Starting phenix.real_space_refine on Sun Feb 8 02:18:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n0n_48787/02_2026/9n0n_48787.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n0n_48787/02_2026/9n0n_48787.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9n0n_48787/02_2026/9n0n_48787.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n0n_48787/02_2026/9n0n_48787.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9n0n_48787/02_2026/9n0n_48787.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n0n_48787/02_2026/9n0n_48787.map" } resolution = 3.3 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= 0.018 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: 5 Type Number sf(0) Gaussians S 70 5.16 5 C 12251 2.51 5 N 3425 2.21 5 O 3520 1.98 5 H 18923 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 38189 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 545, 8637 Classifications: {'peptide': 545} Link IDs: {'PTRANS': 22, 'TRANS': 522} Chain: "B" Number of atoms: 10464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 657, 10464 Classifications: {'peptide': 657} Link IDs: {'PTRANS': 23, 'TRANS': 633} Chain breaks: 7 Chain: "C" Number of atoms: 10587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 668, 10587 Classifications: {'peptide': 668} Link IDs: {'PTRANS': 25, 'TRANS': 642} Chain breaks: 6 Chain: "D" Number of atoms: 8501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 538, 8501 Classifications: {'peptide': 538} Link IDs: {'PTRANS': 22, 'TRANS': 515} Chain breaks: 1 Time building chain proxies: 5.98, per 1000 atoms: 0.16 Number of scatterers: 38189 At special positions: 0 Unit cell: (143.28, 140.4, 97.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 70 16.00 O 3520 8.00 N 3425 7.00 C 12251 6.00 H 18923 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.40 Conformation dependent library (CDL) restraints added in 1.1 seconds 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4590 Finding SS restraints... Secondary structure from input PDB file: 121 helices and 20 sheets defined 55.4% alpha, 8.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'A' and resid 378 through 392 removed outlier: 4.143A pdb=" N THR A 382 " --> pdb=" O ASN A 378 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA A 383 " --> pdb=" O GLY A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 416 Processing helix chain 'A' and resid 437 through 451 removed outlier: 3.584A pdb=" N LEU A 448 " --> pdb=" O ALA A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 457 Processing helix chain 'A' and resid 473 through 485 removed outlier: 3.638A pdb=" N ILE A 484 " --> pdb=" O GLU A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 502 removed outlier: 3.721A pdb=" N ALA A 500 " --> pdb=" O TYR A 497 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N THR A 501 " --> pdb=" O ALA A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 509 Processing helix chain 'A' and resid 510 through 524 removed outlier: 3.635A pdb=" N GLU A 516 " --> pdb=" O MET A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 538 Processing helix chain 'A' and resid 542 through 549 removed outlier: 4.078A pdb=" N VAL A 547 " --> pdb=" O SER A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 573 Processing helix chain 'A' and resid 587 through 592 Processing helix chain 'A' and resid 592 through 604 Processing helix chain 'A' and resid 609 through 615 Processing helix chain 'A' and resid 623 through 648 removed outlier: 3.741A pdb=" N GLY A 627 " --> pdb=" O VAL A 623 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU A 629 " --> pdb=" O ILE A 625 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU A 630 " --> pdb=" O GLU A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 655 removed outlier: 4.209A pdb=" N TRP A 654 " --> pdb=" O LEU A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 659 through 664 removed outlier: 3.614A pdb=" N VAL A 664 " --> pdb=" O GLU A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 669 Processing helix chain 'A' and resid 687 through 694 removed outlier: 4.306A pdb=" N TRP A 691 " --> pdb=" O TRP A 687 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG A 692 " --> pdb=" O ASN A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 722 removed outlier: 4.021A pdb=" N LEU A 722 " --> pdb=" O ARG A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 772 Processing helix chain 'A' and resid 776 through 788 Processing helix chain 'A' and resid 801 through 805 Processing helix chain 'A' and resid 814 through 822 Processing helix chain 'A' and resid 832 through 842 removed outlier: 4.279A pdb=" N GLY A 837 " --> pdb=" O ILE A 833 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N ARG A 838 " --> pdb=" O GLY A 834 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 877 Processing helix chain 'A' and resid 897 through 915 Processing helix chain 'B' and resid 26 through 47 Processing helix chain 'B' and resid 50 through 66 removed outlier: 3.789A pdb=" N ALA B 66 " --> pdb=" O ASP B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 71 Processing helix chain 'B' and resid 75 through 88 removed outlier: 3.911A pdb=" N SER B 88 " --> pdb=" O ALA B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 108 removed outlier: 3.562A pdb=" N GLU B 96 " --> pdb=" O VAL B 92 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N SER B 99 " --> pdb=" O THR B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 112 Processing helix chain 'B' and resid 177 through 183 removed outlier: 3.884A pdb=" N ILE B 180 " --> pdb=" O GLU B 177 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N THR B 181 " --> pdb=" O ASP B 178 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL B 183 " --> pdb=" O ILE B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 235 Processing helix chain 'B' and resid 379 through 392 Processing helix chain 'B' and resid 405 through 416 removed outlier: 3.557A pdb=" N HIS B 409 " --> pdb=" O HIS B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 452 removed outlier: 3.595A pdb=" N ILE B 441 " --> pdb=" O PRO B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 455 No H-bonds generated for 'chain 'B' and resid 453 through 455' Processing helix chain 'B' and resid 473 through 485 removed outlier: 3.723A pdb=" N ALA B 483 " --> pdb=" O GLU B 479 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ILE B 484 " --> pdb=" O GLU B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 510 Processing helix chain 'B' and resid 510 through 524 removed outlier: 3.583A pdb=" N SER B 523 " --> pdb=" O GLU B 519 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR B 524 " --> pdb=" O GLN B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 539 removed outlier: 3.769A pdb=" N SER B 537 " --> pdb=" O ASN B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 541 No H-bonds generated for 'chain 'B' and resid 540 through 541' Processing helix chain 'B' and resid 542 through 549 removed outlier: 4.363A pdb=" N VAL B 547 " --> pdb=" O SER B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 592 Processing helix chain 'B' and resid 592 through 604 Processing helix chain 'B' and resid 616 through 629 removed outlier: 3.687A pdb=" N ARG B 621 " --> pdb=" O ASP B 617 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLN B 622 " --> pdb=" O LEU B 618 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASP B 624 " --> pdb=" O ARG B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 648 Processing helix chain 'B' and resid 648 through 655 removed outlier: 4.365A pdb=" N TRP B 654 " --> pdb=" O LEU B 650 " (cutoff:3.500A) Processing helix chain 'B' and resid 659 through 664 Processing helix chain 'B' and resid 665 through 669 Processing helix chain 'B' and resid 689 through 694 removed outlier: 3.510A pdb=" N ASP B 694 " --> pdb=" O ALA B 690 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 711 Processing helix chain 'B' and resid 713 through 721 Processing helix chain 'B' and resid 747 through 772 Processing helix chain 'B' and resid 774 through 790 removed outlier: 3.746A pdb=" N ILE B 787 " --> pdb=" O HIS B 783 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASP B 790 " --> pdb=" O GLU B 786 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 822 Processing helix chain 'B' and resid 823 through 826 removed outlier: 5.907A pdb=" N ALA B 826 " --> pdb=" O TYR B 823 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 823 through 826' Processing helix chain 'B' and resid 832 through 842 removed outlier: 3.850A pdb=" N GLY B 837 " --> pdb=" O ILE B 833 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ARG B 838 " --> pdb=" O GLY B 834 " (cutoff:3.500A) Processing helix chain 'B' and resid 869 through 879 Processing helix chain 'B' and resid 897 through 910 removed outlier: 3.758A pdb=" N ALA B 910 " --> pdb=" O ALA B 906 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 45 removed outlier: 3.676A pdb=" N ALA C 41 " --> pdb=" O CYS C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 66 removed outlier: 3.794A pdb=" N ALA C 66 " --> pdb=" O ASP C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 71 Processing helix chain 'C' and resid 76 through 88 Processing helix chain 'C' and resid 90 through 108 removed outlier: 3.729A pdb=" N GLU C 96 " --> pdb=" O VAL C 92 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG C 103 " --> pdb=" O SER C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 278 Processing helix chain 'C' and resid 379 through 392 removed outlier: 3.535A pdb=" N ALA C 383 " --> pdb=" O GLY C 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 416 removed outlier: 3.741A pdb=" N HIS C 409 " --> pdb=" O HIS C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 451 removed outlier: 3.590A pdb=" N ILE C 441 " --> pdb=" O PRO C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 453 through 457 Processing helix chain 'C' and resid 473 through 483 Processing helix chain 'C' and resid 497 through 501 removed outlier: 3.728A pdb=" N ALA C 500 " --> pdb=" O TYR C 497 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N THR C 501 " --> pdb=" O ALA C 498 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 497 through 501' Processing helix chain 'C' and resid 503 through 510 Processing helix chain 'C' and resid 510 through 524 removed outlier: 3.558A pdb=" N SER C 523 " --> pdb=" O GLU C 519 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR C 524 " --> pdb=" O GLN C 520 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 539 Processing helix chain 'C' and resid 542 through 547 removed outlier: 4.180A pdb=" N VAL C 547 " --> pdb=" O ARG C 543 " (cutoff:3.500A) Processing helix chain 'C' and resid 587 through 592 Processing helix chain 'C' and resid 592 through 604 Processing helix chain 'C' and resid 611 through 627 removed outlier: 3.712A pdb=" N SER C 615 " --> pdb=" O GLN C 611 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG C 620 " --> pdb=" O LEU C 616 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE C 625 " --> pdb=" O ARG C 621 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU C 626 " --> pdb=" O GLN C 622 " (cutoff:3.500A) Processing helix chain 'C' and resid 629 through 649 removed outlier: 4.575A pdb=" N ARG C 649 " --> pdb=" O VAL C 645 " (cutoff:3.500A) Processing helix chain 'C' and resid 650 through 655 removed outlier: 4.218A pdb=" N TRP C 654 " --> pdb=" O LEU C 650 " (cutoff:3.500A) Processing helix chain 'C' and resid 659 through 664 Processing helix chain 'C' and resid 687 through 694 Processing helix chain 'C' and resid 708 through 711 Processing helix chain 'C' and resid 713 through 722 Processing helix chain 'C' and resid 747 through 772 Processing helix chain 'C' and resid 773 through 790 removed outlier: 3.507A pdb=" N ILE C 787 " --> pdb=" O HIS C 783 " (cutoff:3.500A) Processing helix chain 'C' and resid 814 through 822 Processing helix chain 'C' and resid 823 through 826 removed outlier: 5.841A pdb=" N ALA C 826 " --> pdb=" O TYR C 823 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 823 through 826' Processing helix chain 'C' and resid 832 through 842 removed outlier: 3.992A pdb=" N GLY C 837 " --> pdb=" O ILE C 833 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ARG C 838 " --> pdb=" O GLY C 834 " (cutoff:3.500A) Processing helix chain 'C' and resid 869 through 879 Processing helix chain 'C' and resid 897 through 910 removed outlier: 3.833A pdb=" N ALA C 910 " --> pdb=" O ALA C 906 " (cutoff:3.500A) Processing helix chain 'D' and resid 379 through 392 removed outlier: 3.805A pdb=" N ALA D 383 " --> pdb=" O GLY D 379 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 414 removed outlier: 3.746A pdb=" N HIS D 409 " --> pdb=" O HIS D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 417 No H-bonds generated for 'chain 'D' and resid 415 through 417' Processing helix chain 'D' and resid 437 through 451 Processing helix chain 'D' and resid 453 through 455 No H-bonds generated for 'chain 'D' and resid 453 through 455' Processing helix chain 'D' and resid 473 through 485 removed outlier: 3.679A pdb=" N VAL D 481 " --> pdb=" O VAL D 477 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE D 484 " --> pdb=" O GLU D 480 " (cutoff:3.500A) Processing helix chain 'D' and resid 497 through 502 removed outlier: 3.672A pdb=" N ALA D 500 " --> pdb=" O TYR D 497 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N THR D 501 " --> pdb=" O ALA D 498 " (cutoff:3.500A) Processing helix chain 'D' and resid 506 through 509 Processing helix chain 'D' and resid 510 through 524 Processing helix chain 'D' and resid 524 through 539 Processing helix chain 'D' and resid 542 through 549 removed outlier: 4.284A pdb=" N VAL D 547 " --> pdb=" O SER D 544 " (cutoff:3.500A) Processing helix chain 'D' and resid 587 through 592 Processing helix chain 'D' and resid 592 through 604 Processing helix chain 'D' and resid 617 through 621 removed outlier: 4.511A pdb=" N ARG D 620 " --> pdb=" O ASP D 617 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ARG D 621 " --> pdb=" O LEU D 618 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 617 through 621' Processing helix chain 'D' and resid 624 through 648 removed outlier: 3.596A pdb=" N ARG D 646 " --> pdb=" O ARG D 642 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 655 removed outlier: 4.109A pdb=" N TRP D 654 " --> pdb=" O LEU D 650 " (cutoff:3.500A) Processing helix chain 'D' and resid 659 through 664 Processing helix chain 'D' and resid 665 through 669 Processing helix chain 'D' and resid 687 through 694 removed outlier: 3.856A pdb=" N TRP D 691 " --> pdb=" O TRP D 687 " (cutoff:3.500A) Processing helix chain 'D' and resid 708 through 711 Processing helix chain 'D' and resid 713 through 721 Processing helix chain 'D' and resid 747 through 771 Processing helix chain 'D' and resid 773 through 787 removed outlier: 3.911A pdb=" N ILE D 787 " --> pdb=" O HIS D 783 " (cutoff:3.500A) Processing helix chain 'D' and resid 814 through 822 Processing helix chain 'D' and resid 832 through 843 removed outlier: 3.734A pdb=" N GLY D 837 " --> pdb=" O ILE D 833 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ARG D 838 " --> pdb=" O GLY D 834 " (cutoff:3.500A) Processing helix chain 'D' and resid 869 through 879 removed outlier: 3.635A pdb=" N GLN D 878 " --> pdb=" O TYR D 874 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU D 879 " --> pdb=" O PHE D 875 " (cutoff:3.500A) Processing helix chain 'D' and resid 897 through 915 Processing sheet with id=AA1, first strand: chain 'A' and resid 374 through 376 removed outlier: 3.523A pdb=" N LEU A 491 " --> pdb=" O LEU A 460 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N ILE A 397 " --> pdb=" O MET A 459 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N LEU A 461 " --> pdb=" O ILE A 397 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N LEU A 399 " --> pdb=" O LEU A 461 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N THR A 463 " --> pdb=" O LEU A 399 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N ASP A 401 " --> pdb=" O THR A 463 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL A 398 " --> pdb=" O MET A 420 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N LEU A 422 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ILE A 400 " --> pdb=" O LEU A 422 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 426 through 427 Processing sheet with id=AA3, first strand: chain 'A' and resid 470 through 471 Processing sheet with id=AA4, first strand: chain 'A' and resid 656 through 657 removed outlier: 3.513A pdb=" N ARG A 656 " --> pdb=" O PHE A 706 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 828 through 831 Processing sheet with id=AA6, first strand: chain 'B' and resid 139 through 142 Processing sheet with id=AA7, first strand: chain 'B' and resid 418 through 422 removed outlier: 6.305A pdb=" N VAL B 398 " --> pdb=" O MET B 420 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N LEU B 422 " --> pdb=" O VAL B 398 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N ILE B 400 " --> pdb=" O LEU B 422 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N ILE B 397 " --> pdb=" O ARG B 458 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LEU B 460 " --> pdb=" O ILE B 397 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LEU B 399 " --> pdb=" O LEU B 460 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N LEU B 462 " --> pdb=" O LEU B 399 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ASP B 401 " --> pdb=" O LEU B 462 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N PHE B 490 " --> pdb=" O TYR B 563 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N THR B 565 " --> pdb=" O PHE B 490 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N TRP B 492 " --> pdb=" O THR B 565 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 470 through 471 removed outlier: 3.625A pdb=" N VAL B 697 " --> pdb=" O VAL B 471 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 656 through 657 removed outlier: 3.520A pdb=" N ARG B 656 " --> pdb=" O PHE B 706 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU B 739 " --> pdb=" O LYS B 732 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LYS B 732 " --> pdb=" O LEU B 739 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ILE B 741 " --> pdb=" O ILE B 730 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N ILE B 730 " --> pdb=" O ILE B 741 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 828 through 831 Processing sheet with id=AB2, first strand: chain 'B' and resid 853 through 854 Processing sheet with id=AB3, first strand: chain 'C' and resid 372 through 376 removed outlier: 3.589A pdb=" N LEU C 491 " --> pdb=" O LEU C 460 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N ILE C 397 " --> pdb=" O MET C 459 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N LEU C 461 " --> pdb=" O ILE C 397 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LEU C 399 " --> pdb=" O LEU C 461 " (cutoff:3.500A) removed outlier: 8.355A pdb=" N THR C 463 " --> pdb=" O LEU C 399 " (cutoff:3.500A) removed outlier: 8.325A pdb=" N ASP C 401 " --> pdb=" O THR C 463 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N VAL C 398 " --> pdb=" O MET C 420 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N LEU C 422 " --> pdb=" O VAL C 398 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ILE C 400 " --> pdb=" O LEU C 422 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 470 through 472 removed outlier: 3.649A pdb=" N VAL C 697 " --> pdb=" O VAL C 471 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 656 through 657 removed outlier: 3.594A pdb=" N LEU C 739 " --> pdb=" O LYS C 732 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N LYS C 732 " --> pdb=" O LEU C 739 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N ILE C 741 " --> pdb=" O ILE C 730 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N ILE C 730 " --> pdb=" O ILE C 741 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 828 through 831 Processing sheet with id=AB7, first strand: chain 'D' and resid 418 through 422 removed outlier: 6.369A pdb=" N VAL D 398 " --> pdb=" O MET D 420 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N LEU D 422 " --> pdb=" O VAL D 398 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ILE D 400 " --> pdb=" O LEU D 422 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N ILE D 397 " --> pdb=" O ARG D 458 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N LEU D 460 " --> pdb=" O ILE D 397 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LEU D 399 " --> pdb=" O LEU D 460 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N LEU D 462 " --> pdb=" O LEU D 399 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N ASP D 401 " --> pdb=" O LEU D 462 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N CYS D 489 " --> pdb=" O ARG D 458 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU D 491 " --> pdb=" O LEU D 460 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 426 through 427 Processing sheet with id=AB9, first strand: chain 'D' and resid 470 through 472 removed outlier: 3.521A pdb=" N VAL D 697 " --> pdb=" O VAL D 471 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 656 through 657 removed outlier: 3.577A pdb=" N ARG D 656 " --> pdb=" O PHE D 706 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N LYS D 732 " --> pdb=" O LEU D 739 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 828 through 831 906 hydrogen bonds defined for protein. 2562 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: 9.13 Time building geometry restraints manager: 4.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.80 - 1.01: 18904 1.01 - 1.21: 19 1.21 - 1.41: 8344 1.41 - 1.61: 11233 1.61 - 1.81: 121 Bond restraints: 38621 Sorted by residual: bond pdb=" ND2 ASN D 688 " pdb="HD22 ASN D 688 " ideal model delta sigma weight residual 0.860 0.805 0.055 2.00e-02 2.50e+03 7.60e+00 bond pdb=" ND2 ASN B 464 " pdb="HD22 ASN B 464 " ideal model delta sigma weight residual 0.860 0.808 0.052 2.00e-02 2.50e+03 6.77e+00 bond pdb=" NE2 GLN B 453 " pdb="HE22 GLN B 453 " ideal model delta sigma weight residual 0.860 0.813 0.047 2.00e-02 2.50e+03 5.54e+00 bond pdb=" ND2 ASN C 378 " pdb="HD22 ASN C 378 " ideal model delta sigma weight residual 0.860 0.813 0.047 2.00e-02 2.50e+03 5.43e+00 bond pdb=" ND2 ASN C 688 " pdb="HD22 ASN C 688 " ideal model delta sigma weight residual 0.860 0.816 0.044 2.00e-02 2.50e+03 4.94e+00 ... (remaining 38616 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.50: 69384 7.50 - 15.00: 9 15.00 - 22.51: 8 22.51 - 30.01: 52 30.01 - 37.51: 27 Bond angle restraints: 69480 Sorted by residual: angle pdb=" CD GLN D 695 " pdb=" NE2 GLN D 695 " pdb="HE22 GLN D 695 " ideal model delta sigma weight residual 120.00 157.51 -37.51 3.00e+00 1.11e-01 1.56e+02 angle pdb=" CD GLN C 508 " pdb=" NE2 GLN C 508 " pdb="HE22 GLN C 508 " ideal model delta sigma weight residual 120.00 156.85 -36.85 3.00e+00 1.11e-01 1.51e+02 angle pdb=" CD GLN D 729 " pdb=" NE2 GLN D 729 " pdb="HE22 GLN D 729 " ideal model delta sigma weight residual 120.00 156.61 -36.61 3.00e+00 1.11e-01 1.49e+02 angle pdb=" CD GLN A 681 " pdb=" NE2 GLN A 681 " pdb="HE22 GLN A 681 " ideal model delta sigma weight residual 120.00 156.43 -36.43 3.00e+00 1.11e-01 1.47e+02 angle pdb=" CD GLN A 622 " pdb=" NE2 GLN A 622 " pdb="HE22 GLN A 622 " ideal model delta sigma weight residual 120.00 156.06 -36.06 3.00e+00 1.11e-01 1.44e+02 ... (remaining 69475 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 16459 17.91 - 35.81: 1084 35.81 - 53.72: 377 53.72 - 71.63: 196 71.63 - 89.53: 58 Dihedral angle restraints: 18174 sinusoidal: 9727 harmonic: 8447 Sorted by residual: dihedral pdb=" CA ARG B 692 " pdb=" C ARG B 692 " pdb=" N SER B 693 " pdb=" CA SER B 693 " ideal model delta harmonic sigma weight residual -180.00 -156.00 -24.00 0 5.00e+00 4.00e-02 2.30e+01 dihedral pdb=" CA PRO A 419 " pdb=" C PRO A 419 " pdb=" N MET A 420 " pdb=" CA MET A 420 " ideal model delta harmonic sigma weight residual 180.00 156.08 23.92 0 5.00e+00 4.00e-02 2.29e+01 dihedral pdb=" CA TRP C 368 " pdb=" C TRP C 368 " pdb=" N ASN C 369 " pdb=" CA ASN C 369 " ideal model delta harmonic sigma weight residual -180.00 -157.29 -22.71 0 5.00e+00 4.00e-02 2.06e+01 ... (remaining 18171 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 2166 0.042 - 0.085: 615 0.085 - 0.127: 200 0.127 - 0.170: 20 0.170 - 0.212: 2 Chirality restraints: 3003 Sorted by residual: chirality pdb=" CB ILE D 730 " pdb=" CA ILE D 730 " pdb=" CG1 ILE D 730 " pdb=" CG2 ILE D 730 " both_signs ideal model delta sigma weight residual False 2.64 2.86 -0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA HIS D 603 " pdb=" N HIS D 603 " pdb=" C HIS D 603 " pdb=" CB HIS D 603 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.88e-01 chirality pdb=" CA PHE B 499 " pdb=" N PHE B 499 " pdb=" C PHE B 499 " pdb=" CB PHE B 499 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.56e-01 ... (remaining 3000 not shown) Planarity restraints: 5745 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN D 443 " -0.048 2.00e-02 2.50e+03 9.93e-02 1.48e+02 pdb=" CD GLN D 443 " 0.118 2.00e-02 2.50e+03 pdb=" OE1 GLN D 443 " 0.010 2.00e-02 2.50e+03 pdb=" NE2 GLN D 443 " -0.164 2.00e-02 2.50e+03 pdb="HE21 GLN D 443 " -0.036 2.00e-02 2.50e+03 pdb="HE22 GLN D 443 " 0.120 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 731 " 0.048 2.00e-02 2.50e+03 9.88e-02 1.46e+02 pdb=" CG ASN D 731 " -0.117 2.00e-02 2.50e+03 pdb=" OD1 ASN D 731 " -0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN D 731 " 0.164 2.00e-02 2.50e+03 pdb="HD21 ASN D 731 " 0.034 2.00e-02 2.50e+03 pdb="HD22 ASN D 731 " -0.120 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 688 " 0.044 2.00e-02 2.50e+03 9.88e-02 1.46e+02 pdb=" CG ASN C 688 " -0.118 2.00e-02 2.50e+03 pdb=" OD1 ASN C 688 " -0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN C 688 " 0.163 2.00e-02 2.50e+03 pdb="HD21 ASN C 688 " 0.041 2.00e-02 2.50e+03 pdb="HD22 ASN C 688 " -0.121 2.00e-02 2.50e+03 ... (remaining 5742 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 1571 2.17 - 2.78: 76234 2.78 - 3.39: 108561 3.39 - 3.99: 139390 3.99 - 4.60: 218514 Nonbonded interactions: 544270 Sorted by model distance: nonbonded pdb=" OE1 GLU C 598 " pdb=" HH TYR D 823 " model vdw 1.564 2.450 nonbonded pdb=" OD1 ASP C 542 " pdb=" H GLU C 545 " model vdw 1.616 2.450 nonbonded pdb=" HH TYR D 527 " pdb=" O PRO D 553 " model vdw 1.618 2.450 nonbonded pdb=" O GLU B 529 " pdb="HD21 ASN B 533 " model vdw 1.619 2.450 nonbonded pdb=" HH TYR A 527 " pdb=" O PRO A 553 " model vdw 1.620 2.450 ... (remaining 544265 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 376 through 408 or (resid 409 and (name N or name CA or na \ me C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or nam \ e HE2)) or resid 410 through 414 or (resid 415 and (name N or name CA or name C \ or name O or name CB )) or (resid 416 and (name N or name CA or name C or name O \ )) or resid 417 through 472 or (resid 473 and (name N or name CA or name C or n \ ame O or name CB or name CG or name OD1 or name ND2 or name H or name HA )) or r \ esid 474 through 611 or (resid 612 through 613 and (name N or name CA or name C \ or name O or name CB or name CG or name CD1 or name CD2 or name H or name HA )) \ or resid 614 through 620 or (resid 621 and (name N or name CA or name C or name \ O or name CB or name CG or name CD or name NE or name CZ or name NH1 or name NH2 \ or name H or name HA )) or resid 622 through 673 or resid 678 through 917)) selection = (chain 'D' and (resid 376 through 404 or (resid 405 and (name N or name CA or na \ me C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or nam \ e HE2)) or resid 406 through 622 or (resid 623 and (name N or name CA or name C \ or name O or name CB or name CG1 or name CG2 or name H or name HA )) or (resid 6 \ 24 and (name N or name CA or name C or name O or name CB or name CG or name OD1 \ or name OD2 or name H or name HA )) or (resid 625 and (name N or name CA or name \ C or name O or name CB or name CG1 or name CG2 or name CD1 or name H or name HA \ )) or resid 626 through 720 or (resid 721 and (name N or name CA or name C or n \ ame O or name CB or name CG1 or name CG2 or name CD1 or name H or name HA )) or \ resid 722 through 917)) } ncs_group { reference = (chain 'B' and (resid 25 through 84 or (resid 85 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE \ 2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name H \ E2)) or resid 86 through 110 or resid 138 through 143 or resid 169 through 196 o \ r resid 238 through 239 or resid 363 through 408 or (resid 409 and (name N or na \ me CA or name C or name O or name CB or name CG or name ND1 or name CD2 or name \ CE1 or name NE2 or name H or name HA or name HB2 or name HB3 or name HD1 or name \ HD2 or name HE1)) or resid 410 through 576 or (resid 577 and (name N or name CA \ or name C or name O or name CB or name CG or name CD or name OE1 or name NE2 or \ name H or name HA )) or resid 578 through 632 or (resid 633 and (name N or name \ CA or name C or name O or name CB or name CG or name ND1 or name CD2 or name CE \ 1 or name NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name H \ E1 or name HE2)) or resid 634 through 911)) selection = (chain 'C' and (resid 25 through 143 or resid 169 through 183 or resid 194 throu \ gh 196 or resid 284 through 285 or resid 363 through 606 or (resid 607 and (name \ N or name CA or name C or name O or name CB or name OG )) or (resid 608 and (na \ me N or name CA or name C or name O or name CB or name CG or name CD )) or (resi \ d 609 and (name N or name CA or name C or name O or name CB or name CG or name O \ D1 or name ND2)) or resid 615 through 655 or (resid 656 and (name N or name CA o \ r name C or name O or name CB or name CG or name CD or name NE or name CZ or nam \ e NH1 or name NH2 or name H or name HA )) or resid 657 through 669 or resid 687 \ through 724 or (resid 725 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name NE or name CZ or name NH1 or name NH2 or name H or \ name HA )) or resid 726 through 911)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.570 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: 0.220 Extract box with map and model: 0.600 Check model and map are aligned: 0.120 Set scattering table: 0.110 Process input model: 34.970 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.060 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 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 : 0.005 0.057 19698 Z= 0.214 Angle : 0.720 14.105 26764 Z= 0.409 Chirality : 0.044 0.212 3003 Planarity : 0.008 0.105 3451 Dihedral : 14.653 88.640 7146 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.05 % Favored : 95.83 % Rotamer: Outliers : 0.20 % Allowed : 9.61 % Favored : 90.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.17), residues: 2372 helix: 0.13 (0.15), residues: 1107 sheet: -1.60 (0.30), residues: 265 loop : -0.49 (0.20), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 692 TYR 0.039 0.002 TYR C 497 PHE 0.029 0.002 PHE C 467 TRP 0.026 0.002 TRP C 505 HIS 0.014 0.002 HIS D 603 Details of bonding type rmsd covalent geometry : bond 0.00489 (19698) covalent geometry : angle 0.72021 (26764) hydrogen bonds : bond 0.15835 ( 906) hydrogen bonds : angle 6.79623 ( 2562) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 623 is missing expected H atoms. Skipping. Residue ILE 625 is missing expected H atoms. Skipping. Residue ILE 721 is missing expected H atoms. Skipping. Residue LEU 612 is missing expected H atoms. Skipping. Residue LEU 613 is missing expected H atoms. Skipping. Evaluate side-chains 210 residues out of total 2030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 206 time to evaluate : 1.051 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 600 PHE cc_start: 0.8761 (OUTLIER) cc_final: 0.8278 (t80) REVERT: D 712 MET cc_start: 0.7605 (ttt) cc_final: 0.7357 (ttt) outliers start: 4 outliers final: 2 residues processed: 210 average time/residue: 0.4212 time to fit residues: 126.4535 Evaluate side-chains 199 residues out of total 2030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 196 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 600 PHE Chi-restraints excluded: chain C residue 606 THR Chi-restraints excluded: chain D residue 726 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 216 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 3.9990 chunk 107 optimal weight: 0.0980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 0.8980 chunk 235 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 609 ASN A 731 ASN B 378 ASN B 609 ASN C 609 ASN C 611 GLN C 752 HIS D 384 ASN D 409 HIS D 473 ASN D 508 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.181145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.152397 restraints weight = 73060.064| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 2.06 r_work: 0.3683 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3560 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.0822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 19698 Z= 0.127 Angle : 0.538 6.617 26764 Z= 0.294 Chirality : 0.039 0.156 3003 Planarity : 0.004 0.067 3451 Dihedral : 5.332 57.946 2690 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.07 % Favored : 97.89 % Rotamer: Outliers : 0.69 % Allowed : 8.92 % Favored : 90.39 % 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: 0.18 (0.17), residues: 2372 helix: 0.93 (0.15), residues: 1105 sheet: -1.30 (0.31), residues: 238 loop : -0.29 (0.20), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 584 TYR 0.020 0.001 TYR D 527 PHE 0.009 0.001 PHE A 797 TRP 0.015 0.001 TRP C 505 HIS 0.005 0.001 HIS D 603 Details of bonding type rmsd covalent geometry : bond 0.00277 (19698) covalent geometry : angle 0.53802 (26764) hydrogen bonds : bond 0.04588 ( 906) hydrogen bonds : angle 5.19976 ( 2562) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 623 is missing expected H atoms. Skipping. Residue ILE 625 is missing expected H atoms. Skipping. Residue ILE 721 is missing expected H atoms. Skipping. Residue LEU 612 is missing expected H atoms. Skipping. Residue LEU 613 is missing expected H atoms. Skipping. Evaluate side-chains 232 residues out of total 2030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 218 time to evaluate : 0.981 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: B 600 PHE cc_start: 0.8715 (OUTLIER) cc_final: 0.8183 (t80) REVERT: B 609 ASN cc_start: 0.6271 (t0) cc_final: 0.5981 (t0) REVERT: B 749 SER cc_start: 0.8621 (OUTLIER) cc_final: 0.8362 (p) REVERT: D 874 TYR cc_start: 0.8183 (t80) cc_final: 0.6674 (m-10) outliers start: 14 outliers final: 8 residues processed: 227 average time/residue: 0.4582 time to fit residues: 147.0451 Evaluate side-chains 209 residues out of total 2030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 199 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 HIS Chi-restraints excluded: chain B residue 600 PHE Chi-restraints excluded: chain B residue 749 SER Chi-restraints excluded: chain B residue 763 ILE Chi-restraints excluded: chain C residue 580 MET Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain D residue 613 LEU Chi-restraints excluded: chain D residue 659 ASP Chi-restraints excluded: chain D residue 726 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 129 optimal weight: 0.7980 chunk 105 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 193 optimal weight: 2.9990 chunk 182 optimal weight: 0.8980 chunk 207 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 168 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 172 optimal weight: 0.3980 chunk 165 optimal weight: 0.8980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 378 ASN C 31 ASN D 473 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.179810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.151676 restraints weight = 73109.724| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 2.06 r_work: 0.3689 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3566 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.1235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19698 Z= 0.120 Angle : 0.487 6.568 26764 Z= 0.264 Chirality : 0.038 0.150 3003 Planarity : 0.004 0.051 3451 Dihedral : 5.002 55.615 2689 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.57 % Favored : 97.39 % Rotamer: Outliers : 0.84 % Allowed : 9.46 % Favored : 89.70 % 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: 0.46 (0.17), residues: 2372 helix: 1.35 (0.16), residues: 1106 sheet: -1.48 (0.31), residues: 244 loop : -0.31 (0.20), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 767 TYR 0.019 0.001 TYR D 527 PHE 0.009 0.001 PHE B 499 TRP 0.016 0.001 TRP C 505 HIS 0.008 0.001 HIS B 85 Details of bonding type rmsd covalent geometry : bond 0.00271 (19698) covalent geometry : angle 0.48663 (26764) hydrogen bonds : bond 0.04031 ( 906) hydrogen bonds : angle 4.83171 ( 2562) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 623 is missing expected H atoms. Skipping. Residue ILE 625 is missing expected H atoms. Skipping. Residue ILE 721 is missing expected H atoms. Skipping. Residue LEU 612 is missing expected H atoms. Skipping. Residue LEU 613 is missing expected H atoms. Skipping. Evaluate side-chains 229 residues out of total 2030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 212 time to evaluate : 1.089 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: B 600 PHE cc_start: 0.8785 (OUTLIER) cc_final: 0.8222 (t80) REVERT: B 609 ASN cc_start: 0.5959 (t0) cc_final: 0.5750 (t0) REVERT: B 749 SER cc_start: 0.8635 (OUTLIER) cc_final: 0.8377 (p) REVERT: C 694 ASP cc_start: 0.7408 (t0) cc_final: 0.7125 (m-30) REVERT: C 763 ILE cc_start: 0.8037 (mm) cc_final: 0.7836 (mt) REVERT: D 649 ARG cc_start: 0.8239 (ptt180) cc_final: 0.7497 (mtt180) REVERT: D 874 TYR cc_start: 0.8201 (t80) cc_final: 0.6712 (m-10) outliers start: 17 outliers final: 11 residues processed: 224 average time/residue: 0.4542 time to fit residues: 142.9719 Evaluate side-chains 204 residues out of total 2030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 191 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 HIS Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 600 PHE Chi-restraints excluded: chain B residue 629 GLU Chi-restraints excluded: chain B residue 749 SER Chi-restraints excluded: chain B residue 763 ILE Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 580 MET Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain D residue 613 LEU Chi-restraints excluded: chain D residue 659 ASP Chi-restraints excluded: chain D residue 726 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 175 optimal weight: 3.9990 chunk 187 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 223 optimal weight: 5.9990 chunk 104 optimal weight: 3.9990 chunk 131 optimal weight: 8.9990 chunk 102 optimal weight: 1.9990 chunk 127 optimal weight: 7.9990 chunk 117 optimal weight: 6.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 389 GLN B 378 ASN C 577 GLN D 464 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.172208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.144086 restraints weight = 74257.207| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 2.00 r_work: 0.3581 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3463 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 19698 Z= 0.257 Angle : 0.596 6.827 26764 Z= 0.329 Chirality : 0.043 0.219 3003 Planarity : 0.005 0.051 3451 Dihedral : 5.377 53.102 2689 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.71 % Favored : 96.25 % Rotamer: Outliers : 1.38 % Allowed : 10.30 % Favored : 88.33 % 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: -0.12 (0.17), residues: 2372 helix: 0.88 (0.15), residues: 1107 sheet: -1.48 (0.31), residues: 238 loop : -0.71 (0.19), residues: 1027 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 702 TYR 0.027 0.002 TYR D 527 PHE 0.021 0.002 PHE C 668 TRP 0.028 0.002 TRP C 505 HIS 0.012 0.002 HIS B 603 Details of bonding type rmsd covalent geometry : bond 0.00600 (19698) covalent geometry : angle 0.59589 (26764) hydrogen bonds : bond 0.04701 ( 906) hydrogen bonds : angle 4.99632 ( 2562) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 623 is missing expected H atoms. Skipping. Residue ILE 625 is missing expected H atoms. Skipping. Residue ILE 721 is missing expected H atoms. Skipping. Residue LEU 612 is missing expected H atoms. Skipping. Residue LEU 613 is missing expected H atoms. Skipping. Evaluate side-chains 230 residues out of total 2030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 202 time to evaluate : 0.985 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: A 776 ASP cc_start: 0.4853 (OUTLIER) cc_final: 0.4423 (m-30) REVERT: B 140 LEU cc_start: 0.8061 (mp) cc_final: 0.7800 (mm) REVERT: B 815 MET cc_start: 0.8679 (ttp) cc_final: 0.8418 (ttp) REVERT: C 649 ARG cc_start: 0.7800 (ptt180) cc_final: 0.7159 (tpm170) REVERT: C 815 MET cc_start: 0.8731 (ttp) cc_final: 0.8466 (ttp) REVERT: D 403 ASN cc_start: 0.7611 (p0) cc_final: 0.7208 (p0) REVERT: D 649 ARG cc_start: 0.8307 (ptt180) cc_final: 0.7585 (mtt180) REVERT: D 874 TYR cc_start: 0.8263 (t80) cc_final: 0.6758 (m-10) outliers start: 28 outliers final: 16 residues processed: 220 average time/residue: 0.4486 time to fit residues: 139.0849 Evaluate side-chains 210 residues out of total 2030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 193 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 776 ASP Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 629 GLU Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 749 SER Chi-restraints excluded: chain B residue 753 TYR Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 432 ILE Chi-restraints excluded: chain C residue 521 MET Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 580 MET Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain D residue 613 LEU Chi-restraints excluded: chain D residue 659 ASP Chi-restraints excluded: chain D residue 726 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 138 optimal weight: 2.9990 chunk 172 optimal weight: 0.9980 chunk 209 optimal weight: 0.0570 chunk 126 optimal weight: 6.9990 chunk 170 optimal weight: 1.9990 chunk 211 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 111 optimal weight: 6.9990 chunk 13 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 overall best weight: 1.2102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.175312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.147496 restraints weight = 73453.670| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 1.99 r_work: 0.3625 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3505 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19698 Z= 0.125 Angle : 0.492 5.933 26764 Z= 0.266 Chirality : 0.038 0.148 3003 Planarity : 0.004 0.040 3451 Dihedral : 4.922 51.342 2687 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.41 % Favored : 96.54 % Rotamer: Outliers : 0.94 % Allowed : 11.18 % Favored : 87.88 % 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: 0.20 (0.17), residues: 2372 helix: 1.27 (0.16), residues: 1102 sheet: -1.53 (0.32), residues: 223 loop : -0.67 (0.19), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 576 TYR 0.018 0.001 TYR D 527 PHE 0.009 0.001 PHE D 628 TRP 0.015 0.001 TRP C 505 HIS 0.005 0.001 HIS D 603 Details of bonding type rmsd covalent geometry : bond 0.00284 (19698) covalent geometry : angle 0.49233 (26764) hydrogen bonds : bond 0.03793 ( 906) hydrogen bonds : angle 4.69200 ( 2562) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 623 is missing expected H atoms. Skipping. Residue ILE 625 is missing expected H atoms. Skipping. Residue ILE 721 is missing expected H atoms. Skipping. Residue LEU 612 is missing expected H atoms. Skipping. Residue LEU 613 is missing expected H atoms. Skipping. Evaluate side-chains 221 residues out of total 2030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 202 time to evaluate : 1.096 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: A 776 ASP cc_start: 0.4616 (OUTLIER) cc_final: 0.4263 (m-30) REVERT: B 140 LEU cc_start: 0.8023 (mp) cc_final: 0.7688 (mm) REVERT: B 749 SER cc_start: 0.8644 (OUTLIER) cc_final: 0.8366 (p) REVERT: C 649 ARG cc_start: 0.7645 (ptt180) cc_final: 0.7099 (tpm170) REVERT: C 694 ASP cc_start: 0.7636 (t0) cc_final: 0.7308 (m-30) REVERT: C 870 LYS cc_start: 0.7368 (mppt) cc_final: 0.6383 (mmtm) REVERT: D 874 TYR cc_start: 0.8221 (t80) cc_final: 0.6725 (m-10) outliers start: 19 outliers final: 13 residues processed: 214 average time/residue: 0.4305 time to fit residues: 131.6086 Evaluate side-chains 206 residues out of total 2030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 191 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 776 ASP Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 521 MET Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 749 SER Chi-restraints excluded: chain B residue 753 TYR Chi-restraints excluded: chain C residue 432 ILE Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 580 MET Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain D residue 423 ASP Chi-restraints excluded: chain D residue 613 LEU Chi-restraints excluded: chain D residue 659 ASP Chi-restraints excluded: chain D residue 726 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 174 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 212 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 119 optimal weight: 5.9990 chunk 181 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.173409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.145462 restraints weight = 73941.219| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 2.00 r_work: 0.3599 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3480 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 19698 Z= 0.169 Angle : 0.512 5.965 26764 Z= 0.278 Chirality : 0.040 0.147 3003 Planarity : 0.004 0.065 3451 Dihedral : 4.920 49.814 2687 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.22 % Favored : 95.74 % Rotamer: Outliers : 1.23 % Allowed : 11.67 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.10 (0.17), residues: 2372 helix: 1.20 (0.16), residues: 1107 sheet: -1.65 (0.31), residues: 235 loop : -0.69 (0.19), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 621 TYR 0.018 0.001 TYR B 73 PHE 0.012 0.001 PHE C 668 TRP 0.014 0.001 TRP C 505 HIS 0.006 0.001 HIS D 603 Details of bonding type rmsd covalent geometry : bond 0.00395 (19698) covalent geometry : angle 0.51162 (26764) hydrogen bonds : bond 0.03938 ( 906) hydrogen bonds : angle 4.67770 ( 2562) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 623 is missing expected H atoms. Skipping. Residue ILE 625 is missing expected H atoms. Skipping. Residue ILE 721 is missing expected H atoms. Skipping. Residue LEU 612 is missing expected H atoms. Skipping. Residue LEU 613 is missing expected H atoms. Skipping. Evaluate side-chains 224 residues out of total 2030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 199 time to evaluate : 1.163 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: A 776 ASP cc_start: 0.4631 (OUTLIER) cc_final: 0.4265 (m-30) REVERT: B 140 LEU cc_start: 0.8025 (mp) cc_final: 0.7710 (mm) REVERT: B 576 ARG cc_start: 0.7565 (ttp80) cc_final: 0.7318 (ttp-170) REVERT: B 749 SER cc_start: 0.8657 (OUTLIER) cc_final: 0.8389 (p) REVERT: C 576 ARG cc_start: 0.6823 (OUTLIER) cc_final: 0.6380 (ttp-110) REVERT: C 649 ARG cc_start: 0.7831 (ptt180) cc_final: 0.7293 (tpm170) REVERT: C 870 LYS cc_start: 0.7509 (mppt) cc_final: 0.6651 (mmtm) REVERT: D 835 LEU cc_start: 0.8516 (mm) cc_final: 0.8198 (mp) REVERT: D 874 TYR cc_start: 0.8215 (t80) cc_final: 0.6714 (m-10) outliers start: 25 outliers final: 18 residues processed: 213 average time/residue: 0.4397 time to fit residues: 134.1068 Evaluate side-chains 217 residues out of total 2030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 196 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 776 ASP Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 521 MET Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 749 SER Chi-restraints excluded: chain B residue 753 TYR Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain C residue 432 ILE Chi-restraints excluded: chain C residue 521 MET Chi-restraints excluded: chain C residue 576 ARG Chi-restraints excluded: chain C residue 580 MET Chi-restraints excluded: chain C residue 840 LEU Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain D residue 423 ASP Chi-restraints excluded: chain D residue 613 LEU Chi-restraints excluded: chain D residue 659 ASP Chi-restraints excluded: chain D residue 726 PHE Chi-restraints excluded: chain D residue 747 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 26 optimal weight: 1.9990 chunk 148 optimal weight: 0.7980 chunk 220 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 188 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 167 optimal weight: 0.7980 chunk 215 optimal weight: 2.9990 chunk 221 optimal weight: 0.8980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 622 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.173017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.145090 restraints weight = 74128.863| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 2.03 r_work: 0.3593 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3476 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19698 Z= 0.133 Angle : 0.486 5.644 26764 Z= 0.261 Chirality : 0.038 0.144 3003 Planarity : 0.004 0.046 3451 Dihedral : 4.776 49.404 2687 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.67 % Favored : 96.29 % Rotamer: Outliers : 1.28 % Allowed : 11.58 % Favored : 87.14 % 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: 0.29 (0.18), residues: 2372 helix: 1.40 (0.16), residues: 1101 sheet: -1.52 (0.32), residues: 236 loop : -0.66 (0.20), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 621 TYR 0.017 0.001 TYR B 73 PHE 0.010 0.001 PHE C 628 TRP 0.013 0.001 TRP C 505 HIS 0.004 0.001 HIS D 603 Details of bonding type rmsd covalent geometry : bond 0.00307 (19698) covalent geometry : angle 0.48553 (26764) hydrogen bonds : bond 0.03618 ( 906) hydrogen bonds : angle 4.56337 ( 2562) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 623 is missing expected H atoms. Skipping. Residue ILE 625 is missing expected H atoms. Skipping. Residue ILE 721 is missing expected H atoms. Skipping. Residue LEU 612 is missing expected H atoms. Skipping. Residue LEU 613 is missing expected H atoms. Skipping. Evaluate side-chains 231 residues out of total 2030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 205 time to evaluate : 1.085 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: A 776 ASP cc_start: 0.4653 (OUTLIER) cc_final: 0.4311 (m-30) REVERT: B 140 LEU cc_start: 0.8011 (mp) cc_final: 0.7774 (mm) REVERT: B 576 ARG cc_start: 0.7437 (ttp80) cc_final: 0.7199 (ttp-170) REVERT: B 749 SER cc_start: 0.8657 (OUTLIER) cc_final: 0.8402 (p) REVERT: C 576 ARG cc_start: 0.6857 (OUTLIER) cc_final: 0.6425 (ttp-110) REVERT: C 649 ARG cc_start: 0.7844 (ptt180) cc_final: 0.7295 (tpm170) REVERT: C 694 ASP cc_start: 0.7720 (t0) cc_final: 0.7423 (m-30) REVERT: C 870 LYS cc_start: 0.7413 (mppt) cc_final: 0.6577 (mmtm) REVERT: D 835 LEU cc_start: 0.8520 (mm) cc_final: 0.8220 (mp) REVERT: D 874 TYR cc_start: 0.8210 (t80) cc_final: 0.6730 (m-10) outliers start: 26 outliers final: 15 residues processed: 220 average time/residue: 0.4358 time to fit residues: 137.3278 Evaluate side-chains 219 residues out of total 2030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 201 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 776 ASP Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 521 MET Chi-restraints excluded: chain B residue 629 GLU Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 749 SER Chi-restraints excluded: chain B residue 753 TYR Chi-restraints excluded: chain C residue 432 ILE Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 576 ARG Chi-restraints excluded: chain C residue 580 MET Chi-restraints excluded: chain C residue 840 LEU Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain D residue 423 ASP Chi-restraints excluded: chain D residue 659 ASP Chi-restraints excluded: chain D residue 747 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 56 optimal weight: 7.9990 chunk 159 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 66 optimal weight: 10.0000 chunk 233 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 133 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 186 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 783 HIS ** C 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.172879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.145208 restraints weight = 73673.896| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 1.98 r_work: 0.3595 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3477 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19698 Z= 0.135 Angle : 0.482 5.432 26764 Z= 0.260 Chirality : 0.038 0.143 3003 Planarity : 0.004 0.044 3451 Dihedral : 4.590 24.683 2685 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.22 % Favored : 95.74 % Rotamer: Outliers : 1.23 % Allowed : 11.72 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.35 (0.18), residues: 2372 helix: 1.46 (0.16), residues: 1100 sheet: -1.52 (0.32), residues: 240 loop : -0.63 (0.20), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 621 TYR 0.015 0.001 TYR A 527 PHE 0.011 0.001 PHE D 726 TRP 0.012 0.001 TRP C 505 HIS 0.004 0.001 HIS D 603 Details of bonding type rmsd covalent geometry : bond 0.00313 (19698) covalent geometry : angle 0.48230 (26764) hydrogen bonds : bond 0.03600 ( 906) hydrogen bonds : angle 4.52504 ( 2562) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 623 is missing expected H atoms. Skipping. Residue ILE 625 is missing expected H atoms. Skipping. Residue ILE 721 is missing expected H atoms. Skipping. Residue LEU 612 is missing expected H atoms. Skipping. Residue LEU 613 is missing expected H atoms. Skipping. Evaluate side-chains 235 residues out of total 2030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 210 time to evaluate : 1.044 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: A 776 ASP cc_start: 0.4702 (OUTLIER) cc_final: 0.4352 (m-30) REVERT: B 140 LEU cc_start: 0.8001 (mp) cc_final: 0.7760 (mm) REVERT: B 539 ASP cc_start: 0.6786 (p0) cc_final: 0.6554 (p0) REVERT: B 576 ARG cc_start: 0.7457 (ttp80) cc_final: 0.7245 (ttp-170) REVERT: B 749 SER cc_start: 0.8667 (OUTLIER) cc_final: 0.8388 (p) REVERT: C 576 ARG cc_start: 0.6863 (OUTLIER) cc_final: 0.6441 (ttp-110) REVERT: C 649 ARG cc_start: 0.7851 (ptt180) cc_final: 0.7311 (tpm170) REVERT: C 694 ASP cc_start: 0.7745 (t0) cc_final: 0.7448 (m-30) REVERT: C 839 ARG cc_start: 0.7172 (mmt180) cc_final: 0.6838 (mmt90) REVERT: C 870 LYS cc_start: 0.7387 (mppt) cc_final: 0.6550 (mmtm) REVERT: D 835 LEU cc_start: 0.8542 (mm) cc_final: 0.8238 (mp) REVERT: D 874 TYR cc_start: 0.8205 (t80) cc_final: 0.6738 (m-10) outliers start: 25 outliers final: 20 residues processed: 222 average time/residue: 0.4383 time to fit residues: 138.7071 Evaluate side-chains 223 residues out of total 2030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 200 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 776 ASP Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 521 MET Chi-restraints excluded: chain B residue 629 GLU Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 749 SER Chi-restraints excluded: chain B residue 753 TYR Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain C residue 432 ILE Chi-restraints excluded: chain C residue 521 MET Chi-restraints excluded: chain C residue 566 HIS Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 576 ARG Chi-restraints excluded: chain C residue 580 MET Chi-restraints excluded: chain C residue 616 LEU Chi-restraints excluded: chain C residue 840 LEU Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain D residue 423 ASP Chi-restraints excluded: chain D residue 659 ASP Chi-restraints excluded: chain D residue 698 LEU Chi-restraints excluded: chain D residue 747 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 177 optimal weight: 4.9990 chunk 188 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 215 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 123 optimal weight: 2.9990 chunk 212 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 150 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 783 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.172997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.145050 restraints weight = 74263.386| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 2.03 r_work: 0.3591 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3473 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19698 Z= 0.135 Angle : 0.485 5.434 26764 Z= 0.262 Chirality : 0.038 0.142 3003 Planarity : 0.004 0.065 3451 Dihedral : 4.555 24.745 2685 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.05 % Favored : 95.91 % Rotamer: Outliers : 1.08 % Allowed : 12.22 % Favored : 86.70 % 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: 0.36 (0.18), residues: 2372 helix: 1.49 (0.16), residues: 1101 sheet: -1.50 (0.32), residues: 236 loop : -0.65 (0.20), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 781 TYR 0.016 0.001 TYR B 73 PHE 0.009 0.001 PHE C 628 TRP 0.012 0.001 TRP C 505 HIS 0.005 0.001 HIS C 89 Details of bonding type rmsd covalent geometry : bond 0.00312 (19698) covalent geometry : angle 0.48483 (26764) hydrogen bonds : bond 0.03544 ( 906) hydrogen bonds : angle 4.49945 ( 2562) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 623 is missing expected H atoms. Skipping. Residue ILE 625 is missing expected H atoms. Skipping. Residue ILE 721 is missing expected H atoms. Skipping. Residue LEU 612 is missing expected H atoms. Skipping. Residue LEU 613 is missing expected H atoms. Skipping. Evaluate side-chains 224 residues out of total 2030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 202 time to evaluate : 0.868 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: A 776 ASP cc_start: 0.4689 (OUTLIER) cc_final: 0.4363 (m-30) REVERT: B 140 LEU cc_start: 0.8017 (mp) cc_final: 0.7771 (mm) REVERT: B 539 ASP cc_start: 0.6840 (p0) cc_final: 0.6609 (p0) REVERT: B 749 SER cc_start: 0.8662 (OUTLIER) cc_final: 0.8379 (p) REVERT: C 576 ARG cc_start: 0.6902 (OUTLIER) cc_final: 0.6483 (ttp-110) REVERT: C 649 ARG cc_start: 0.7839 (ptt180) cc_final: 0.7310 (tpm170) REVERT: C 839 ARG cc_start: 0.7211 (mmt180) cc_final: 0.6886 (mmt90) REVERT: C 870 LYS cc_start: 0.7364 (mppt) cc_final: 0.6373 (mmtm) REVERT: D 835 LEU cc_start: 0.8564 (mm) cc_final: 0.8313 (mp) REVERT: D 874 TYR cc_start: 0.8207 (t80) cc_final: 0.6738 (m-10) outliers start: 22 outliers final: 18 residues processed: 213 average time/residue: 0.4067 time to fit residues: 123.8394 Evaluate side-chains 223 residues out of total 2030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 202 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 776 ASP Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 521 MET Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 749 SER Chi-restraints excluded: chain B residue 753 TYR Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain C residue 432 ILE Chi-restraints excluded: chain C residue 566 HIS Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 576 ARG Chi-restraints excluded: chain C residue 580 MET Chi-restraints excluded: chain C residue 616 LEU Chi-restraints excluded: chain C residue 840 LEU Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain D residue 423 ASP Chi-restraints excluded: chain D residue 659 ASP Chi-restraints excluded: chain D residue 698 LEU Chi-restraints excluded: chain D residue 747 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 189 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 153 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 173 optimal weight: 0.9980 chunk 110 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 222 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 783 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.173619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.145744 restraints weight = 73837.821| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 2.00 r_work: 0.3602 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3484 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 19698 Z= 0.154 Angle : 0.497 5.391 26764 Z= 0.269 Chirality : 0.039 0.143 3003 Planarity : 0.004 0.038 3451 Dihedral : 4.602 24.457 2685 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.68 % Favored : 95.28 % Rotamer: Outliers : 1.08 % Allowed : 12.27 % Favored : 86.65 % 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: 0.30 (0.18), residues: 2372 helix: 1.44 (0.16), residues: 1101 sheet: -1.50 (0.32), residues: 239 loop : -0.70 (0.20), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 576 TYR 0.017 0.001 TYR A 527 PHE 0.024 0.001 PHE C 499 TRP 0.012 0.001 TRP C 505 HIS 0.008 0.001 HIS C 89 Details of bonding type rmsd covalent geometry : bond 0.00359 (19698) covalent geometry : angle 0.49741 (26764) hydrogen bonds : bond 0.03653 ( 906) hydrogen bonds : angle 4.53192 ( 2562) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 623 is missing expected H atoms. Skipping. Residue ILE 625 is missing expected H atoms. Skipping. Residue ILE 721 is missing expected H atoms. Skipping. Residue LEU 612 is missing expected H atoms. Skipping. Residue LEU 613 is missing expected H atoms. Skipping. Evaluate side-chains 228 residues out of total 2030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 206 time to evaluate : 0.962 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: B 140 LEU cc_start: 0.8054 (mp) cc_final: 0.7812 (mm) REVERT: B 749 SER cc_start: 0.8656 (OUTLIER) cc_final: 0.8372 (p) REVERT: C 576 ARG cc_start: 0.6895 (OUTLIER) cc_final: 0.6452 (ttp-110) REVERT: C 649 ARG cc_start: 0.7858 (ptt180) cc_final: 0.7341 (tpm170) REVERT: C 694 ASP cc_start: 0.7773 (t0) cc_final: 0.7465 (m-30) REVERT: C 839 ARG cc_start: 0.7194 (mmt180) cc_final: 0.6886 (mmt90) REVERT: C 870 LYS cc_start: 0.7389 (mppt) cc_final: 0.6531 (mmtp) REVERT: D 835 LEU cc_start: 0.8578 (mm) cc_final: 0.8343 (mp) REVERT: D 874 TYR cc_start: 0.8207 (t80) cc_final: 0.6720 (m-10) outliers start: 22 outliers final: 19 residues processed: 217 average time/residue: 0.4426 time to fit residues: 135.6663 Evaluate side-chains 224 residues out of total 2030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 203 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 521 MET Chi-restraints excluded: chain B residue 629 GLU Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 749 SER Chi-restraints excluded: chain B residue 753 TYR Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain C residue 432 ILE Chi-restraints excluded: chain C residue 566 HIS Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 576 ARG Chi-restraints excluded: chain C residue 580 MET Chi-restraints excluded: chain C residue 616 LEU Chi-restraints excluded: chain C residue 840 LEU Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain D residue 423 ASP Chi-restraints excluded: chain D residue 659 ASP Chi-restraints excluded: chain D residue 698 LEU Chi-restraints excluded: chain D residue 747 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 163 optimal weight: 4.9990 chunk 216 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 162 optimal weight: 0.6980 chunk 189 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 145 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 783 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.173685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.145919 restraints weight = 73598.946| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 1.99 r_work: 0.3606 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3487 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19698 Z= 0.147 Angle : 0.493 5.405 26764 Z= 0.266 Chirality : 0.039 0.143 3003 Planarity : 0.004 0.062 3451 Dihedral : 4.589 24.616 2685 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.09 % Favored : 95.87 % Rotamer: Outliers : 1.03 % Allowed : 12.41 % Favored : 86.55 % 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: 0.32 (0.18), residues: 2372 helix: 1.47 (0.16), residues: 1101 sheet: -1.48 (0.32), residues: 239 loop : -0.71 (0.20), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 646 TYR 0.016 0.001 TYR A 527 PHE 0.022 0.001 PHE C 499 TRP 0.012 0.001 TRP C 505 HIS 0.005 0.001 HIS C 89 Details of bonding type rmsd covalent geometry : bond 0.00343 (19698) covalent geometry : angle 0.49259 (26764) hydrogen bonds : bond 0.03590 ( 906) hydrogen bonds : angle 4.51121 ( 2562) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9196.66 seconds wall clock time: 156 minutes 42.05 seconds (9402.05 seconds total)