Starting phenix.real_space_refine on Sun Jan 19 18:41:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b35_44128/01_2025/9b35_44128.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b35_44128/01_2025/9b35_44128.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b35_44128/01_2025/9b35_44128.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b35_44128/01_2025/9b35_44128.map" model { file = "/net/cci-nas-00/data/ceres_data/9b35_44128/01_2025/9b35_44128.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b35_44128/01_2025/9b35_44128.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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: 4 Type Number sf(0) Gaussians S 92 5.16 5 C 9102 2.51 5 N 2316 2.21 5 O 2622 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 14132 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3525 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 444, 3518 Classifications: {'peptide': 444} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 426} Conformer: "B" Number of residues, atoms: 444, 3518 Classifications: {'peptide': 444} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 426} bond proxies already assigned to first conformer: 3587 Chain: "B" Number of atoms: 3521 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 444, 3518 Classifications: {'peptide': 444} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 426} Conformer: "B" Number of residues, atoms: 444, 3518 Classifications: {'peptide': 444} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 426} bond proxies already assigned to first conformer: 3592 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Restraints were copied for chains: D, C Time building chain proxies: 14.61, per 1000 atoms: 1.03 Number of scatterers: 14132 At special positions: 0 Unit cell: (128.127, 87.6655, 140.265, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 92 16.00 O 2622 8.00 N 2316 7.00 C 9102 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 750 " - pdb=" SG CYS A 804 " distance=2.03 Simple disulfide: pdb=" SG CYS B 750 " - pdb=" SG CYS B 804 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.59 Conformation dependent library (CDL) restraints added in 3.7 seconds 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3308 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 16 sheets defined 51.1% alpha, 4.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.32 Creating SS restraints... Processing helix chain 'A' and resid 461 through 475 removed outlier: 3.558A pdb=" N GLU A 469 " --> pdb=" O ASP A 465 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR A 472 " --> pdb=" O ARG A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 507 removed outlier: 3.531A pdb=" N ASP A 507 " --> pdb=" O ARG A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 525 removed outlier: 3.886A pdb=" N LYS A 525 " --> pdb=" O TYR A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 557 removed outlier: 3.854A pdb=" N LEU A 556 " --> pdb=" O PHE A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 585 removed outlier: 3.952A pdb=" N SER A 575 " --> pdb=" O CYS A 571 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N CYS A 576 " --> pdb=" O LEU A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 620 removed outlier: 3.837A pdb=" N TRP A 613 " --> pdb=" O LEU A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 660 removed outlier: 3.591A pdb=" N ILE A 635 " --> pdb=" O LEU A 631 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N VAL A 636 " --> pdb=" O SER A 632 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA A 656 " --> pdb=" O THR A 652 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ALA A 657 " --> pdb=" O ALA A 653 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE A 658 " --> pdb=" O ASN A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 676 removed outlier: 4.080A pdb=" N LYS A 676 " --> pdb=" O ASP A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 697 removed outlier: 3.572A pdb=" N PHE A 694 " --> pdb=" O THR A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 710 Processing helix chain 'A' and resid 720 through 731 removed outlier: 3.972A pdb=" N VAL A 728 " --> pdb=" O GLY A 724 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 746 removed outlier: 3.821A pdb=" N PHE A 744 " --> pdb=" O THR A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 788 removed outlier: 4.080A pdb=" N LYS A 777 " --> pdb=" O PRO A 773 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE A 778 " --> pdb=" O TYR A 774 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU A 783 " --> pdb=" O THR A 779 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU A 785 " --> pdb=" O ALA A 781 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU A 788 " --> pdb=" O GLN A 784 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 800 removed outlier: 4.061A pdb=" N LYS A 795 " --> pdb=" O LEU A 791 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 820 removed outlier: 3.716A pdb=" N ASN A 819 " --> pdb=" O GLY A 816 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE A 820 " --> pdb=" O VAL A 817 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 816 through 820' Processing helix chain 'A' and resid 821 through 849 removed outlier: 3.650A pdb=" N ILE A 825 " --> pdb=" O GLY A 821 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N PHE A 836 " --> pdb=" O VAL A 832 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL A 837 " --> pdb=" O LEU A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 852 No H-bonds generated for 'chain 'A' and resid 850 through 852' Processing helix chain 'A' and resid 855 through 868 removed outlier: 3.899A pdb=" N ALA A 860 " --> pdb=" O SER A 856 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N MET A 861 " --> pdb=" O PHE A 857 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 457 No H-bonds generated for 'chain 'B' and resid 455 through 457' Processing helix chain 'B' and resid 461 through 474 Processing helix chain 'B' and resid 500 through 507 removed outlier: 3.704A pdb=" N GLU B 504 " --> pdb=" O GLY B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 525 removed outlier: 3.537A pdb=" N LYS B 525 " --> pdb=" O TYR B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 583 removed outlier: 3.884A pdb=" N LEU B 568 " --> pdb=" O TRP B 564 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N CYS B 576 " --> pdb=" O LEU B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 620 removed outlier: 3.833A pdb=" N PHE B 612 " --> pdb=" O LEU B 608 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TRP B 613 " --> pdb=" O LEU B 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 655 removed outlier: 3.654A pdb=" N ARG B 634 " --> pdb=" O ALA B 630 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL B 636 " --> pdb=" O SER B 632 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN B 654 " --> pdb=" O SER B 650 " (cutoff:3.500A) Processing helix chain 'B' and resid 670 through 676 removed outlier: 3.870A pdb=" N LEU B 674 " --> pdb=" O SER B 670 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA B 675 " --> pdb=" O ALA B 671 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 696 Processing helix chain 'B' and resid 699 through 712 removed outlier: 3.606A pdb=" N LYS B 704 " --> pdb=" O SER B 700 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N MET B 709 " --> pdb=" O MET B 705 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N SER B 711 " --> pdb=" O ALA B 707 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG B 712 " --> pdb=" O PHE B 708 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 716 Processing helix chain 'B' and resid 721 through 730 Processing helix chain 'B' and resid 739 through 749 removed outlier: 3.552A pdb=" N PHE B 744 " --> pdb=" O THR B 740 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLN B 747 " --> pdb=" O GLU B 743 " (cutoff:3.500A) Processing helix chain 'B' and resid 774 through 789 Processing helix chain 'B' and resid 789 through 800 Processing helix chain 'B' and resid 821 through 849 removed outlier: 3.562A pdb=" N ILE B 825 " --> pdb=" O GLY B 821 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL B 832 " --> pdb=" O ALA B 828 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASN B 849 " --> pdb=" O LYS B 845 " (cutoff:3.500A) Processing helix chain 'B' and resid 856 through 870 removed outlier: 3.635A pdb=" N MET B 867 " --> pdb=" O GLU B 863 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LYS B 870 " --> pdb=" O ARG B 866 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 475 removed outlier: 3.558A pdb=" N GLU C 469 " --> pdb=" O ASP C 465 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR C 472 " --> pdb=" O ARG C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 507 removed outlier: 3.532A pdb=" N ASP C 507 " --> pdb=" O ARG C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 525 removed outlier: 3.885A pdb=" N LYS C 525 " --> pdb=" O TYR C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 553 through 557 removed outlier: 3.854A pdb=" N LEU C 556 " --> pdb=" O PHE C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 562 through 585 removed outlier: 3.952A pdb=" N SER C 575 " --> pdb=" O CYS C 571 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N CYS C 576 " --> pdb=" O LEU C 572 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 620 removed outlier: 3.836A pdb=" N TRP C 613 " --> pdb=" O LEU C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 660 removed outlier: 3.592A pdb=" N ILE C 635 " --> pdb=" O LEU C 631 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N VAL C 636 " --> pdb=" O SER C 632 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA C 656 " --> pdb=" O THR C 652 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ALA C 657 " --> pdb=" O ALA C 653 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE C 658 " --> pdb=" O ASN C 654 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 676 removed outlier: 4.080A pdb=" N LYS C 676 " --> pdb=" O ASP C 672 " (cutoff:3.500A) Processing helix chain 'C' and resid 688 through 697 removed outlier: 3.573A pdb=" N PHE C 694 " --> pdb=" O THR C 690 " (cutoff:3.500A) Processing helix chain 'C' and resid 699 through 710 Processing helix chain 'C' and resid 720 through 731 removed outlier: 3.973A pdb=" N VAL C 728 " --> pdb=" O GLY C 724 " (cutoff:3.500A) Processing helix chain 'C' and resid 739 through 746 removed outlier: 3.822A pdb=" N PHE C 744 " --> pdb=" O THR C 740 " (cutoff:3.500A) Processing helix chain 'C' and resid 773 through 788 removed outlier: 4.080A pdb=" N LYS C 777 " --> pdb=" O PRO C 773 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE C 778 " --> pdb=" O TYR C 774 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU C 783 " --> pdb=" O THR C 779 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU C 785 " --> pdb=" O ALA C 781 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU C 788 " --> pdb=" O GLN C 784 " (cutoff:3.500A) Processing helix chain 'C' and resid 789 through 800 removed outlier: 4.060A pdb=" N LYS C 795 " --> pdb=" O LEU C 791 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 820 removed outlier: 3.716A pdb=" N ASN C 819 " --> pdb=" O GLY C 816 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE C 820 " --> pdb=" O VAL C 817 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 816 through 820' Processing helix chain 'C' and resid 821 through 849 removed outlier: 3.651A pdb=" N ILE C 825 " --> pdb=" O GLY C 821 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N PHE C 836 " --> pdb=" O VAL C 832 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL C 837 " --> pdb=" O LEU C 833 " (cutoff:3.500A) Processing helix chain 'C' and resid 850 through 852 No H-bonds generated for 'chain 'C' and resid 850 through 852' Processing helix chain 'C' and resid 855 through 868 removed outlier: 3.899A pdb=" N ALA C 860 " --> pdb=" O SER C 856 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N MET C 861 " --> pdb=" O PHE C 857 " (cutoff:3.500A) Processing helix chain 'D' and resid 455 through 457 No H-bonds generated for 'chain 'D' and resid 455 through 457' Processing helix chain 'D' and resid 461 through 474 Processing helix chain 'D' and resid 500 through 507 removed outlier: 3.704A pdb=" N GLU D 504 " --> pdb=" O GLY D 500 " (cutoff:3.500A) Processing helix chain 'D' and resid 520 through 525 removed outlier: 3.537A pdb=" N LYS D 525 " --> pdb=" O TYR D 521 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 583 removed outlier: 3.883A pdb=" N LEU D 568 " --> pdb=" O TRP D 564 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N CYS D 576 " --> pdb=" O LEU D 572 " (cutoff:3.500A) Processing helix chain 'D' and resid 607 through 620 removed outlier: 3.833A pdb=" N PHE D 612 " --> pdb=" O LEU D 608 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N TRP D 613 " --> pdb=" O LEU D 609 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 655 removed outlier: 3.654A pdb=" N ARG D 634 " --> pdb=" O ALA D 630 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL D 636 " --> pdb=" O SER D 632 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN D 654 " --> pdb=" O SER D 650 " (cutoff:3.500A) Processing helix chain 'D' and resid 670 through 676 removed outlier: 3.870A pdb=" N LEU D 674 " --> pdb=" O SER D 670 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA D 675 " --> pdb=" O ALA D 671 " (cutoff:3.500A) Processing helix chain 'D' and resid 688 through 696 Processing helix chain 'D' and resid 699 through 712 removed outlier: 3.605A pdb=" N LYS D 704 " --> pdb=" O SER D 700 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N MET D 709 " --> pdb=" O MET D 705 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N SER D 711 " --> pdb=" O ALA D 707 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG D 712 " --> pdb=" O PHE D 708 " (cutoff:3.500A) Processing helix chain 'D' and resid 712 through 716 Processing helix chain 'D' and resid 721 through 730 Processing helix chain 'D' and resid 739 through 749 removed outlier: 3.549A pdb=" N PHE D 744 " --> pdb=" O THR D 740 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLN D 747 " --> pdb=" O GLU D 743 " (cutoff:3.500A) Processing helix chain 'D' and resid 774 through 789 Processing helix chain 'D' and resid 789 through 800 Processing helix chain 'D' and resid 821 through 849 removed outlier: 3.561A pdb=" N ILE D 825 " --> pdb=" O GLY D 821 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL D 832 " --> pdb=" O ALA D 828 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASN D 849 " --> pdb=" O LYS D 845 " (cutoff:3.500A) Processing helix chain 'D' and resid 856 through 870 removed outlier: 3.635A pdb=" N MET D 867 " --> pdb=" O GLU D 863 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LYS D 870 " --> pdb=" O ARG D 866 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 445 through 446 Processing sheet with id=AA2, first strand: chain 'A' and resid 532 through 535 removed outlier: 6.590A pdb=" N TYR A 764 " --> pdb=" O PHE A 533 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 735 through 738 removed outlier: 3.694A pdb=" N ILE A 540 " --> pdb=" O ILE A 755 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 434 through 435 Processing sheet with id=AA5, first strand: chain 'B' and resid 445 through 446 Processing sheet with id=AA6, first strand: chain 'B' and resid 535 through 536 Processing sheet with id=AA7, first strand: chain 'B' and resid 717 through 718 removed outlier: 8.155A pdb=" N VAL B 718 " --> pdb=" O TYR B 682 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ALA B 684 " --> pdb=" O VAL B 718 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N GLU B 681 " --> pdb=" O ALA B 734 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N LEU B 736 " --> pdb=" O GLU B 681 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N GLY B 683 " --> pdb=" O LEU B 736 " (cutoff:3.500A) removed outlier: 8.536A pdb=" N GLU B 738 " --> pdb=" O GLY B 683 " (cutoff:3.500A) removed outlier: 10.349A pdb=" N VAL B 685 " --> pdb=" O GLU B 738 " (cutoff:3.500A) removed outlier: 8.684A pdb=" N TYR B 733 " --> pdb=" O ARG B 543 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N ARG B 543 " --> pdb=" O TYR B 733 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ILE B 540 " --> pdb=" O ILE B 755 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 548 through 549 removed outlier: 4.212A pdb=" N GLU B 662 " --> pdb=" O ASN B 549 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 445 through 446 Processing sheet with id=AB1, first strand: chain 'C' and resid 532 through 535 removed outlier: 6.591A pdb=" N TYR C 764 " --> pdb=" O PHE C 533 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 735 through 738 removed outlier: 3.694A pdb=" N ILE C 540 " --> pdb=" O ILE C 755 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 434 through 435 Processing sheet with id=AB4, first strand: chain 'D' and resid 445 through 446 Processing sheet with id=AB5, first strand: chain 'D' and resid 535 through 536 Processing sheet with id=AB6, first strand: chain 'D' and resid 717 through 718 removed outlier: 8.155A pdb=" N VAL D 718 " --> pdb=" O TYR D 682 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ALA D 684 " --> pdb=" O VAL D 718 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N GLU D 681 " --> pdb=" O ALA D 734 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N LEU D 736 " --> pdb=" O GLU D 681 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N GLY D 683 " --> pdb=" O LEU D 736 " (cutoff:3.500A) removed outlier: 8.534A pdb=" N GLU D 738 " --> pdb=" O GLY D 683 " (cutoff:3.500A) removed outlier: 10.350A pdb=" N VAL D 685 " --> pdb=" O GLU D 738 " (cutoff:3.500A) removed outlier: 8.683A pdb=" N TYR D 733 " --> pdb=" O ARG D 543 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N ARG D 543 " --> pdb=" O TYR D 733 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ILE D 540 " --> pdb=" O ILE D 755 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 548 through 549 removed outlier: 4.211A pdb=" N GLU D 662 " --> pdb=" O ASN D 549 " (cutoff:3.500A) 580 hydrogen bonds defined for protein. 1706 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: 3.91 Time building geometry restraints manager: 4.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4425 1.34 - 1.46: 3140 1.46 - 1.58: 6729 1.58 - 1.70: 0 1.70 - 1.81: 152 Bond restraints: 14446 Sorted by residual: bond pdb=" C ASN C 557 " pdb=" N PRO C 558 " ideal model delta sigma weight residual 1.337 1.381 -0.045 1.11e-02 8.12e+03 1.63e+01 bond pdb=" C ASN A 557 " pdb=" N PRO A 558 " ideal model delta sigma weight residual 1.337 1.381 -0.044 1.11e-02 8.12e+03 1.59e+01 bond pdb=" C ASN B 557 " pdb=" N PRO B 558 " ideal model delta sigma weight residual 1.337 1.379 -0.043 1.11e-02 8.12e+03 1.49e+01 bond pdb=" C ASN D 557 " pdb=" N PRO D 558 " ideal model delta sigma weight residual 1.337 1.379 -0.043 1.11e-02 8.12e+03 1.48e+01 bond pdb=" C LEU B 626 " pdb=" N MET B 627 " ideal model delta sigma weight residual 1.332 1.290 0.042 1.40e-02 5.10e+03 9.21e+00 ... (remaining 14441 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 18332 2.33 - 4.66: 1002 4.66 - 6.99: 158 6.99 - 9.32: 42 9.32 - 11.65: 12 Bond angle restraints: 19546 Sorted by residual: angle pdb=" CA LYS C 676 " pdb=" C LYS C 676 " pdb=" N GLN C 677 " ideal model delta sigma weight residual 117.79 124.86 -7.07 1.22e+00 6.72e-01 3.36e+01 angle pdb=" CA LYS A 676 " pdb=" C LYS A 676 " pdb=" N GLN A 677 " ideal model delta sigma weight residual 117.79 124.83 -7.04 1.22e+00 6.72e-01 3.33e+01 angle pdb=" C ASP C 492 " pdb=" N ASP C 493 " pdb=" CA ASP C 493 " ideal model delta sigma weight residual 121.54 132.01 -10.47 1.91e+00 2.74e-01 3.00e+01 angle pdb=" C ASP A 492 " pdb=" N ASP A 493 " pdb=" CA ASP A 493 " ideal model delta sigma weight residual 121.54 131.89 -10.35 1.91e+00 2.74e-01 2.93e+01 angle pdb=" N LYS B 629 " pdb=" CA LYS B 629 " pdb=" C LYS B 629 " ideal model delta sigma weight residual 109.96 101.71 8.25 1.58e+00 4.01e-01 2.72e+01 ... (remaining 19541 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.39: 8215 17.39 - 34.79: 351 34.79 - 52.18: 64 52.18 - 69.57: 8 69.57 - 86.97: 6 Dihedral angle restraints: 8644 sinusoidal: 3484 harmonic: 5160 Sorted by residual: dihedral pdb=" CB CYS B 750 " pdb=" SG CYS B 750 " pdb=" SG CYS B 804 " pdb=" CB CYS B 804 " ideal model delta sinusoidal sigma weight residual 93.00 179.97 -86.97 1 1.00e+01 1.00e-02 9.09e+01 dihedral pdb=" CB CYS A 750 " pdb=" SG CYS A 750 " pdb=" SG CYS A 804 " pdb=" CB CYS A 804 " ideal model delta sinusoidal sigma weight residual -86.00 -162.20 76.20 1 1.00e+01 1.00e-02 7.31e+01 dihedral pdb=" CA ASP D 493 " pdb=" C ASP D 493 " pdb=" N VAL D 494 " pdb=" CA VAL D 494 " ideal model delta harmonic sigma weight residual -180.00 -145.47 -34.53 0 5.00e+00 4.00e-02 4.77e+01 ... (remaining 8641 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1730 0.069 - 0.138: 368 0.138 - 0.207: 58 0.207 - 0.276: 12 0.276 - 0.345: 4 Chirality restraints: 2172 Sorted by residual: chirality pdb=" CG LEU C 568 " pdb=" CB LEU C 568 " pdb=" CD1 LEU C 568 " pdb=" CD2 LEU C 568 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.34 2.00e-01 2.50e+01 2.97e+00 chirality pdb=" CG LEU A 568 " pdb=" CB LEU A 568 " pdb=" CD1 LEU A 568 " pdb=" CD2 LEU A 568 " both_signs ideal model delta sigma weight residual False -2.59 -2.25 -0.34 2.00e-01 2.50e+01 2.91e+00 chirality pdb=" CB ILE B 438 " pdb=" CA ILE B 438 " pdb=" CG1 ILE B 438 " pdb=" CG2 ILE B 438 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.63e+00 ... (remaining 2169 not shown) Planarity restraints: 2474 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP C 492 " 0.016 2.00e-02 2.50e+03 3.24e-02 1.05e+01 pdb=" C ASP C 492 " -0.056 2.00e-02 2.50e+03 pdb=" O ASP C 492 " 0.021 2.00e-02 2.50e+03 pdb=" N ASP C 493 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 492 " 0.016 2.00e-02 2.50e+03 3.23e-02 1.05e+01 pdb=" C ASP A 492 " -0.056 2.00e-02 2.50e+03 pdb=" O ASP A 492 " 0.021 2.00e-02 2.50e+03 pdb=" N ASP A 493 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG D 481 " -0.014 2.00e-02 2.50e+03 2.76e-02 7.62e+00 pdb=" C ARG D 481 " 0.048 2.00e-02 2.50e+03 pdb=" O ARG D 481 " -0.018 2.00e-02 2.50e+03 pdb=" N LEU D 482 " -0.016 2.00e-02 2.50e+03 ... (remaining 2471 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 160 2.60 - 3.18: 11897 3.18 - 3.75: 21599 3.75 - 4.33: 30493 4.33 - 4.90: 49336 Nonbonded interactions: 113485 Sorted by model distance: nonbonded pdb=" SG CYS D 750 " pdb=" SG CYS D 804 " model vdw 2.030 3.760 nonbonded pdb=" SG CYS C 750 " pdb=" SG CYS C 804 " model vdw 2.030 3.760 nonbonded pdb=" O ARG B 727 " pdb=" OG SER B 731 " model vdw 2.244 3.040 nonbonded pdb=" O ARG D 727 " pdb=" OG SER D 731 " model vdw 2.244 3.040 nonbonded pdb=" O LYS D 629 " pdb=" OG1 THR D 633 " model vdw 2.280 3.040 ... (remaining 113480 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: 0.07 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'A' selection = chain 'C' } 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=0.38 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 41.010 Find NCS groups from input model: 0.260 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.075 14446 Z= 0.505 Angle : 1.245 11.648 19546 Z= 0.728 Chirality : 0.060 0.345 2172 Planarity : 0.008 0.059 2474 Dihedral : 10.750 71.111 5330 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.90 % Allowed : 11.65 % Favored : 87.44 % Rotamer: Outliers : 0.65 % Allowed : 4.77 % Favored : 94.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.35 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.51 (0.14), residues: 1774 helix: -3.92 (0.09), residues: 858 sheet: -3.17 (0.37), residues: 164 loop : -3.26 (0.19), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.004 TRP A 799 HIS 0.022 0.003 HIS A 593 PHE 0.041 0.003 PHE B 735 TYR 0.036 0.004 TYR B 488 ARG 0.010 0.001 ARG A 866 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 378 time to evaluate : 1.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 465 ASP cc_start: 0.8006 (t70) cc_final: 0.7754 (t0) REVERT: A 565 MET cc_start: 0.8243 (mmm) cc_final: 0.7952 (mmt) REVERT: A 861 MET cc_start: 0.8239 (mmp) cc_final: 0.7781 (mtm) REVERT: B 465 ASP cc_start: 0.8494 (m-30) cc_final: 0.8232 (m-30) REVERT: B 469 GLU cc_start: 0.8373 (mm-30) cc_final: 0.8093 (mm-30) REVERT: B 572 LEU cc_start: 0.9141 (mm) cc_final: 0.8516 (mm) REVERT: B 576 CYS cc_start: 0.7820 (m) cc_final: 0.7434 (m) REVERT: B 580 VAL cc_start: 0.9300 (t) cc_final: 0.9075 (m) REVERT: B 584 PHE cc_start: 0.7503 (t80) cc_final: 0.6995 (m-10) REVERT: B 590 TYR cc_start: 0.7756 (p90) cc_final: 0.7276 (p90) REVERT: B 627 MET cc_start: 0.7846 (tpp) cc_final: 0.7416 (mmt) REVERT: B 639 ILE cc_start: 0.9186 (tp) cc_final: 0.8828 (pt) REVERT: B 655 LEU cc_start: 0.8641 (tp) cc_final: 0.8418 (tp) REVERT: B 792 HIS cc_start: 0.8346 (t70) cc_final: 0.7607 (t70) REVERT: B 861 MET cc_start: 0.7093 (ttt) cc_final: 0.6881 (ttt) REVERT: B 863 GLU cc_start: 0.7460 (mm-30) cc_final: 0.7035 (mt-10) REVERT: C 565 MET cc_start: 0.8134 (mmm) cc_final: 0.7929 (mmt) REVERT: C 639 ILE cc_start: 0.8799 (mm) cc_final: 0.8471 (tp) REVERT: C 761 SER cc_start: 0.8795 (t) cc_final: 0.8298 (m) REVERT: C 805 PRO cc_start: 0.8504 (Cg_exo) cc_final: 0.8269 (Cg_endo) REVERT: D 465 ASP cc_start: 0.8462 (m-30) cc_final: 0.8233 (m-30) REVERT: D 572 LEU cc_start: 0.9149 (mm) cc_final: 0.8552 (mm) REVERT: D 576 CYS cc_start: 0.7873 (m) cc_final: 0.7443 (m) REVERT: D 580 VAL cc_start: 0.9274 (t) cc_final: 0.9047 (m) REVERT: D 590 TYR cc_start: 0.7726 (p90) cc_final: 0.7227 (p90) REVERT: D 639 ILE cc_start: 0.9160 (tp) cc_final: 0.8832 (pt) REVERT: D 655 LEU cc_start: 0.8653 (tp) cc_final: 0.8444 (tp) REVERT: D 792 HIS cc_start: 0.8401 (t70) cc_final: 0.7830 (t70) REVERT: D 861 MET cc_start: 0.6936 (ttt) cc_final: 0.6722 (ttt) outliers start: 2 outliers final: 0 residues processed: 380 average time/residue: 0.2796 time to fit residues: 152.8949 Evaluate side-chains 215 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 1.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 6.9990 chunk 133 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 137 optimal weight: 0.5980 chunk 53 optimal weight: 0.8980 chunk 83 optimal weight: 0.9990 chunk 102 optimal weight: 0.7980 chunk 159 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 596 ASN A 604 ASN A 802 ASN B 549 ASN B 610 ASN B 792 HIS B 819 ASN C 596 ASN C 604 ASN C 802 ASN D 549 ASN D 604 ASN D 610 ASN D 819 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.141982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.103141 restraints weight = 88875.204| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 5.91 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3373 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3373 r_free = 0.3373 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3373 r_free = 0.3373 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3373 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 14446 Z= 0.239 Angle : 0.768 8.453 19546 Z= 0.398 Chirality : 0.044 0.159 2172 Planarity : 0.006 0.053 2474 Dihedral : 6.438 44.776 1936 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.40 % Allowed : 11.76 % Favored : 87.84 % Rotamer: Outliers : 2.26 % Allowed : 10.00 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.46 (0.17), residues: 1774 helix: -1.61 (0.15), residues: 866 sheet: -2.95 (0.43), residues: 130 loop : -2.93 (0.20), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 798 HIS 0.015 0.002 HIS C 593 PHE 0.026 0.002 PHE B 476 TYR 0.022 0.002 TYR D 566 ARG 0.008 0.001 ARG C 583 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 260 time to evaluate : 1.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 534 MET cc_start: 0.8948 (ttm) cc_final: 0.8684 (ttp) REVERT: A 565 MET cc_start: 0.8532 (mmm) cc_final: 0.8262 (mmt) REVERT: A 635 ILE cc_start: 0.8877 (OUTLIER) cc_final: 0.8642 (mp) REVERT: A 668 ILE cc_start: 0.8728 (mm) cc_final: 0.8286 (pt) REVERT: A 800 ARG cc_start: 0.7714 (ptp90) cc_final: 0.7456 (mtm110) REVERT: A 836 PHE cc_start: 0.7946 (m-80) cc_final: 0.7709 (m-10) REVERT: A 841 GLU cc_start: 0.7472 (mt-10) cc_final: 0.7200 (mt-10) REVERT: A 861 MET cc_start: 0.8456 (mmp) cc_final: 0.7855 (mtm) REVERT: A 866 ARG cc_start: 0.6837 (OUTLIER) cc_final: 0.5975 (tmm-80) REVERT: B 465 ASP cc_start: 0.8858 (m-30) cc_final: 0.8495 (m-30) REVERT: B 469 GLU cc_start: 0.8591 (mm-30) cc_final: 0.8091 (mm-30) REVERT: B 563 ILE cc_start: 0.9102 (mm) cc_final: 0.8894 (mt) REVERT: B 572 LEU cc_start: 0.9237 (mm) cc_final: 0.8386 (mm) REVERT: B 576 CYS cc_start: 0.8502 (m) cc_final: 0.7856 (m) REVERT: B 580 VAL cc_start: 0.9384 (t) cc_final: 0.9025 (m) REVERT: B 584 PHE cc_start: 0.7918 (t80) cc_final: 0.6872 (m-10) REVERT: B 590 TYR cc_start: 0.7697 (p90) cc_final: 0.7232 (p90) REVERT: B 609 LEU cc_start: 0.8901 (tt) cc_final: 0.8309 (mt) REVERT: B 612 PHE cc_start: 0.8496 (m-80) cc_final: 0.8148 (t80) REVERT: B 626 LEU cc_start: 0.8462 (mt) cc_final: 0.8143 (mt) REVERT: B 639 ILE cc_start: 0.9014 (tp) cc_final: 0.8784 (pt) REVERT: B 655 LEU cc_start: 0.8846 (tp) cc_final: 0.8617 (tp) REVERT: B 709 MET cc_start: 0.8952 (mtt) cc_final: 0.8604 (mtt) REVERT: B 792 HIS cc_start: 0.8555 (t-90) cc_final: 0.8352 (t-170) REVERT: B 800 ARG cc_start: 0.8338 (tpp80) cc_final: 0.8001 (mmm160) REVERT: C 565 MET cc_start: 0.8588 (mmm) cc_final: 0.8273 (mmt) REVERT: C 635 ILE cc_start: 0.8762 (OUTLIER) cc_final: 0.8508 (mp) REVERT: C 667 PRO cc_start: 0.9066 (Cg_exo) cc_final: 0.8645 (Cg_endo) REVERT: C 761 SER cc_start: 0.8765 (t) cc_final: 0.8320 (m) REVERT: C 805 PRO cc_start: 0.8339 (Cg_exo) cc_final: 0.7931 (Cg_endo) REVERT: C 841 GLU cc_start: 0.7587 (mt-10) cc_final: 0.7249 (mt-10) REVERT: D 469 GLU cc_start: 0.8455 (mm-30) cc_final: 0.8215 (mm-30) REVERT: D 535 THR cc_start: 0.9161 (OUTLIER) cc_final: 0.8940 (p) REVERT: D 556 LEU cc_start: 0.9088 (mm) cc_final: 0.8796 (mp) REVERT: D 572 LEU cc_start: 0.9244 (mm) cc_final: 0.8410 (mm) REVERT: D 576 CYS cc_start: 0.8404 (m) cc_final: 0.7995 (m) REVERT: D 590 TYR cc_start: 0.7650 (p90) cc_final: 0.7187 (p90) REVERT: D 627 MET cc_start: 0.8147 (tpp) cc_final: 0.7324 (tpp) REVERT: D 639 ILE cc_start: 0.9011 (tp) cc_final: 0.8761 (tp) REVERT: D 792 HIS cc_start: 0.8707 (t70) cc_final: 0.8446 (t-170) REVERT: D 800 ARG cc_start: 0.8436 (tpp80) cc_final: 0.7929 (mmm160) outliers start: 27 outliers final: 14 residues processed: 280 average time/residue: 0.2407 time to fit residues: 101.6774 Evaluate side-chains 226 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 208 time to evaluate : 1.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 458 ARG Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 866 ARG Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 591 ASN Chi-restraints excluded: chain B residue 725 ILE Chi-restraints excluded: chain C residue 458 ARG Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 575 SER Chi-restraints excluded: chain C residue 635 ILE Chi-restraints excluded: chain D residue 444 VAL Chi-restraints excluded: chain D residue 535 THR Chi-restraints excluded: chain D residue 770 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 31 optimal weight: 2.9990 chunk 155 optimal weight: 6.9990 chunk 28 optimal weight: 0.9990 chunk 156 optimal weight: 1.9990 chunk 92 optimal weight: 0.7980 chunk 62 optimal weight: 0.6980 chunk 121 optimal weight: 0.8980 chunk 107 optimal weight: 5.9990 chunk 173 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 168 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 508 HIS B 604 ASN C 508 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.137429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.098900 restraints weight = 69148.562| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 5.48 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3378 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3378 r_free = 0.3378 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3378 r_free = 0.3378 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3378 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14446 Z= 0.248 Angle : 0.719 8.078 19546 Z= 0.369 Chirality : 0.044 0.180 2172 Planarity : 0.005 0.053 2474 Dihedral : 5.961 41.126 1936 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.28 % Allowed : 11.54 % Favored : 88.18 % Rotamer: Outliers : 2.65 % Allowed : 12.00 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.19), residues: 1774 helix: -0.56 (0.16), residues: 880 sheet: -2.68 (0.43), residues: 126 loop : -2.73 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 589 HIS 0.015 0.002 HIS C 593 PHE 0.023 0.002 PHE B 476 TYR 0.020 0.002 TYR A 651 ARG 0.007 0.001 ARG C 583 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 236 time to evaluate : 1.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 488 TYR cc_start: 0.8192 (m-80) cc_final: 0.7681 (m-80) REVERT: A 534 MET cc_start: 0.8974 (ttm) cc_final: 0.8696 (ttp) REVERT: A 565 MET cc_start: 0.8557 (mmm) cc_final: 0.8247 (mmt) REVERT: A 635 ILE cc_start: 0.8861 (OUTLIER) cc_final: 0.8605 (mp) REVERT: A 651 TYR cc_start: 0.8798 (t80) cc_final: 0.8545 (t80) REVERT: A 668 ILE cc_start: 0.8701 (mm) cc_final: 0.8254 (pt) REVERT: A 755 ILE cc_start: 0.9230 (mp) cc_final: 0.8838 (mp) REVERT: A 761 SER cc_start: 0.8875 (t) cc_final: 0.8310 (m) REVERT: A 810 LYS cc_start: 0.9136 (tmtm) cc_final: 0.8914 (mmtt) REVERT: A 836 PHE cc_start: 0.8011 (m-80) cc_final: 0.7663 (m-10) REVERT: A 841 GLU cc_start: 0.7451 (mt-10) cc_final: 0.7163 (mt-10) REVERT: A 861 MET cc_start: 0.8418 (mmp) cc_final: 0.7710 (mtm) REVERT: B 465 ASP cc_start: 0.8776 (m-30) cc_final: 0.8570 (m-30) REVERT: B 469 GLU cc_start: 0.8621 (mm-30) cc_final: 0.8238 (mm-30) REVERT: B 572 LEU cc_start: 0.9222 (mm) cc_final: 0.8416 (mm) REVERT: B 576 CYS cc_start: 0.8543 (m) cc_final: 0.7883 (m) REVERT: B 580 VAL cc_start: 0.9385 (t) cc_final: 0.9049 (m) REVERT: B 584 PHE cc_start: 0.7912 (t80) cc_final: 0.7032 (m-10) REVERT: B 590 TYR cc_start: 0.7510 (p90) cc_final: 0.6865 (p90) REVERT: B 609 LEU cc_start: 0.8800 (tt) cc_final: 0.8130 (mt) REVERT: B 612 PHE cc_start: 0.8461 (m-80) cc_final: 0.8125 (t80) REVERT: B 639 ILE cc_start: 0.9029 (tp) cc_final: 0.8721 (tp) REVERT: B 709 MET cc_start: 0.9002 (mtt) cc_final: 0.8679 (mtt) REVERT: C 501 MET cc_start: 0.7866 (mtm) cc_final: 0.7643 (mtm) REVERT: C 565 MET cc_start: 0.8579 (mmm) cc_final: 0.8343 (mmm) REVERT: C 589 TRP cc_start: 0.8280 (m100) cc_final: 0.8027 (m100) REVERT: C 635 ILE cc_start: 0.8803 (OUTLIER) cc_final: 0.8562 (mp) REVERT: C 668 ILE cc_start: 0.8897 (mm) cc_final: 0.8426 (pt) REVERT: C 698 LYS cc_start: 0.9363 (mmtt) cc_final: 0.8885 (mmtt) REVERT: C 761 SER cc_start: 0.8839 (t) cc_final: 0.8338 (m) REVERT: C 841 GLU cc_start: 0.7805 (mt-10) cc_final: 0.7472 (mt-10) REVERT: D 556 LEU cc_start: 0.9137 (mm) cc_final: 0.8870 (mp) REVERT: D 572 LEU cc_start: 0.9170 (mm) cc_final: 0.8351 (mm) REVERT: D 576 CYS cc_start: 0.8498 (m) cc_final: 0.8001 (m) REVERT: D 590 TYR cc_start: 0.7434 (p90) cc_final: 0.6651 (p90) REVERT: D 612 PHE cc_start: 0.8442 (m-80) cc_final: 0.7995 (t80) REVERT: D 625 GLU cc_start: 0.8335 (pt0) cc_final: 0.8133 (pt0) REVERT: D 639 ILE cc_start: 0.9024 (tp) cc_final: 0.8738 (tp) outliers start: 33 outliers final: 19 residues processed: 253 average time/residue: 0.2350 time to fit residues: 89.6098 Evaluate side-chains 233 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 212 time to evaluate : 1.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 458 ARG Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 866 ARG Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 565 MET Chi-restraints excluded: chain B residue 591 ASN Chi-restraints excluded: chain B residue 725 ILE Chi-restraints excluded: chain B residue 831 LEU Chi-restraints excluded: chain C residue 458 ARG Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 571 CYS Chi-restraints excluded: chain C residue 635 ILE Chi-restraints excluded: chain D residue 444 VAL Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 565 MET Chi-restraints excluded: chain D residue 831 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 48 optimal weight: 4.9990 chunk 104 optimal weight: 0.0980 chunk 148 optimal weight: 0.5980 chunk 60 optimal weight: 0.0010 chunk 64 optimal weight: 0.6980 chunk 53 optimal weight: 0.0020 chunk 152 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 174 optimal weight: 7.9990 chunk 160 optimal weight: 0.9990 chunk 86 optimal weight: 10.0000 overall best weight: 0.2794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 792 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.141303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.102660 restraints weight = 79193.010| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 5.80 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3431 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3431 r_free = 0.3431 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3431 r_free = 0.3431 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3431 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.3669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14446 Z= 0.164 Angle : 0.674 9.049 19546 Z= 0.344 Chirality : 0.042 0.148 2172 Planarity : 0.005 0.053 2474 Dihedral : 5.584 42.903 1936 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.28 % Allowed : 10.46 % Favored : 89.25 % Rotamer: Outliers : 2.32 % Allowed : 12.90 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.19), residues: 1774 helix: 0.12 (0.17), residues: 866 sheet: -3.06 (0.40), residues: 124 loop : -2.46 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 589 HIS 0.013 0.002 HIS A 593 PHE 0.031 0.001 PHE D 584 TYR 0.017 0.001 TYR A 651 ARG 0.008 0.001 ARG A 800 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 250 time to evaluate : 1.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 534 MET cc_start: 0.8902 (ttm) cc_final: 0.8639 (ttp) REVERT: A 565 MET cc_start: 0.8514 (mmm) cc_final: 0.8221 (mmt) REVERT: A 635 ILE cc_start: 0.8841 (OUTLIER) cc_final: 0.8626 (mp) REVERT: A 651 TYR cc_start: 0.8675 (t80) cc_final: 0.8425 (t80) REVERT: A 668 ILE cc_start: 0.8628 (mm) cc_final: 0.8200 (pt) REVERT: A 755 ILE cc_start: 0.9091 (mp) cc_final: 0.8732 (mp) REVERT: A 761 SER cc_start: 0.8860 (t) cc_final: 0.8326 (m) REVERT: A 810 LYS cc_start: 0.9133 (tmtm) cc_final: 0.8899 (mmtt) REVERT: A 836 PHE cc_start: 0.8038 (m-80) cc_final: 0.7738 (m-10) REVERT: A 841 GLU cc_start: 0.7692 (mt-10) cc_final: 0.7026 (mm-30) REVERT: A 861 MET cc_start: 0.8372 (mmp) cc_final: 0.7721 (mtm) REVERT: A 866 ARG cc_start: 0.7136 (OUTLIER) cc_final: 0.6269 (tmm160) REVERT: B 443 TYR cc_start: 0.8021 (m-80) cc_final: 0.7465 (m-80) REVERT: B 465 ASP cc_start: 0.8809 (m-30) cc_final: 0.8558 (m-30) REVERT: B 469 GLU cc_start: 0.8461 (mm-30) cc_final: 0.7961 (mm-30) REVERT: B 572 LEU cc_start: 0.9159 (mm) cc_final: 0.8394 (mm) REVERT: B 576 CYS cc_start: 0.8650 (m) cc_final: 0.7992 (m) REVERT: B 580 VAL cc_start: 0.9349 (t) cc_final: 0.9015 (m) REVERT: B 584 PHE cc_start: 0.7941 (t80) cc_final: 0.6971 (m-10) REVERT: B 590 TYR cc_start: 0.7255 (p90) cc_final: 0.6822 (p90) REVERT: B 612 PHE cc_start: 0.8392 (m-80) cc_final: 0.8082 (t80) REVERT: B 639 ILE cc_start: 0.8993 (tp) cc_final: 0.8697 (tp) REVERT: C 501 MET cc_start: 0.7742 (mtm) cc_final: 0.7479 (mtm) REVERT: C 565 MET cc_start: 0.8564 (mmm) cc_final: 0.8278 (mmt) REVERT: C 612 PHE cc_start: 0.8562 (m-10) cc_final: 0.8324 (m-80) REVERT: C 761 SER cc_start: 0.8828 (t) cc_final: 0.8363 (m) REVERT: C 810 LYS cc_start: 0.8248 (mmtt) cc_final: 0.7727 (mmpt) REVERT: C 841 GLU cc_start: 0.7851 (mt-10) cc_final: 0.7138 (mm-30) REVERT: D 556 LEU cc_start: 0.9100 (mm) cc_final: 0.8806 (mp) REVERT: D 572 LEU cc_start: 0.9135 (mm) cc_final: 0.8338 (mm) REVERT: D 576 CYS cc_start: 0.8493 (m) cc_final: 0.7828 (m) REVERT: D 580 VAL cc_start: 0.9378 (t) cc_final: 0.8967 (m) REVERT: D 590 TYR cc_start: 0.7578 (p90) cc_final: 0.7204 (p90) REVERT: D 612 PHE cc_start: 0.8413 (m-80) cc_final: 0.7937 (t80) REVERT: D 639 ILE cc_start: 0.8953 (tp) cc_final: 0.8663 (tp) REVERT: D 800 ARG cc_start: 0.8561 (tpp80) cc_final: 0.8021 (tpt90) REVERT: D 861 MET cc_start: 0.8485 (ppp) cc_final: 0.7674 (ttt) outliers start: 28 outliers final: 15 residues processed: 268 average time/residue: 0.2542 time to fit residues: 101.5900 Evaluate side-chains 235 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 218 time to evaluate : 1.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 458 ARG Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 866 ARG Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 565 MET Chi-restraints excluded: chain B residue 831 LEU Chi-restraints excluded: chain C residue 458 ARG Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain D residue 444 VAL Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 565 MET Chi-restraints excluded: chain D residue 831 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 32 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 33 optimal weight: 0.0770 chunk 162 optimal weight: 4.9990 chunk 90 optimal weight: 0.7980 chunk 115 optimal weight: 7.9990 chunk 121 optimal weight: 1.9990 chunk 158 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 173 optimal weight: 1.9990 overall best weight: 0.9142 ------------------------------------------------------------------------------- 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 = 0.3959 r_free = 0.3959 target = 0.138919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.099717 restraints weight = 78012.082| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 5.63 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3376 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3376 r_free = 0.3376 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3376 r_free = 0.3376 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3376 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.3919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14446 Z= 0.216 Angle : 0.685 10.179 19546 Z= 0.346 Chirality : 0.043 0.177 2172 Planarity : 0.005 0.070 2474 Dihedral : 5.471 41.295 1936 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.28 % Allowed : 10.86 % Favored : 88.86 % Rotamer: Outliers : 2.06 % Allowed : 14.65 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.20), residues: 1774 helix: 0.38 (0.17), residues: 876 sheet: -2.80 (0.43), residues: 108 loop : -2.46 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 706 HIS 0.011 0.002 HIS A 593 PHE 0.025 0.002 PHE B 476 TYR 0.016 0.002 TYR A 521 ARG 0.005 0.001 ARG B 855 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 226 time to evaluate : 1.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 534 MET cc_start: 0.8914 (ttm) cc_final: 0.8609 (ttp) REVERT: A 565 MET cc_start: 0.8523 (mmm) cc_final: 0.8257 (mmt) REVERT: A 755 ILE cc_start: 0.9124 (mp) cc_final: 0.8834 (mp) REVERT: A 761 SER cc_start: 0.8877 (t) cc_final: 0.8335 (m) REVERT: A 810 LYS cc_start: 0.9109 (tmtm) cc_final: 0.8902 (mmtt) REVERT: A 836 PHE cc_start: 0.8050 (m-80) cc_final: 0.7721 (m-10) REVERT: A 841 GLU cc_start: 0.7739 (mt-10) cc_final: 0.7100 (mm-30) REVERT: A 861 MET cc_start: 0.8408 (mmp) cc_final: 0.7678 (mtm) REVERT: B 443 TYR cc_start: 0.8164 (m-80) cc_final: 0.7598 (m-80) REVERT: B 469 GLU cc_start: 0.8474 (mm-30) cc_final: 0.8261 (mm-30) REVERT: B 572 LEU cc_start: 0.9134 (mm) cc_final: 0.8380 (mm) REVERT: B 576 CYS cc_start: 0.8588 (m) cc_final: 0.8131 (m) REVERT: B 584 PHE cc_start: 0.7963 (t80) cc_final: 0.6899 (m-10) REVERT: B 590 TYR cc_start: 0.7448 (p90) cc_final: 0.6860 (p90) REVERT: B 609 LEU cc_start: 0.8792 (tt) cc_final: 0.7976 (mt) REVERT: B 612 PHE cc_start: 0.8390 (m-80) cc_final: 0.8090 (t80) REVERT: B 625 GLU cc_start: 0.8189 (pt0) cc_final: 0.7913 (pt0) REVERT: B 709 MET cc_start: 0.8953 (mtt) cc_final: 0.8625 (mtt) REVERT: B 800 ARG cc_start: 0.8639 (tpp80) cc_final: 0.7627 (tpt170) REVERT: B 861 MET cc_start: 0.8283 (ppp) cc_final: 0.7639 (ttt) REVERT: C 501 MET cc_start: 0.7861 (mtm) cc_final: 0.7631 (mtm) REVERT: C 565 MET cc_start: 0.8562 (mmm) cc_final: 0.8292 (mmt) REVERT: C 612 PHE cc_start: 0.8591 (m-10) cc_final: 0.8381 (m-80) REVERT: C 668 ILE cc_start: 0.8747 (mm) cc_final: 0.8445 (pt) REVERT: C 698 LYS cc_start: 0.9351 (mmtt) cc_final: 0.8926 (mmtt) REVERT: C 761 SER cc_start: 0.8817 (t) cc_final: 0.8316 (m) REVERT: C 810 LYS cc_start: 0.8156 (mmtt) cc_final: 0.7658 (mmpt) REVERT: C 841 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7044 (mm-30) REVERT: D 556 LEU cc_start: 0.9169 (mm) cc_final: 0.8930 (mp) REVERT: D 572 LEU cc_start: 0.9223 (mm) cc_final: 0.8413 (mm) REVERT: D 576 CYS cc_start: 0.8499 (m) cc_final: 0.8044 (m) REVERT: D 590 TYR cc_start: 0.7940 (p90) cc_final: 0.7409 (p90) REVERT: D 609 LEU cc_start: 0.8753 (tt) cc_final: 0.7927 (mt) REVERT: D 612 PHE cc_start: 0.8440 (m-80) cc_final: 0.7882 (t80) REVERT: D 639 ILE cc_start: 0.9042 (tp) cc_final: 0.8761 (tp) REVERT: D 800 ARG cc_start: 0.8509 (tpp80) cc_final: 0.7799 (tpt170) REVERT: D 861 MET cc_start: 0.8520 (ppp) cc_final: 0.7715 (ttt) outliers start: 24 outliers final: 15 residues processed: 238 average time/residue: 0.2481 time to fit residues: 90.0137 Evaluate side-chains 222 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 207 time to evaluate : 1.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 458 ARG Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 565 MET Chi-restraints excluded: chain B residue 831 LEU Chi-restraints excluded: chain C residue 458 ARG Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain D residue 444 VAL Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 565 MET Chi-restraints excluded: chain D residue 823 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 157 optimal weight: 3.9990 chunk 119 optimal weight: 0.9990 chunk 160 optimal weight: 0.9980 chunk 66 optimal weight: 0.0670 chunk 37 optimal weight: 0.7980 chunk 106 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 chunk 125 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 85 optimal weight: 6.9990 chunk 79 optimal weight: 0.9980 overall best weight: 0.7720 ------------------------------------------------------------------------------- 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 = 0.3964 r_free = 0.3964 target = 0.139665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.101274 restraints weight = 72760.573| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 5.50 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3380 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3380 r_free = 0.3380 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3380 r_free = 0.3380 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3380 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.4133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14446 Z= 0.199 Angle : 0.669 10.253 19546 Z= 0.339 Chirality : 0.043 0.187 2172 Planarity : 0.005 0.070 2474 Dihedral : 5.356 41.147 1936 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.75 % Favored : 89.08 % Rotamer: Outliers : 2.00 % Allowed : 15.42 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.20), residues: 1774 helix: 0.64 (0.18), residues: 878 sheet: -2.76 (0.42), residues: 108 loop : -2.44 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 589 HIS 0.010 0.001 HIS A 593 PHE 0.028 0.002 PHE B 476 TYR 0.022 0.001 TYR C 651 ARG 0.004 0.000 ARG A 583 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 220 time to evaluate : 2.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 534 MET cc_start: 0.8907 (ttm) cc_final: 0.8531 (ttp) REVERT: A 565 MET cc_start: 0.8521 (mmm) cc_final: 0.8275 (mmt) REVERT: A 651 TYR cc_start: 0.8829 (t80) cc_final: 0.8550 (t80) REVERT: A 755 ILE cc_start: 0.9090 (mp) cc_final: 0.8814 (mp) REVERT: A 761 SER cc_start: 0.8868 (t) cc_final: 0.8334 (m) REVERT: A 836 PHE cc_start: 0.8048 (m-80) cc_final: 0.7696 (m-10) REVERT: A 841 GLU cc_start: 0.7682 (mt-10) cc_final: 0.7118 (mm-30) REVERT: A 861 MET cc_start: 0.8383 (mmp) cc_final: 0.7626 (mtm) REVERT: B 443 TYR cc_start: 0.8069 (m-80) cc_final: 0.7513 (m-80) REVERT: B 572 LEU cc_start: 0.9220 (mm) cc_final: 0.8447 (mm) REVERT: B 576 CYS cc_start: 0.8645 (m) cc_final: 0.8175 (m) REVERT: B 584 PHE cc_start: 0.7979 (t80) cc_final: 0.6911 (m-10) REVERT: B 590 TYR cc_start: 0.7215 (p90) cc_final: 0.6498 (p90) REVERT: B 609 LEU cc_start: 0.8754 (tt) cc_final: 0.7972 (mt) REVERT: B 612 PHE cc_start: 0.8394 (m-80) cc_final: 0.8080 (t80) REVERT: B 709 MET cc_start: 0.8933 (mtt) cc_final: 0.8600 (mtt) REVERT: B 800 ARG cc_start: 0.8617 (tpp80) cc_final: 0.7658 (tpt170) REVERT: B 861 MET cc_start: 0.8385 (ppp) cc_final: 0.7627 (ttt) REVERT: C 501 MET cc_start: 0.7766 (mtm) cc_final: 0.7496 (mtm) REVERT: C 565 MET cc_start: 0.8564 (mmm) cc_final: 0.8293 (mmt) REVERT: C 589 TRP cc_start: 0.8175 (m100) cc_final: 0.7915 (m100) REVERT: C 612 PHE cc_start: 0.8596 (m-10) cc_final: 0.8388 (m-80) REVERT: C 698 LYS cc_start: 0.9389 (mmtt) cc_final: 0.8989 (mmtm) REVERT: C 761 SER cc_start: 0.8838 (t) cc_final: 0.8336 (m) REVERT: C 810 LYS cc_start: 0.8119 (mmtt) cc_final: 0.7624 (mmpt) REVERT: C 836 PHE cc_start: 0.8055 (m-80) cc_final: 0.7725 (m-10) REVERT: C 841 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7054 (mm-30) REVERT: D 572 LEU cc_start: 0.9225 (mm) cc_final: 0.8410 (mm) REVERT: D 576 CYS cc_start: 0.8527 (m) cc_final: 0.8065 (m) REVERT: D 590 TYR cc_start: 0.7978 (p90) cc_final: 0.7506 (p90) REVERT: D 609 LEU cc_start: 0.8724 (tt) cc_final: 0.7917 (mt) REVERT: D 612 PHE cc_start: 0.8388 (m-80) cc_final: 0.7897 (t80) REVERT: D 639 ILE cc_start: 0.9047 (tp) cc_final: 0.8774 (tp) REVERT: D 793 MET cc_start: 0.8569 (ptp) cc_final: 0.8233 (pmm) REVERT: D 861 MET cc_start: 0.8469 (ppp) cc_final: 0.7742 (ttt) outliers start: 23 outliers final: 17 residues processed: 229 average time/residue: 0.2302 time to fit residues: 81.8609 Evaluate side-chains 221 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 204 time to evaluate : 1.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 458 ARG Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 571 CYS Chi-restraints excluded: chain A residue 867 MET Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 565 MET Chi-restraints excluded: chain B residue 823 ILE Chi-restraints excluded: chain B residue 831 LEU Chi-restraints excluded: chain C residue 458 ARG Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain D residue 444 VAL Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 565 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 124 optimal weight: 0.0770 chunk 173 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 108 optimal weight: 4.9990 chunk 113 optimal weight: 4.9990 chunk 12 optimal weight: 0.7980 chunk 161 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 24 optimal weight: 6.9990 chunk 82 optimal weight: 0.5980 chunk 112 optimal weight: 0.7980 overall best weight: 0.6338 ------------------------------------------------------------------------------- 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 = 0.3943 r_free = 0.3943 target = 0.137801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.099598 restraints weight = 60671.240| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 4.90 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3400 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3400 r_free = 0.3400 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3400 r_free = 0.3400 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3400 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.4335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14446 Z= 0.184 Angle : 0.656 9.620 19546 Z= 0.333 Chirality : 0.042 0.143 2172 Planarity : 0.005 0.070 2474 Dihedral : 5.270 40.972 1936 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.92 % Favored : 88.86 % Rotamer: Outliers : 1.81 % Allowed : 15.42 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.20), residues: 1774 helix: 0.81 (0.18), residues: 886 sheet: -2.87 (0.45), residues: 98 loop : -2.29 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 589 HIS 0.009 0.001 HIS A 593 PHE 0.023 0.001 PHE D 476 TYR 0.013 0.001 TYR A 521 ARG 0.004 0.000 ARG C 583 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 228 time to evaluate : 1.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 534 MET cc_start: 0.8475 (ttm) cc_final: 0.8087 (ttp) REVERT: A 565 MET cc_start: 0.8474 (mmm) cc_final: 0.8202 (mmt) REVERT: A 651 TYR cc_start: 0.8837 (t80) cc_final: 0.8637 (t80) REVERT: A 686 GLU cc_start: 0.6536 (tp30) cc_final: 0.6242 (tt0) REVERT: A 755 ILE cc_start: 0.9015 (mp) cc_final: 0.8745 (mp) REVERT: A 761 SER cc_start: 0.8825 (t) cc_final: 0.8283 (m) REVERT: A 810 LYS cc_start: 0.8267 (mmtt) cc_final: 0.8060 (mmtm) REVERT: A 836 PHE cc_start: 0.8089 (m-80) cc_final: 0.7719 (m-10) REVERT: A 841 GLU cc_start: 0.7392 (mt-10) cc_final: 0.6929 (mm-30) REVERT: A 861 MET cc_start: 0.8398 (mmp) cc_final: 0.7554 (mtm) REVERT: B 443 TYR cc_start: 0.8039 (m-80) cc_final: 0.7508 (m-80) REVERT: B 572 LEU cc_start: 0.9247 (mm) cc_final: 0.8457 (mm) REVERT: B 576 CYS cc_start: 0.8559 (m) cc_final: 0.8114 (m) REVERT: B 584 PHE cc_start: 0.8074 (t80) cc_final: 0.6995 (m-10) REVERT: B 590 TYR cc_start: 0.7314 (p90) cc_final: 0.6558 (p90) REVERT: B 609 LEU cc_start: 0.8763 (tt) cc_final: 0.7959 (mt) REVERT: B 612 PHE cc_start: 0.8380 (m-80) cc_final: 0.8049 (t80) REVERT: B 709 MET cc_start: 0.8944 (mtt) cc_final: 0.8620 (mtt) REVERT: B 800 ARG cc_start: 0.8575 (tpp80) cc_final: 0.7658 (tpt170) REVERT: B 861 MET cc_start: 0.8457 (ppp) cc_final: 0.7707 (ttt) REVERT: C 501 MET cc_start: 0.7746 (mtm) cc_final: 0.7470 (mtm) REVERT: C 565 MET cc_start: 0.8555 (mmm) cc_final: 0.8316 (mmt) REVERT: C 612 PHE cc_start: 0.8551 (m-10) cc_final: 0.8349 (m-80) REVERT: C 698 LYS cc_start: 0.9413 (mmtt) cc_final: 0.9008 (mmtm) REVERT: C 761 SER cc_start: 0.8820 (t) cc_final: 0.8313 (m) REVERT: C 841 GLU cc_start: 0.7677 (mt-10) cc_final: 0.6963 (mm-30) REVERT: D 572 LEU cc_start: 0.9248 (mm) cc_final: 0.8401 (mm) REVERT: D 576 CYS cc_start: 0.8486 (m) cc_final: 0.8054 (m) REVERT: D 590 TYR cc_start: 0.7742 (p90) cc_final: 0.7314 (p90) REVERT: D 609 LEU cc_start: 0.8684 (tt) cc_final: 0.7908 (mt) REVERT: D 612 PHE cc_start: 0.8296 (m-80) cc_final: 0.7863 (t80) REVERT: D 639 ILE cc_start: 0.8922 (tp) cc_final: 0.8642 (tp) REVERT: D 778 ILE cc_start: 0.9285 (mt) cc_final: 0.9059 (mm) REVERT: D 861 MET cc_start: 0.8352 (ppp) cc_final: 0.7639 (ttt) outliers start: 20 outliers final: 17 residues processed: 235 average time/residue: 0.2285 time to fit residues: 84.1308 Evaluate side-chains 223 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 206 time to evaluate : 1.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 458 ARG Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 571 CYS Chi-restraints excluded: chain A residue 867 MET Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 565 MET Chi-restraints excluded: chain B residue 823 ILE Chi-restraints excluded: chain B residue 831 LEU Chi-restraints excluded: chain C residue 458 ARG Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain D residue 444 VAL Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 565 MET Chi-restraints excluded: chain D residue 569 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 104 optimal weight: 0.0060 chunk 81 optimal weight: 9.9990 chunk 18 optimal weight: 5.9990 chunk 147 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 45 optimal weight: 0.7980 chunk 80 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 118 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 56 optimal weight: 0.2980 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 610 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.138044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.099528 restraints weight = 61415.624| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 4.95 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3399 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3399 r_free = 0.3399 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3399 r_free = 0.3399 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3399 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.4481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14446 Z= 0.179 Angle : 0.658 9.733 19546 Z= 0.332 Chirality : 0.042 0.191 2172 Planarity : 0.005 0.055 2474 Dihedral : 5.199 41.131 1936 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.69 % Favored : 89.20 % Rotamer: Outliers : 1.74 % Allowed : 16.45 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.21), residues: 1774 helix: 0.86 (0.18), residues: 904 sheet: -2.82 (0.47), residues: 86 loop : -2.29 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 589 HIS 0.008 0.001 HIS A 593 PHE 0.024 0.001 PHE B 658 TYR 0.012 0.001 TYR A 521 ARG 0.004 0.000 ARG C 583 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 215 time to evaluate : 1.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 534 MET cc_start: 0.8605 (ttm) cc_final: 0.8216 (ttp) REVERT: A 565 MET cc_start: 0.8486 (mmm) cc_final: 0.8275 (mmt) REVERT: A 702 TYR cc_start: 0.9148 (m-10) cc_final: 0.8750 (m-80) REVERT: A 761 SER cc_start: 0.8836 (t) cc_final: 0.8309 (m) REVERT: A 836 PHE cc_start: 0.8085 (m-80) cc_final: 0.7720 (m-10) REVERT: A 841 GLU cc_start: 0.7460 (mt-10) cc_final: 0.7117 (mm-30) REVERT: A 861 MET cc_start: 0.8422 (mmp) cc_final: 0.7588 (mtm) REVERT: B 443 TYR cc_start: 0.7997 (m-80) cc_final: 0.7447 (m-80) REVERT: B 572 LEU cc_start: 0.9236 (mm) cc_final: 0.8452 (mm) REVERT: B 576 CYS cc_start: 0.8592 (m) cc_final: 0.8125 (m) REVERT: B 584 PHE cc_start: 0.8223 (t80) cc_final: 0.7052 (m-10) REVERT: B 590 TYR cc_start: 0.7262 (p90) cc_final: 0.6484 (p90) REVERT: B 609 LEU cc_start: 0.8783 (tt) cc_final: 0.8003 (mt) REVERT: B 612 PHE cc_start: 0.8307 (m-80) cc_final: 0.8035 (t80) REVERT: B 709 MET cc_start: 0.8946 (mtt) cc_final: 0.8625 (mtt) REVERT: B 778 ILE cc_start: 0.9291 (mt) cc_final: 0.9045 (mm) REVERT: B 800 ARG cc_start: 0.8575 (tpp80) cc_final: 0.7651 (tpt170) REVERT: B 861 MET cc_start: 0.8447 (ppp) cc_final: 0.7715 (ttt) REVERT: C 501 MET cc_start: 0.7751 (mtm) cc_final: 0.7471 (mtm) REVERT: C 556 LEU cc_start: 0.9118 (mt) cc_final: 0.8906 (mp) REVERT: C 565 MET cc_start: 0.8553 (mmm) cc_final: 0.8321 (mmt) REVERT: C 612 PHE cc_start: 0.8538 (m-10) cc_final: 0.8314 (m-80) REVERT: C 698 LYS cc_start: 0.9384 (mmtt) cc_final: 0.9005 (mmtm) REVERT: C 705 MET cc_start: 0.8790 (mmt) cc_final: 0.8434 (mmm) REVERT: C 761 SER cc_start: 0.8814 (t) cc_final: 0.8297 (m) REVERT: C 841 GLU cc_start: 0.7607 (mt-10) cc_final: 0.7066 (mm-30) REVERT: D 572 LEU cc_start: 0.9242 (mm) cc_final: 0.8428 (mm) REVERT: D 576 CYS cc_start: 0.8523 (m) cc_final: 0.8098 (m) REVERT: D 590 TYR cc_start: 0.7890 (p90) cc_final: 0.7335 (p90) REVERT: D 612 PHE cc_start: 0.8303 (m-80) cc_final: 0.7850 (t80) REVERT: D 639 ILE cc_start: 0.8937 (tp) cc_final: 0.8647 (tp) REVERT: D 778 ILE cc_start: 0.9273 (mt) cc_final: 0.9055 (mm) REVERT: D 800 ARG cc_start: 0.8407 (tpp80) cc_final: 0.7752 (tpt170) REVERT: D 861 MET cc_start: 0.8283 (ppp) cc_final: 0.7607 (ttt) outliers start: 19 outliers final: 17 residues processed: 221 average time/residue: 0.2249 time to fit residues: 77.0490 Evaluate side-chains 223 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 206 time to evaluate : 1.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 458 ARG Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 867 MET Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 565 MET Chi-restraints excluded: chain B residue 823 ILE Chi-restraints excluded: chain B residue 831 LEU Chi-restraints excluded: chain C residue 458 ARG Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain D residue 444 VAL Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 565 MET Chi-restraints excluded: chain D residue 569 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 104 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 118 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 167 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 131 optimal weight: 0.3980 chunk 100 optimal weight: 0.9990 chunk 103 optimal weight: 0.6980 chunk 64 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 621 GLN B 622 GLN ** D 593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 622 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.138974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.100639 restraints weight = 66200.875| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 5.07 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3404 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3404 r_free = 0.3404 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3404 r_free = 0.3404 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3404 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.4597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14446 Z= 0.181 Angle : 0.656 9.863 19546 Z= 0.333 Chirality : 0.042 0.169 2172 Planarity : 0.005 0.070 2474 Dihedral : 5.186 41.151 1936 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.86 % Favored : 89.03 % Rotamer: Outliers : 1.74 % Allowed : 16.65 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.21), residues: 1774 helix: 0.94 (0.18), residues: 906 sheet: -2.53 (0.46), residues: 96 loop : -2.29 (0.23), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 589 HIS 0.008 0.001 HIS A 593 PHE 0.017 0.001 PHE D 584 TYR 0.019 0.001 TYR C 542 ARG 0.004 0.000 ARG C 583 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 214 time to evaluate : 1.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 488 TYR cc_start: 0.8170 (m-80) cc_final: 0.7771 (m-80) REVERT: A 534 MET cc_start: 0.8696 (ttm) cc_final: 0.8397 (ttp) REVERT: A 565 MET cc_start: 0.8502 (mmm) cc_final: 0.8272 (mmt) REVERT: A 761 SER cc_start: 0.8859 (t) cc_final: 0.8335 (m) REVERT: A 836 PHE cc_start: 0.8074 (m-80) cc_final: 0.7703 (m-10) REVERT: A 861 MET cc_start: 0.8425 (mmp) cc_final: 0.7577 (mtm) REVERT: B 441 GLU cc_start: 0.8768 (mt-10) cc_final: 0.8293 (tt0) REVERT: B 443 TYR cc_start: 0.8053 (m-80) cc_final: 0.7552 (m-80) REVERT: B 572 LEU cc_start: 0.9229 (mm) cc_final: 0.8447 (mm) REVERT: B 576 CYS cc_start: 0.8602 (m) cc_final: 0.8135 (m) REVERT: B 584 PHE cc_start: 0.8268 (t80) cc_final: 0.7114 (m-10) REVERT: B 590 TYR cc_start: 0.7309 (p90) cc_final: 0.6710 (p90) REVERT: B 609 LEU cc_start: 0.8776 (tt) cc_final: 0.8002 (mt) REVERT: B 612 PHE cc_start: 0.8355 (m-80) cc_final: 0.8048 (t80) REVERT: B 709 MET cc_start: 0.8914 (mtt) cc_final: 0.8572 (mtt) REVERT: B 778 ILE cc_start: 0.9277 (mt) cc_final: 0.9028 (mm) REVERT: B 800 ARG cc_start: 0.8548 (tpp80) cc_final: 0.7624 (tpt170) REVERT: B 861 MET cc_start: 0.8547 (ppp) cc_final: 0.7887 (ttt) REVERT: C 501 MET cc_start: 0.7780 (mtm) cc_final: 0.7501 (mtm) REVERT: C 556 LEU cc_start: 0.9120 (mt) cc_final: 0.8902 (mp) REVERT: C 565 MET cc_start: 0.8560 (mmm) cc_final: 0.8326 (mmt) REVERT: C 612 PHE cc_start: 0.8549 (m-10) cc_final: 0.8318 (m-80) REVERT: C 698 LYS cc_start: 0.9380 (mmtt) cc_final: 0.8864 (mmtm) REVERT: C 761 SER cc_start: 0.8802 (t) cc_final: 0.8284 (m) REVERT: C 841 GLU cc_start: 0.7647 (mt-10) cc_final: 0.7213 (mm-30) REVERT: D 564 TRP cc_start: 0.8767 (m100) cc_final: 0.8212 (m100) REVERT: D 572 LEU cc_start: 0.9239 (mm) cc_final: 0.8435 (mm) REVERT: D 576 CYS cc_start: 0.8548 (m) cc_final: 0.8127 (m) REVERT: D 590 TYR cc_start: 0.7870 (p90) cc_final: 0.7290 (p90) REVERT: D 612 PHE cc_start: 0.8298 (m-80) cc_final: 0.7838 (t80) REVERT: D 639 ILE cc_start: 0.8930 (tp) cc_final: 0.8650 (tp) REVERT: D 778 ILE cc_start: 0.9258 (mt) cc_final: 0.9041 (mm) REVERT: D 800 ARG cc_start: 0.8419 (tpp80) cc_final: 0.7994 (tpt90) REVERT: D 810 LYS cc_start: 0.6440 (tmtt) cc_final: 0.6237 (tmtt) REVERT: D 861 MET cc_start: 0.8326 (ppp) cc_final: 0.7689 (ttt) outliers start: 19 outliers final: 17 residues processed: 220 average time/residue: 0.2287 time to fit residues: 78.5701 Evaluate side-chains 230 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 213 time to evaluate : 1.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 458 ARG Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 867 MET Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 565 MET Chi-restraints excluded: chain B residue 810 LYS Chi-restraints excluded: chain B residue 823 ILE Chi-restraints excluded: chain B residue 831 LEU Chi-restraints excluded: chain C residue 458 ARG Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain D residue 444 VAL Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 569 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 64 optimal weight: 0.5980 chunk 92 optimal weight: 0.9980 chunk 171 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 12 optimal weight: 0.0020 chunk 25 optimal weight: 6.9990 chunk 57 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 130 optimal weight: 0.2980 chunk 3 optimal weight: 2.9990 chunk 117 optimal weight: 0.7980 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.139799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.101304 restraints weight = 70314.528| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 5.16 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3408 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3408 r_free = 0.3408 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3408 r_free = 0.3408 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3408 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.4721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14446 Z= 0.174 Angle : 0.656 9.604 19546 Z= 0.333 Chirality : 0.042 0.211 2172 Planarity : 0.005 0.056 2474 Dihedral : 5.152 41.697 1936 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.41 % Favored : 89.48 % Rotamer: Outliers : 1.61 % Allowed : 16.97 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.21), residues: 1774 helix: 1.00 (0.18), residues: 908 sheet: -2.51 (0.45), residues: 96 loop : -2.23 (0.23), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.002 TRP A 589 HIS 0.007 0.001 HIS A 593 PHE 0.017 0.001 PHE D 584 TYR 0.017 0.001 TYR C 542 ARG 0.004 0.000 ARG C 583 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 224 time to evaluate : 1.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 488 TYR cc_start: 0.8062 (m-80) cc_final: 0.7689 (m-80) REVERT: A 534 MET cc_start: 0.8690 (ttm) cc_final: 0.8401 (ttp) REVERT: A 565 MET cc_start: 0.8531 (mmm) cc_final: 0.8292 (mmt) REVERT: A 702 TYR cc_start: 0.9113 (m-10) cc_final: 0.8712 (m-80) REVERT: A 723 GLU cc_start: 0.7864 (mp0) cc_final: 0.7204 (mp0) REVERT: A 761 SER cc_start: 0.8843 (t) cc_final: 0.8321 (m) REVERT: A 836 PHE cc_start: 0.8064 (m-80) cc_final: 0.7703 (m-10) REVERT: A 861 MET cc_start: 0.8431 (mmp) cc_final: 0.7572 (mtm) REVERT: B 441 GLU cc_start: 0.8762 (mt-10) cc_final: 0.8286 (tt0) REVERT: B 443 TYR cc_start: 0.8008 (m-80) cc_final: 0.7493 (m-80) REVERT: B 572 LEU cc_start: 0.9256 (mm) cc_final: 0.8498 (mm) REVERT: B 576 CYS cc_start: 0.8624 (m) cc_final: 0.8163 (m) REVERT: B 584 PHE cc_start: 0.8211 (t80) cc_final: 0.7067 (m-10) REVERT: B 590 TYR cc_start: 0.7529 (p90) cc_final: 0.6951 (p90) REVERT: B 609 LEU cc_start: 0.8736 (tt) cc_final: 0.8003 (mt) REVERT: B 612 PHE cc_start: 0.8346 (m-80) cc_final: 0.8043 (t80) REVERT: B 709 MET cc_start: 0.8934 (mtt) cc_final: 0.8609 (mtt) REVERT: B 778 ILE cc_start: 0.9266 (mt) cc_final: 0.9032 (mm) REVERT: B 800 ARG cc_start: 0.8523 (tpp80) cc_final: 0.7605 (tpt170) REVERT: B 861 MET cc_start: 0.8534 (ppp) cc_final: 0.7893 (ttt) REVERT: C 501 MET cc_start: 0.7827 (mtm) cc_final: 0.7533 (mtm) REVERT: C 565 MET cc_start: 0.8597 (mmm) cc_final: 0.8353 (mmt) REVERT: C 612 PHE cc_start: 0.8545 (m-10) cc_final: 0.8313 (m-80) REVERT: C 698 LYS cc_start: 0.9334 (mmtt) cc_final: 0.8914 (mmtt) REVERT: C 761 SER cc_start: 0.8831 (t) cc_final: 0.8318 (m) REVERT: C 841 GLU cc_start: 0.7652 (mt-10) cc_final: 0.7313 (mm-30) REVERT: D 564 TRP cc_start: 0.8773 (m100) cc_final: 0.8234 (m100) REVERT: D 572 LEU cc_start: 0.9248 (mm) cc_final: 0.8442 (mm) REVERT: D 576 CYS cc_start: 0.8531 (m) cc_final: 0.8113 (m) REVERT: D 589 TRP cc_start: 0.8122 (m100) cc_final: 0.7586 (m100) REVERT: D 590 TYR cc_start: 0.7860 (p90) cc_final: 0.7298 (p90) REVERT: D 612 PHE cc_start: 0.8289 (m-80) cc_final: 0.7827 (t80) REVERT: D 639 ILE cc_start: 0.8931 (tp) cc_final: 0.8647 (tp) REVERT: D 800 ARG cc_start: 0.8380 (tpp80) cc_final: 0.7964 (tpt90) REVERT: D 810 LYS cc_start: 0.6448 (tmtt) cc_final: 0.6233 (tmtt) REVERT: D 861 MET cc_start: 0.8311 (ppp) cc_final: 0.7687 (ttt) outliers start: 17 outliers final: 17 residues processed: 230 average time/residue: 0.2610 time to fit residues: 93.1564 Evaluate side-chains 226 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 209 time to evaluate : 1.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 458 ARG Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 867 MET Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 565 MET Chi-restraints excluded: chain B residue 810 LYS Chi-restraints excluded: chain B residue 823 ILE Chi-restraints excluded: chain B residue 831 LEU Chi-restraints excluded: chain C residue 458 ARG Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain D residue 444 VAL Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 565 MET Chi-restraints excluded: chain D residue 569 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 158 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 64 optimal weight: 0.7980 chunk 5 optimal weight: 4.9990 chunk 139 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 59 optimal weight: 0.2980 chunk 27 optimal weight: 1.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 610 ASN ** D 593 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 = 0.3907 r_free = 0.3907 target = 0.135082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.096057 restraints weight = 56537.600| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 4.99 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3341 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3341 r_free = 0.3341 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3341 r_free = 0.3341 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3341 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.4674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 14446 Z= 0.308 Angle : 0.714 9.328 19546 Z= 0.362 Chirality : 0.045 0.196 2172 Planarity : 0.005 0.074 2474 Dihedral : 5.291 38.770 1936 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.17 % Allowed : 11.09 % Favored : 88.74 % Rotamer: Outliers : 1.87 % Allowed : 16.52 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.21), residues: 1774 helix: 0.86 (0.18), residues: 902 sheet: -2.35 (0.47), residues: 94 loop : -2.25 (0.22), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.003 TRP A 589 HIS 0.008 0.001 HIS A 593 PHE 0.017 0.002 PHE C 533 TYR 0.015 0.002 TYR C 542 ARG 0.012 0.001 ARG C 800 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5884.03 seconds wall clock time: 106 minutes 12.65 seconds (6372.65 seconds total)