evaluate side-chains 284 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 256 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 706 LYS Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 851 PHE Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 330 ASN Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 407 GLU Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 674 GLN Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 851 PHE Chi-restraints excluded: chain B residue 866 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 105 optimal weight: 4.9990 chunk 101 optimal weight: 0.9980 chunk 118 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 139 optimal weight: 1.9990 chunk 24 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 chunk 135 optimal weight: 6.9990 chunk 73 optimal weight: 9.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 330 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.104943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.089068 restraints weight = 37319.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.090774 restraints weight = 23764.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.091875 restraints weight = 17516.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.092412 restraints weight = 14321.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.092961 restraints weight = 12808.515| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.4559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 12304 Z= 0.162 Angle : 0.859 12.213 16676 Z= 0.435 Chirality : 0.050 0.444 1816 Planarity : 0.005 0.052 2066 Dihedral : 5.727 34.890 1594 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.62 % Favored : 90.10 % Rotamer: Outliers : 2.38 % Allowed : 30.83 % Favored : 66.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.50 (0.21), residues: 1414 helix: -0.47 (0.18), residues: 808 sheet: -2.27 (0.72), residues: 44 loop : -3.46 (0.23), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 420 TYR 0.027 0.001 TYR A 528 PHE 0.052 0.002 PHE B 485 TRP 0.030 0.001 TRP A 273 HIS 0.002 0.000 HIS A 129 Details of bonding type rmsd covalent geometry : bond 0.00374 (12298) covalent geometry : angle 0.85908 (16664) SS BOND : bond 0.00263 ( 6) SS BOND : angle 0.96852 ( 12) hydrogen bonds : bond 0.04763 ( 524) hydrogen bonds : angle 5.25015 ( 1566) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 268 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 ASP cc_start: 0.8548 (m-30) cc_final: 0.8187 (m-30) REVERT: A 133 GLU cc_start: 0.7976 (tp30) cc_final: 0.7556 (tp30) REVERT: A 294 GLU cc_start: 0.8195 (tp30) cc_final: 0.7962 (tp30) REVERT: A 415 GLN cc_start: 0.6724 (mp10) cc_final: 0.6130 (pm20) REVERT: A 428 ASN cc_start: 0.8073 (p0) cc_final: 0.7723 (p0) REVERT: A 463 TRP cc_start: 0.6948 (t-100) cc_final: 0.6655 (t-100) REVERT: A 553 MET cc_start: 0.7899 (tpt) cc_final: 0.7031 (tpp) REVERT: A 558 PHE cc_start: 0.8372 (t80) cc_final: 0.7871 (t80) REVERT: A 685 PHE cc_start: 0.8652 (t80) cc_final: 0.8141 (t80) REVERT: A 773 MET cc_start: 0.8302 (mtm) cc_final: 0.7538 (mpp) REVERT: A 851 PHE cc_start: 0.8425 (OUTLIER) cc_final: 0.8112 (m-80) REVERT: B 123 LEU cc_start: 0.6865 (OUTLIER) cc_final: 0.6429 (mm) REVERT: B 133 GLU cc_start: 0.7883 (tp30) cc_final: 0.7324 (tp30) REVERT: B 235 ARG cc_start: 0.7903 (mmm160) cc_final: 0.7163 (ttm-80) REVERT: B 396 PHE cc_start: 0.8476 (t80) cc_final: 0.7942 (m-80) REVERT: B 463 TRP cc_start: 0.7043 (t-100) cc_final: 0.6733 (t-100) REVERT: B 685 PHE cc_start: 0.8534 (t80) cc_final: 0.8274 (t80) REVERT: B 687 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8886 (mm) REVERT: B 697 ILE cc_start: 0.9406 (pt) cc_final: 0.9125 (mm) REVERT: B 851 PHE cc_start: 0.8392 (OUTLIER) cc_final: 0.7891 (m-80) outliers start: 31 outliers final: 21 residues processed: 288 average time/residue: 0.0883 time to fit residues: 39.2911 Evaluate side-chains 284 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 259 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 706 LYS Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 851 PHE Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 407 GLU Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 851 PHE Chi-restraints excluded: chain B residue 866 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 66 optimal weight: 5.9990 chunk 100 optimal weight: 0.9980 chunk 15 optimal weight: 9.9990 chunk 95 optimal weight: 0.9990 chunk 38 optimal weight: 8.9990 chunk 83 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 84 optimal weight: 6.9990 chunk 124 optimal weight: 5.9990 chunk 59 optimal weight: 0.9990 chunk 136 optimal weight: 0.3980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 275 HIS B 674 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.106182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.090065 restraints weight = 36964.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.091836 restraints weight = 23368.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.092979 restraints weight = 17114.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.093613 restraints weight = 13914.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.094187 restraints weight = 12329.473| |-----------------------------------------------------------------------------| r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.4732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 12304 Z= 0.153 Angle : 0.845 12.330 16676 Z= 0.426 Chirality : 0.048 0.341 1816 Planarity : 0.005 0.052 2066 Dihedral : 5.663 35.365 1594 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.34 % Favored : 90.38 % Rotamer: Outliers : 2.45 % Allowed : 30.90 % Favored : 66.64 % 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 are not related in a simple way. whole: -2.45 (0.21), residues: 1414 helix: -0.44 (0.18), residues: 808 sheet: -2.10 (0.76), residues: 44 loop : -3.43 (0.23), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 420 TYR 0.024 0.001 TYR A 528 PHE 0.050 0.001 PHE B 485 TRP 0.024 0.001 TRP A 273 HIS 0.003 0.000 HIS B 143 Details of bonding type rmsd covalent geometry : bond 0.00352 (12298) covalent geometry : angle 0.84483 (16664) SS BOND : bond 0.00256 ( 6) SS BOND : angle 0.89229 ( 12) hydrogen bonds : bond 0.04617 ( 524) hydrogen bonds : angle 5.18051 ( 1566) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1933.13 seconds wall clock time: 34 minutes 24.73 seconds (2064.73 seconds total)