Starting phenix.real_space_refine on Fri May 16 06:44:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b35_44128/05_2025/9b35_44128.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b35_44128/05_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_44128/05_2025/9b35_44128.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b35_44128/05_2025/9b35_44128.map" model { file = "/net/cci-nas-00/data/ceres_data/9b35_44128/05_2025/9b35_44128.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b35_44128/05_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 13.75, per 1000 atoms: 0.97 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=4, 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 Simple disulfide: pdb=" SG CYS C 750 " - pdb=" SG CYS C 804 " distance=2.03 Simple disulfide: pdb=" SG CYS D 750 " - pdb=" SG CYS D 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: 2.96 Conformation dependent library (CDL) restraints added in 3.2 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: 1.41 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: 3.80 Time building geometry restraints manager: 3.58 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 - 17.40: 8218 17.40 - 34.80: 352 34.80 - 52.19: 64 52.19 - 69.59: 8 69.59 - 86.99: 8 Dihedral angle restraints: 8650 sinusoidal: 3490 harmonic: 5160 Sorted by residual: dihedral pdb=" CB CYS D 750 " pdb=" SG CYS D 750 " pdb=" SG CYS D 804 " pdb=" CB CYS D 804 " ideal model delta sinusoidal sigma weight residual 93.00 179.99 -86.99 1 1.00e+01 1.00e-02 9.10e+01 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 ... (remaining 8647 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: 2.24 - 2.77: 3164 2.77 - 3.31: 13151 3.31 - 3.84: 23053 3.84 - 4.37: 27548 4.37 - 4.90: 46563 Nonbonded interactions: 113479 Sorted by model distance: 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 nonbonded pdb=" O LYS B 629 " pdb=" OG1 THR B 633 " model vdw 2.280 3.040 nonbonded pdb=" OE1 GLU A 841 " pdb=" OG SER D 585 " model vdw 2.296 3.040 ... (remaining 113474 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: 0.05 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: 1.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 38.180 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.050 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.930 ------------------------------------------------------------------------------- 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 14450 Z= 0.357 Angle : 1.245 11.648 19554 Z= 0.728 Chirality : 0.060 0.345 2172 Planarity : 0.008 0.059 2474 Dihedral : 10.750 71.111 5330 Min Nonbonded Distance : 2.244 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 Details of bonding type rmsd hydrogen bonds : bond 0.28344 ( 580) hydrogen bonds : angle 10.36580 ( 1706) SS BOND : bond 0.00096 ( 4) SS BOND : angle 1.19260 ( 8) covalent geometry : bond 0.00784 (14446) covalent geometry : angle 1.24465 (19546) *********************** 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 : 1.688 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: 0.2611 time to fit residues: 143.3021 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 : 1.541 ------------------------------------------------------------------------------- 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 = 0.3974 r_free = 0.3974 target = 0.142499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.103603 restraints weight = 88890.954| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 5.87 r_work (final): 0.3399 ------------------------------------------------------------------------------- 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: 0.8033 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 14450 Z= 0.167 Angle : 0.759 8.431 19554 Z= 0.392 Chirality : 0.044 0.162 2172 Planarity : 0.006 0.053 2474 Dihedral : 6.352 45.673 1936 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.40 % Allowed : 11.54 % Favored : 88.07 % Rotamer: Outliers : 2.06 % Allowed : 10.97 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -3.52 (0.17), residues: 1774 helix: -1.66 (0.14), residues: 876 sheet: -2.92 (0.46), residues: 120 loop : -2.99 (0.20), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 798 HIS 0.016 0.003 HIS C 593 PHE 0.025 0.002 PHE D 735 TYR 0.017 0.002 TYR D 566 ARG 0.007 0.001 ARG C 583 Details of bonding type rmsd hydrogen bonds : bond 0.03840 ( 580) hydrogen bonds : angle 4.82383 ( 1706) SS BOND : bond 0.00094 ( 4) SS BOND : angle 0.66200 ( 8) covalent geometry : bond 0.00372 (14446) covalent geometry : angle 0.75925 (19546) *********************** 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 288 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 264 time to evaluate : 1.567 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: 0.8183 (m-80) cc_final: 0.7783 (m-80) REVERT: A 534 MET cc_start: 0.8953 (ttm) cc_final: 0.8674 (ttp) REVERT: A 565 MET cc_start: 0.8522 (mmm) cc_final: 0.8243 (mmt) REVERT: A 635 ILE cc_start: 0.8890 (OUTLIER) cc_final: 0.8678 (mp) REVERT: A 761 SER cc_start: 0.8763 (t) cc_final: 0.8235 (m) REVERT: A 800 ARG cc_start: 0.7555 (ptp90) cc_final: 0.7346 (mtm110) REVERT: A 836 PHE cc_start: 0.7917 (m-80) cc_final: 0.7674 (m-10) REVERT: A 841 GLU cc_start: 0.7503 (mt-10) cc_final: 0.7138 (mt-10) REVERT: A 861 MET cc_start: 0.8439 (mmp) cc_final: 0.7827 (mtm) REVERT: A 866 ARG cc_start: 0.6829 (OUTLIER) cc_final: 0.6049 (tmm160) REVERT: B 465 ASP cc_start: 0.8828 (m-30) cc_final: 0.8565 (m-30) REVERT: B 469 GLU cc_start: 0.8553 (mm-30) cc_final: 0.8057 (mm-30) REVERT: B 535 THR cc_start: 0.9162 (OUTLIER) cc_final: 0.8935 (p) REVERT: B 563 ILE cc_start: 0.9107 (mm) cc_final: 0.8896 (mt) REVERT: B 572 LEU cc_start: 0.9248 (mm) cc_final: 0.8440 (mm) REVERT: B 576 CYS cc_start: 0.8512 (m) cc_final: 0.8101 (m) REVERT: B 584 PHE cc_start: 0.7843 (t80) cc_final: 0.6844 (m-10) REVERT: B 590 TYR cc_start: 0.7702 (p90) cc_final: 0.7239 (p90) REVERT: B 609 LEU cc_start: 0.8884 (tt) cc_final: 0.8308 (mt) REVERT: B 612 PHE cc_start: 0.8460 (m-80) cc_final: 0.8127 (t80) REVERT: B 626 LEU cc_start: 0.8455 (mt) cc_final: 0.8074 (mt) REVERT: B 639 ILE cc_start: 0.8981 (tp) cc_final: 0.8776 (pt) REVERT: B 655 LEU cc_start: 0.8829 (tp) cc_final: 0.8592 (tp) REVERT: B 709 MET cc_start: 0.8969 (mtt) cc_final: 0.8617 (mtt) REVERT: B 800 ARG cc_start: 0.8397 (tpp80) cc_final: 0.8005 (mmm160) REVERT: C 534 MET cc_start: 0.8345 (ttm) cc_final: 0.8137 (ttp) REVERT: C 565 MET cc_start: 0.8570 (mmm) cc_final: 0.8263 (mmt) REVERT: C 635 ILE cc_start: 0.8826 (OUTLIER) cc_final: 0.8597 (mp) REVERT: C 667 PRO cc_start: 0.8989 (Cg_exo) cc_final: 0.8560 (Cg_endo) REVERT: C 761 SER cc_start: 0.8742 (t) cc_final: 0.8309 (m) REVERT: C 805 PRO cc_start: 0.8204 (Cg_exo) cc_final: 0.7928 (Cg_endo) REVERT: C 841 GLU cc_start: 0.7783 (mt-10) cc_final: 0.7342 (mt-10) REVERT: C 867 MET cc_start: 0.5914 (mmp) cc_final: 0.5437 (mmp) REVERT: D 469 GLU cc_start: 0.8425 (mm-30) cc_final: 0.8203 (mm-30) REVERT: D 556 LEU cc_start: 0.9044 (mm) cc_final: 0.8739 (mp) REVERT: D 572 LEU cc_start: 0.9200 (mm) cc_final: 0.8396 (mm) REVERT: D 576 CYS cc_start: 0.8382 (m) cc_final: 0.7994 (m) REVERT: D 590 TYR cc_start: 0.7679 (p90) cc_final: 0.7232 (p90) REVERT: D 639 ILE cc_start: 0.8993 (tp) cc_final: 0.8746 (tp) REVERT: D 792 HIS cc_start: 0.8745 (t70) cc_final: 0.8472 (t-170) REVERT: D 800 ARG cc_start: 0.8462 (tpp80) cc_final: 0.7976 (mmm160) outliers start: 24 outliers final: 10 residues processed: 282 average time/residue: 0.2326 time to fit residues: 98.6656 Evaluate side-chains 223 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 209 time to evaluate : 1.600 ------------------------------------------------------------------------------- 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 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 535 THR 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 635 ILE Chi-restraints excluded: chain D residue 444 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 31 optimal weight: 0.8980 chunk 155 optimal weight: 6.9990 chunk 28 optimal weight: 0.8980 chunk 156 optimal weight: 0.6980 chunk 92 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 173 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 168 optimal weight: 4.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 508 HIS C 508 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.137663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.099042 restraints weight = 68998.620| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 5.50 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3379 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3379 r_free = 0.3379 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 = 0.3379 r_free = 0.3379 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3379 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.3264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14450 Z= 0.164 Angle : 0.715 9.643 19554 Z= 0.365 Chirality : 0.044 0.164 2172 Planarity : 0.006 0.064 2474 Dihedral : 5.901 41.367 1936 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.28 % Allowed : 11.60 % Favored : 88.12 % Rotamer: Outliers : 2.71 % Allowed : 12.58 % Favored : 84.71 % 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: -2.43 (0.19), residues: 1774 helix: -0.58 (0.16), residues: 880 sheet: -2.60 (0.44), residues: 126 loop : -2.68 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 589 HIS 0.014 0.002 HIS C 593 PHE 0.023 0.002 PHE B 476 TYR 0.020 0.002 TYR C 651 ARG 0.006 0.001 ARG C 583 Details of bonding type rmsd hydrogen bonds : bond 0.03575 ( 580) hydrogen bonds : angle 4.44253 ( 1706) SS BOND : bond 0.00022 ( 4) SS BOND : angle 0.45230 ( 8) covalent geometry : bond 0.00384 (14446) covalent geometry : angle 0.71459 (19546) *********************** 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 260 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 226 time to evaluate : 1.438 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: 0.8187 (m-80) cc_final: 0.7718 (m-80) REVERT: A 534 MET cc_start: 0.9015 (ttm) cc_final: 0.8735 (ttp) REVERT: A 565 MET cc_start: 0.8540 (mmm) cc_final: 0.8241 (mmt) REVERT: A 651 TYR cc_start: 0.8851 (t80) cc_final: 0.8650 (t80) REVERT: A 761 SER cc_start: 0.8900 (t) cc_final: 0.8340 (m) REVERT: A 836 PHE cc_start: 0.8175 (m-80) cc_final: 0.7738 (m-10) REVERT: A 841 GLU cc_start: 0.7609 (mt-10) cc_final: 0.7374 (mt-10) REVERT: A 861 MET cc_start: 0.8330 (mmp) cc_final: 0.7698 (mtm) REVERT: B 465 ASP cc_start: 0.8828 (m-30) cc_final: 0.8588 (m-30) REVERT: B 563 ILE cc_start: 0.9105 (mm) cc_final: 0.8896 (mt) REVERT: B 572 LEU cc_start: 0.9193 (mm) cc_final: 0.8372 (mm) REVERT: B 576 CYS cc_start: 0.8559 (m) cc_final: 0.7835 (m) REVERT: B 580 VAL cc_start: 0.9367 (t) cc_final: 0.8932 (m) REVERT: B 584 PHE cc_start: 0.7934 (t80) cc_final: 0.6934 (m-10) REVERT: B 590 TYR cc_start: 0.7439 (p90) cc_final: 0.6822 (p90) REVERT: B 612 PHE cc_start: 0.8472 (m-80) cc_final: 0.8121 (t80) REVERT: B 639 ILE cc_start: 0.9019 (tp) cc_final: 0.8698 (tp) REVERT: B 709 MET cc_start: 0.9016 (mtt) cc_final: 0.8687 (mtt) REVERT: C 501 MET cc_start: 0.7872 (mtm) cc_final: 0.7662 (mtm) REVERT: C 534 MET cc_start: 0.8553 (ttm) cc_final: 0.8177 (ttp) REVERT: C 565 MET cc_start: 0.8595 (mmm) cc_final: 0.8362 (mmm) REVERT: C 589 TRP cc_start: 0.8223 (m100) cc_final: 0.7847 (m100) REVERT: C 635 ILE cc_start: 0.8720 (OUTLIER) cc_final: 0.8503 (mp) REVERT: C 698 LYS cc_start: 0.9362 (mmtt) cc_final: 0.8902 (mmtt) REVERT: C 761 SER cc_start: 0.8834 (t) cc_final: 0.8347 (m) REVERT: C 805 PRO cc_start: 0.8261 (Cg_exo) cc_final: 0.7966 (Cg_endo) REVERT: C 841 GLU cc_start: 0.7795 (mt-10) cc_final: 0.7502 (mt-10) REVERT: D 556 LEU cc_start: 0.9108 (mm) cc_final: 0.8847 (mp) REVERT: D 572 LEU cc_start: 0.9176 (mm) cc_final: 0.8377 (mm) REVERT: D 576 CYS cc_start: 0.8553 (m) cc_final: 0.8045 (m) REVERT: D 590 TYR cc_start: 0.7432 (p90) cc_final: 0.6664 (p90) REVERT: D 612 PHE cc_start: 0.8451 (m-80) cc_final: 0.8000 (t80) REVERT: D 625 GLU cc_start: 0.8366 (pt0) cc_final: 0.8139 (pt0) REVERT: D 627 MET cc_start: 0.8116 (tpp) cc_final: 0.7095 (tpp) REVERT: D 639 ILE cc_start: 0.9026 (tp) cc_final: 0.8729 (tp) REVERT: D 792 HIS cc_start: 0.8769 (t70) cc_final: 0.8505 (t-170) outliers start: 34 outliers final: 19 residues processed: 245 average time/residue: 0.2183 time to fit residues: 82.0006 Evaluate side-chains 232 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 212 time to evaluate : 1.566 ------------------------------------------------------------------------------- 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 831 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 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 608 LEU 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: 5.9990 chunk 104 optimal weight: 0.0980 chunk 148 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 chunk 64 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 152 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 chunk 174 optimal weight: 6.9990 chunk 160 optimal weight: 0.9990 chunk 86 optimal weight: 7.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3957 r_free = 0.3957 target = 0.139236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.101499 restraints weight = 79112.691| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 5.21 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3420 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3420 r_free = 0.3420 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3420 r_free = 0.3420 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3420 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.3654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14450 Z= 0.134 Angle : 0.677 8.999 19554 Z= 0.345 Chirality : 0.043 0.163 2172 Planarity : 0.005 0.065 2474 Dihedral : 5.585 41.645 1936 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.28 % Allowed : 10.63 % Favored : 89.08 % Rotamer: Outliers : 2.32 % Allowed : 12.77 % Favored : 84.90 % 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 (0.20), residues: 1774 helix: 0.10 (0.17), residues: 872 sheet: -2.58 (0.41), residues: 136 loop : -2.54 (0.22), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 589 HIS 0.012 0.002 HIS A 593 PHE 0.029 0.001 PHE D 584 TYR 0.011 0.001 TYR A 542 ARG 0.007 0.001 ARG A 800 Details of bonding type rmsd hydrogen bonds : bond 0.03173 ( 580) hydrogen bonds : angle 4.18232 ( 1706) SS BOND : bond 0.00198 ( 4) SS BOND : angle 0.34512 ( 8) covalent geometry : bond 0.00303 (14446) covalent geometry : angle 0.67705 (19546) *********************** 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 263 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 235 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: 0.8897 (ttm) cc_final: 0.8606 (ttp) REVERT: A 565 MET cc_start: 0.8463 (mmm) cc_final: 0.8195 (mmt) REVERT: A 651 TYR cc_start: 0.8702 (t80) cc_final: 0.8448 (t80) REVERT: A 761 SER cc_start: 0.8845 (t) cc_final: 0.8345 (m) REVERT: A 836 PHE cc_start: 0.8026 (m-80) cc_final: 0.7689 (m-10) REVERT: A 841 GLU cc_start: 0.7669 (mt-10) cc_final: 0.7022 (mm-30) REVERT: A 861 MET cc_start: 0.8432 (mmp) cc_final: 0.7718 (mtm) REVERT: A 866 ARG cc_start: 0.7326 (OUTLIER) cc_final: 0.6270 (tmm-80) REVERT: B 443 TYR cc_start: 0.8139 (m-80) cc_final: 0.7649 (m-80) REVERT: B 572 LEU cc_start: 0.9166 (mm) cc_final: 0.8358 (mm) REVERT: B 576 CYS cc_start: 0.8470 (m) cc_final: 0.7837 (m) REVERT: B 580 VAL cc_start: 0.9345 (t) cc_final: 0.8927 (m) REVERT: B 584 PHE cc_start: 0.7870 (t80) cc_final: 0.6888 (m-10) REVERT: B 590 TYR cc_start: 0.7416 (p90) cc_final: 0.6854 (p90) REVERT: B 609 LEU cc_start: 0.8761 (tt) cc_final: 0.8059 (mt) REVERT: B 612 PHE cc_start: 0.8342 (m-80) cc_final: 0.8105 (t80) REVERT: B 639 ILE cc_start: 0.8951 (tp) cc_final: 0.8671 (tp) REVERT: B 709 MET cc_start: 0.8968 (mtt) cc_final: 0.8644 (mtt) REVERT: B 800 ARG cc_start: 0.8516 (tpp80) cc_final: 0.8173 (ttp80) REVERT: C 501 MET cc_start: 0.7755 (mtm) cc_final: 0.7492 (mtm) REVERT: C 534 MET cc_start: 0.8910 (ttm) cc_final: 0.8584 (ttp) REVERT: C 565 MET cc_start: 0.8482 (mmm) cc_final: 0.8225 (mmt) REVERT: C 589 TRP cc_start: 0.8152 (m100) cc_final: 0.7860 (m100) REVERT: C 761 SER cc_start: 0.8793 (t) cc_final: 0.8333 (m) REVERT: C 805 PRO cc_start: 0.8367 (Cg_exo) cc_final: 0.8157 (Cg_endo) REVERT: C 810 LYS cc_start: 0.8228 (mmtt) cc_final: 0.7716 (mmpt) REVERT: C 841 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7050 (mm-30) REVERT: D 556 LEU cc_start: 0.9121 (mm) cc_final: 0.8833 (mp) REVERT: D 572 LEU cc_start: 0.9169 (mm) cc_final: 0.8331 (mm) REVERT: D 576 CYS cc_start: 0.8390 (m) cc_final: 0.7968 (m) REVERT: D 590 TYR cc_start: 0.7721 (p90) cc_final: 0.7375 (p90) REVERT: D 612 PHE cc_start: 0.8362 (m-80) cc_final: 0.7899 (t80) REVERT: D 625 GLU cc_start: 0.8128 (pt0) cc_final: 0.7808 (pt0) REVERT: D 639 ILE cc_start: 0.9022 (tp) cc_final: 0.8783 (tp) REVERT: D 861 MET cc_start: 0.8402 (ppp) cc_final: 0.7529 (ttt) outliers start: 28 outliers final: 15 residues processed: 251 average time/residue: 0.2303 time to fit residues: 87.2627 Evaluate side-chains 224 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 208 time to evaluate : 1.572 ------------------------------------------------------------------------------- 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 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 626 LEU 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 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 626 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 32 optimal weight: 0.9990 chunk 75 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 162 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 115 optimal weight: 8.9990 chunk 121 optimal weight: 3.9990 chunk 158 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 173 optimal weight: 3.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 = 0.3949 r_free = 0.3949 target = 0.138409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.098211 restraints weight = 77775.211| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 5.61 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3374 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3374 r_free = 0.3374 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 = 0.3374 r_free = 0.3374 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3374 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.3932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14450 Z= 0.143 Angle : 0.674 10.196 19554 Z= 0.341 Chirality : 0.043 0.148 2172 Planarity : 0.005 0.067 2474 Dihedral : 5.446 40.999 1936 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.28 % Allowed : 11.03 % Favored : 88.69 % Rotamer: Outliers : 2.32 % Allowed : 13.61 % Favored : 84.06 % 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: -1.47 (0.20), residues: 1774 helix: 0.43 (0.17), residues: 874 sheet: -2.69 (0.45), residues: 108 loop : -2.39 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 589 HIS 0.010 0.001 HIS C 593 PHE 0.022 0.002 PHE D 476 TYR 0.011 0.001 TYR A 542 ARG 0.006 0.001 ARG D 855 Details of bonding type rmsd hydrogen bonds : bond 0.03137 ( 580) hydrogen bonds : angle 4.02783 ( 1706) SS BOND : bond 0.00062 ( 4) SS BOND : angle 0.29095 ( 8) covalent geometry : bond 0.00332 (14446) covalent geometry : angle 0.67397 (19546) *********************** 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 251 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 223 time to evaluate : 1.496 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: 0.8850 (ttm) cc_final: 0.8581 (ttp) REVERT: A 565 MET cc_start: 0.8561 (mmm) cc_final: 0.8271 (mmt) REVERT: A 651 TYR cc_start: 0.8820 (t80) cc_final: 0.8489 (t80) REVERT: A 761 SER cc_start: 0.8875 (t) cc_final: 0.8354 (m) REVERT: A 810 LYS cc_start: 0.8275 (mmtt) cc_final: 0.7888 (mmtm) REVERT: A 836 PHE cc_start: 0.8067 (m-80) cc_final: 0.7729 (m-10) REVERT: A 841 GLU cc_start: 0.7721 (mt-10) cc_final: 0.7080 (mm-30) REVERT: A 861 MET cc_start: 0.8391 (mmp) cc_final: 0.7648 (mtm) REVERT: B 443 TYR cc_start: 0.8124 (m-80) cc_final: 0.7641 (m-80) REVERT: B 572 LEU cc_start: 0.9124 (mm) cc_final: 0.8320 (mm) REVERT: B 576 CYS cc_start: 0.8547 (m) cc_final: 0.7876 (m) REVERT: B 580 VAL cc_start: 0.9332 (t) cc_final: 0.8906 (m) REVERT: B 584 PHE cc_start: 0.7908 (t80) cc_final: 0.6835 (m-10) REVERT: B 590 TYR cc_start: 0.7322 (p90) cc_final: 0.6722 (p90) REVERT: B 612 PHE cc_start: 0.8407 (m-80) cc_final: 0.8083 (t80) REVERT: B 639 ILE cc_start: 0.9019 (tp) cc_final: 0.8714 (tp) REVERT: B 709 MET cc_start: 0.8954 (mtt) cc_final: 0.8612 (mtt) REVERT: B 800 ARG cc_start: 0.8611 (tpp80) cc_final: 0.8038 (tpt90) REVERT: B 861 MET cc_start: 0.8438 (ppp) cc_final: 0.7657 (ttt) REVERT: C 501 MET cc_start: 0.7883 (mtm) cc_final: 0.7646 (mtm) REVERT: C 534 MET cc_start: 0.8965 (ttm) cc_final: 0.8650 (ttp) REVERT: C 565 MET cc_start: 0.8577 (mmm) cc_final: 0.8290 (mmt) REVERT: C 589 TRP cc_start: 0.8212 (m100) cc_final: 0.7890 (m100) REVERT: C 612 PHE cc_start: 0.8442 (m-10) cc_final: 0.8181 (m-80) REVERT: C 651 TYR cc_start: 0.8907 (t80) cc_final: 0.8637 (t80) REVERT: C 668 ILE cc_start: 0.8772 (mm) cc_final: 0.8501 (pt) REVERT: C 698 LYS cc_start: 0.9361 (mmtt) cc_final: 0.8919 (mmtt) REVERT: C 761 SER cc_start: 0.8831 (t) cc_final: 0.8348 (m) REVERT: C 805 PRO cc_start: 0.8363 (Cg_exo) cc_final: 0.8098 (Cg_endo) REVERT: C 810 LYS cc_start: 0.8139 (mmtt) cc_final: 0.7639 (mmpt) REVERT: C 836 PHE cc_start: 0.8091 (m-80) cc_final: 0.7754 (m-10) REVERT: C 841 GLU cc_start: 0.7895 (mt-10) cc_final: 0.7068 (mm-30) REVERT: D 572 LEU cc_start: 0.9141 (mm) cc_final: 0.8338 (mm) REVERT: D 576 CYS cc_start: 0.8539 (m) cc_final: 0.8073 (m) REVERT: D 612 PHE cc_start: 0.8389 (m-80) cc_final: 0.7913 (t80) REVERT: D 625 GLU cc_start: 0.8119 (pt0) cc_final: 0.7825 (pt0) REVERT: D 639 ILE cc_start: 0.9072 (tp) cc_final: 0.8796 (tp) REVERT: D 800 ARG cc_start: 0.8483 (tpp80) cc_final: 0.7739 (tpt170) REVERT: D 861 MET cc_start: 0.8508 (ppp) cc_final: 0.7721 (ttt) outliers start: 28 outliers final: 17 residues processed: 238 average time/residue: 0.2299 time to fit residues: 83.0014 Evaluate side-chains 220 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 203 time to evaluate : 1.746 ------------------------------------------------------------------------------- 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 831 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 157 optimal weight: 6.9990 chunk 119 optimal weight: 0.8980 chunk 160 optimal weight: 6.9990 chunk 66 optimal weight: 0.9990 chunk 37 optimal weight: 10.0000 chunk 106 optimal weight: 0.9990 chunk 104 optimal weight: 0.0070 chunk 125 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 85 optimal weight: 7.9990 chunk 79 optimal weight: 0.7980 overall best weight: 0.7402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 604 ASN D 591 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.139761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.101766 restraints weight = 72413.488| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 5.23 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3406 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3406 r_free = 0.3406 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3406 r_free = 0.3406 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3406 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.4161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14450 Z= 0.132 Angle : 0.658 10.315 19554 Z= 0.332 Chirality : 0.042 0.140 2172 Planarity : 0.005 0.070 2474 Dihedral : 5.330 40.760 1936 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.35 % Favored : 89.48 % Rotamer: Outliers : 2.13 % Allowed : 13.74 % Favored : 84.13 % 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: -1.22 (0.20), residues: 1774 helix: 0.69 (0.18), residues: 878 sheet: -2.51 (0.48), residues: 98 loop : -2.38 (0.22), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 706 HIS 0.009 0.001 HIS A 593 PHE 0.027 0.001 PHE B 476 TYR 0.011 0.001 TYR A 542 ARG 0.004 0.001 ARG D 855 Details of bonding type rmsd hydrogen bonds : bond 0.02979 ( 580) hydrogen bonds : angle 3.97655 ( 1706) SS BOND : bond 0.00051 ( 4) SS BOND : angle 0.30752 ( 8) covalent geometry : bond 0.00305 (14446) covalent geometry : angle 0.65831 (19546) *********************** 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 242 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 217 time to evaluate : 1.727 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: 0.8889 (ttm) cc_final: 0.8607 (ttp) REVERT: A 565 MET cc_start: 0.8476 (mmm) cc_final: 0.8224 (mmt) REVERT: A 651 TYR cc_start: 0.8818 (t80) cc_final: 0.8450 (t80) REVERT: A 755 ILE cc_start: 0.8956 (mp) cc_final: 0.8730 (mp) REVERT: A 761 SER cc_start: 0.8848 (t) cc_final: 0.8343 (m) REVERT: A 810 LYS cc_start: 0.8230 (mmtt) cc_final: 0.7805 (mmtm) REVERT: A 836 PHE cc_start: 0.7998 (m-80) cc_final: 0.7659 (m-10) REVERT: A 841 GLU cc_start: 0.7652 (mt-10) cc_final: 0.7095 (mm-30) REVERT: A 861 MET cc_start: 0.8378 (mmp) cc_final: 0.7553 (mtm) REVERT: B 443 TYR cc_start: 0.8090 (m-80) cc_final: 0.7559 (m-80) REVERT: B 572 LEU cc_start: 0.9239 (mm) cc_final: 0.8453 (mm) REVERT: B 576 CYS cc_start: 0.8549 (m) cc_final: 0.8090 (m) REVERT: B 584 PHE cc_start: 0.7950 (t80) cc_final: 0.6930 (m-10) REVERT: B 590 TYR cc_start: 0.7188 (p90) cc_final: 0.6425 (p90) REVERT: B 609 LEU cc_start: 0.8914 (tt) cc_final: 0.8143 (mt) REVERT: B 612 PHE cc_start: 0.8333 (m-80) cc_final: 0.8119 (t80) REVERT: B 639 ILE cc_start: 0.9018 (tp) cc_final: 0.8732 (tp) REVERT: B 709 MET cc_start: 0.8934 (mtt) cc_final: 0.8594 (mtt) REVERT: B 800 ARG cc_start: 0.8558 (tpp80) cc_final: 0.8045 (tpt90) REVERT: B 861 MET cc_start: 0.8377 (ppp) cc_final: 0.7626 (ttt) REVERT: C 501 MET cc_start: 0.7743 (mtm) cc_final: 0.7492 (mtm) REVERT: C 534 MET cc_start: 0.8581 (ttm) cc_final: 0.8190 (ttp) REVERT: C 565 MET cc_start: 0.8533 (mmm) cc_final: 0.8258 (mmt) REVERT: C 589 TRP cc_start: 0.8207 (m100) cc_final: 0.7912 (m100) REVERT: C 612 PHE cc_start: 0.8428 (m-10) cc_final: 0.8155 (m-80) REVERT: C 698 LYS cc_start: 0.9392 (mmtt) cc_final: 0.8999 (mmtm) REVERT: C 761 SER cc_start: 0.8765 (t) cc_final: 0.8296 (m) REVERT: C 805 PRO cc_start: 0.8329 (Cg_exo) cc_final: 0.8062 (Cg_endo) REVERT: C 810 LYS cc_start: 0.8118 (mmtt) cc_final: 0.7628 (mmpt) REVERT: C 836 PHE cc_start: 0.8000 (m-80) cc_final: 0.7680 (m-10) REVERT: C 841 GLU cc_start: 0.7834 (mt-10) cc_final: 0.7077 (mm-30) REVERT: D 572 LEU cc_start: 0.9228 (mm) cc_final: 0.8386 (mm) REVERT: D 576 CYS cc_start: 0.8519 (m) cc_final: 0.8062 (m) REVERT: D 609 LEU cc_start: 0.8839 (tt) cc_final: 0.8118 (mt) REVERT: D 612 PHE cc_start: 0.8323 (m-80) cc_final: 0.7877 (t80) REVERT: D 625 GLU cc_start: 0.8035 (pt0) cc_final: 0.7817 (pt0) REVERT: D 639 ILE cc_start: 0.9048 (tp) cc_final: 0.8794 (tp) REVERT: D 800 ARG cc_start: 0.8453 (tpp80) cc_final: 0.8005 (tpt90) REVERT: D 861 MET cc_start: 0.8426 (ppp) cc_final: 0.7675 (ttt) outliers start: 25 outliers final: 18 residues processed: 227 average time/residue: 0.2437 time to fit residues: 86.7703 Evaluate side-chains 228 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 210 time to evaluate : 1.744 ------------------------------------------------------------------------------- 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 831 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 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 626 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 124 optimal weight: 0.0070 chunk 173 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 108 optimal weight: 0.0670 chunk 113 optimal weight: 4.9990 chunk 12 optimal weight: 0.6980 chunk 161 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 112 optimal weight: 4.9990 overall best weight: 0.4936 ------------------------------------------------------------------------------- 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 = 0.3949 r_free = 0.3949 target = 0.138128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.099692 restraints weight = 60647.891| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 4.89 r_work (final): 0.3394 ------------------------------------------------------------------------------- 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 = 0.06 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: 0.7968 moved from start: 0.4313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14450 Z= 0.119 Angle : 0.644 9.900 19554 Z= 0.326 Chirality : 0.042 0.368 2172 Planarity : 0.005 0.070 2474 Dihedral : 5.195 41.984 1936 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.75 % Favored : 89.14 % Rotamer: Outliers : 1.74 % Allowed : 14.58 % Favored : 83.68 % 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: -1.04 (0.21), residues: 1774 helix: 0.80 (0.18), residues: 890 sheet: -2.47 (0.48), residues: 98 loop : -2.28 (0.23), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 706 HIS 0.008 0.001 HIS C 593 PHE 0.028 0.001 PHE B 476 TYR 0.010 0.001 TYR C 702 ARG 0.004 0.000 ARG C 583 Details of bonding type rmsd hydrogen bonds : bond 0.02878 ( 580) hydrogen bonds : angle 3.92050 ( 1706) SS BOND : bond 0.00060 ( 4) SS BOND : angle 0.27884 ( 8) covalent geometry : bond 0.00268 (14446) covalent geometry : angle 0.64412 (19546) *********************** 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: 19 poor density : 229 time to evaluate : 1.579 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: 0.8504 (ttm) cc_final: 0.8139 (ttp) REVERT: A 565 MET cc_start: 0.8463 (mmm) cc_final: 0.8235 (mmt) REVERT: A 755 ILE cc_start: 0.8963 (mp) cc_final: 0.8727 (mp) REVERT: A 761 SER cc_start: 0.8818 (t) cc_final: 0.8303 (m) REVERT: A 836 PHE cc_start: 0.8080 (m-80) cc_final: 0.7725 (m-10) REVERT: A 841 GLU cc_start: 0.7383 (mt-10) cc_final: 0.6945 (mm-30) REVERT: A 861 MET cc_start: 0.8361 (mmp) cc_final: 0.7482 (mtm) REVERT: B 443 TYR cc_start: 0.7997 (m-80) cc_final: 0.7437 (m-80) REVERT: B 572 LEU cc_start: 0.9259 (mm) cc_final: 0.8447 (mm) REVERT: B 576 CYS cc_start: 0.8512 (m) cc_final: 0.7877 (m) REVERT: B 580 VAL cc_start: 0.9310 (t) cc_final: 0.8849 (m) REVERT: B 584 PHE cc_start: 0.8163 (t80) cc_final: 0.7038 (m-10) REVERT: B 590 TYR cc_start: 0.7206 (p90) cc_final: 0.6361 (p90) REVERT: B 609 LEU cc_start: 0.8724 (tt) cc_final: 0.7951 (mt) REVERT: B 612 PHE cc_start: 0.8349 (m-80) cc_final: 0.8139 (t80) REVERT: B 709 MET cc_start: 0.8985 (mtt) cc_final: 0.8638 (mtt) REVERT: B 800 ARG cc_start: 0.8523 (tpp80) cc_final: 0.8000 (tpt90) REVERT: B 861 MET cc_start: 0.8376 (ppp) cc_final: 0.7740 (ttt) REVERT: C 501 MET cc_start: 0.7694 (mtm) cc_final: 0.7409 (mtm) REVERT: C 534 MET cc_start: 0.8635 (ttm) cc_final: 0.8255 (ttp) REVERT: C 565 MET cc_start: 0.8564 (mmm) cc_final: 0.8331 (mmt) REVERT: C 698 LYS cc_start: 0.9343 (mmtt) cc_final: 0.8869 (mmtt) REVERT: C 755 ILE cc_start: 0.8714 (pt) cc_final: 0.8464 (mt) REVERT: C 761 SER cc_start: 0.8758 (t) cc_final: 0.8274 (m) REVERT: C 805 PRO cc_start: 0.8417 (Cg_exo) cc_final: 0.8182 (Cg_endo) REVERT: C 810 LYS cc_start: 0.8033 (mmtt) cc_final: 0.7567 (mmpt) REVERT: C 836 PHE cc_start: 0.8023 (m-80) cc_final: 0.7700 (m-10) REVERT: C 841 GLU cc_start: 0.7577 (mt-10) cc_final: 0.7023 (mm-30) REVERT: D 572 LEU cc_start: 0.9244 (mm) cc_final: 0.8412 (mm) REVERT: D 576 CYS cc_start: 0.8486 (m) cc_final: 0.8028 (m) REVERT: D 609 LEU cc_start: 0.8918 (tt) cc_final: 0.8273 (mt) REVERT: D 612 PHE cc_start: 0.8323 (m-80) cc_final: 0.7873 (t80) REVERT: D 639 ILE cc_start: 0.9004 (tp) cc_final: 0.8731 (tp) REVERT: D 800 ARG cc_start: 0.8432 (tpp80) cc_final: 0.8051 (tpt90) REVERT: D 861 MET cc_start: 0.8305 (ppp) cc_final: 0.7574 (ttt) outliers start: 19 outliers final: 17 residues processed: 235 average time/residue: 0.2255 time to fit residues: 81.8577 Evaluate side-chains 222 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 205 time to evaluate : 1.694 ------------------------------------------------------------------------------- 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 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 626 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 104 optimal weight: 8.9990 chunk 81 optimal weight: 9.9990 chunk 18 optimal weight: 2.9990 chunk 147 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 28 optimal weight: 0.0970 chunk 118 optimal weight: 0.7980 chunk 34 optimal weight: 0.1980 chunk 56 optimal weight: 0.0570 overall best weight: 0.6298 ------------------------------------------------------------------------------- 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 = 0.3947 r_free = 0.3947 target = 0.138051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.099484 restraints weight = 61409.554| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 5.06 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3393 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3393 r_free = 0.3393 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3393 r_free = 0.3393 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3393 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.4449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14450 Z= 0.127 Angle : 0.664 9.645 19554 Z= 0.334 Chirality : 0.043 0.295 2172 Planarity : 0.005 0.055 2474 Dihedral : 5.175 41.990 1936 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.69 % Favored : 89.20 % Rotamer: Outliers : 1.61 % Allowed : 15.10 % 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: -0.98 (0.21), residues: 1774 helix: 0.87 (0.18), residues: 890 sheet: -2.61 (0.44), residues: 108 loop : -2.24 (0.23), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP C 589 HIS 0.007 0.001 HIS A 593 PHE 0.028 0.001 PHE B 476 TYR 0.020 0.001 TYR A 702 ARG 0.004 0.000 ARG A 583 Details of bonding type rmsd hydrogen bonds : bond 0.02905 ( 580) hydrogen bonds : angle 3.92962 ( 1706) SS BOND : bond 0.00050 ( 4) SS BOND : angle 0.48183 ( 8) covalent geometry : bond 0.00293 (14446) covalent geometry : angle 0.66438 (19546) *********************** 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 231 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 214 time to evaluate : 1.740 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: 0.8646 (ttm) cc_final: 0.8263 (ttp) REVERT: A 565 MET cc_start: 0.8474 (mmm) cc_final: 0.8248 (mmt) REVERT: A 761 SER cc_start: 0.8780 (t) cc_final: 0.8323 (m) REVERT: A 836 PHE cc_start: 0.8132 (m-80) cc_final: 0.7754 (m-10) REVERT: A 841 GLU cc_start: 0.7395 (mt-10) cc_final: 0.6963 (mm-30) REVERT: A 861 MET cc_start: 0.8346 (mmp) cc_final: 0.7467 (mtm) REVERT: B 443 TYR cc_start: 0.8004 (m-80) cc_final: 0.7442 (m-80) REVERT: B 572 LEU cc_start: 0.9248 (mm) cc_final: 0.8436 (mm) REVERT: B 576 CYS cc_start: 0.8527 (m) cc_final: 0.8069 (m) REVERT: B 584 PHE cc_start: 0.8211 (t80) cc_final: 0.7065 (m-10) REVERT: B 590 TYR cc_start: 0.7135 (p90) cc_final: 0.6300 (p90) REVERT: B 609 LEU cc_start: 0.8714 (tt) cc_final: 0.7947 (mt) REVERT: B 612 PHE cc_start: 0.8354 (m-80) cc_final: 0.8051 (t80) REVERT: B 709 MET cc_start: 0.8979 (mtt) cc_final: 0.8649 (mtt) REVERT: B 778 ILE cc_start: 0.9275 (mt) cc_final: 0.9028 (mm) REVERT: B 800 ARG cc_start: 0.8511 (tpp80) cc_final: 0.7972 (tpt90) REVERT: B 861 MET cc_start: 0.8446 (ppp) cc_final: 0.7822 (ttt) REVERT: C 501 MET cc_start: 0.7690 (mtm) cc_final: 0.7413 (mtm) REVERT: C 534 MET cc_start: 0.8650 (ttm) cc_final: 0.8243 (ttp) REVERT: C 565 MET cc_start: 0.8567 (mmm) cc_final: 0.8327 (mmt) REVERT: C 651 TYR cc_start: 0.8910 (t80) cc_final: 0.8671 (t80) REVERT: C 698 LYS cc_start: 0.9348 (mmtt) cc_final: 0.8865 (mmtt) REVERT: C 755 ILE cc_start: 0.8722 (pt) cc_final: 0.8485 (mt) REVERT: C 761 SER cc_start: 0.8767 (t) cc_final: 0.8268 (m) REVERT: C 805 PRO cc_start: 0.8364 (Cg_exo) cc_final: 0.8129 (Cg_endo) REVERT: C 810 LYS cc_start: 0.8101 (mmtt) cc_final: 0.7627 (mmpt) REVERT: C 836 PHE cc_start: 0.8035 (m-80) cc_final: 0.7694 (m-10) REVERT: C 841 GLU cc_start: 0.7613 (mt-10) cc_final: 0.7070 (mm-30) REVERT: D 440 GLU cc_start: 0.8199 (tp30) cc_final: 0.7816 (tp30) REVERT: D 441 GLU cc_start: 0.8676 (mt-10) cc_final: 0.7995 (tt0) REVERT: D 572 LEU cc_start: 0.9229 (mm) cc_final: 0.8406 (mm) REVERT: D 576 CYS cc_start: 0.8588 (m) cc_final: 0.8124 (m) REVERT: D 612 PHE cc_start: 0.8340 (m-80) cc_final: 0.7860 (t80) REVERT: D 639 ILE cc_start: 0.9006 (tp) cc_final: 0.8737 (tp) REVERT: D 664 MET cc_start: 0.8671 (mtm) cc_final: 0.8456 (ptp) REVERT: D 778 ILE cc_start: 0.9296 (mt) cc_final: 0.9069 (mm) REVERT: D 800 ARG cc_start: 0.8439 (tpp80) cc_final: 0.8012 (tpt90) REVERT: D 861 MET cc_start: 0.8295 (ppp) cc_final: 0.7622 (ttt) outliers start: 17 outliers final: 17 residues processed: 220 average time/residue: 0.2185 time to fit residues: 74.7964 Evaluate side-chains 218 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 201 time to evaluate : 1.592 ------------------------------------------------------------------------------- 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 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 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 626 LEU Chi-restraints excluded: chain D residue 823 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 104 optimal weight: 0.7980 chunk 18 optimal weight: 4.9990 chunk 21 optimal weight: 0.5980 chunk 118 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 chunk 167 optimal weight: 0.9980 chunk 30 optimal weight: 4.9990 chunk 131 optimal weight: 9.9990 chunk 100 optimal weight: 0.0050 chunk 103 optimal weight: 0.7980 chunk 64 optimal weight: 0.9980 overall best weight: 0.6394 ------------------------------------------------------------------------------- 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 = 0.3949 r_free = 0.3949 target = 0.138228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.099789 restraints weight = 66135.784| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 5.18 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3395 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3395 r_free = 0.3395 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3395 r_free = 0.3395 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3395 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.4577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14450 Z= 0.126 Angle : 0.666 10.388 19554 Z= 0.335 Chirality : 0.043 0.274 2172 Planarity : 0.005 0.072 2474 Dihedral : 5.133 42.388 1936 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.58 % Favored : 89.31 % Rotamer: Outliers : 1.68 % Allowed : 15.42 % Favored : 82.90 % 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: -0.88 (0.21), residues: 1774 helix: 0.93 (0.18), residues: 894 sheet: -2.58 (0.45), residues: 108 loop : -2.17 (0.23), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP A 589 HIS 0.007 0.001 HIS A 593 PHE 0.017 0.001 PHE D 584 TYR 0.016 0.001 TYR A 702 ARG 0.004 0.000 ARG C 583 Details of bonding type rmsd hydrogen bonds : bond 0.02922 ( 580) hydrogen bonds : angle 3.91602 ( 1706) SS BOND : bond 0.00049 ( 4) SS BOND : angle 0.52213 ( 8) covalent geometry : bond 0.00291 (14446) covalent geometry : angle 0.66633 (19546) *********************** 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 227 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 209 time to evaluate : 1.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 565 MET cc_start: 0.8482 (mmm) cc_final: 0.8247 (mmt) REVERT: A 761 SER cc_start: 0.8821 (t) cc_final: 0.8381 (m) REVERT: A 836 PHE cc_start: 0.8127 (m-80) cc_final: 0.7749 (m-10) REVERT: A 841 GLU cc_start: 0.7440 (mt-10) cc_final: 0.7124 (mm-30) REVERT: A 861 MET cc_start: 0.8389 (mmp) cc_final: 0.7515 (mtm) REVERT: B 443 TYR cc_start: 0.8060 (m-80) cc_final: 0.7519 (m-80) REVERT: B 572 LEU cc_start: 0.9251 (mm) cc_final: 0.8454 (mm) REVERT: B 576 CYS cc_start: 0.8557 (m) cc_final: 0.8097 (m) REVERT: B 584 PHE cc_start: 0.8231 (t80) cc_final: 0.7086 (m-10) REVERT: B 590 TYR cc_start: 0.7383 (p90) cc_final: 0.6780 (p90) REVERT: B 609 LEU cc_start: 0.8799 (tt) cc_final: 0.7995 (mt) REVERT: B 612 PHE cc_start: 0.8344 (m-80) cc_final: 0.8039 (t80) REVERT: B 709 MET cc_start: 0.8951 (mtt) cc_final: 0.8620 (mtt) REVERT: B 778 ILE cc_start: 0.9234 (mt) cc_final: 0.9021 (mm) REVERT: B 800 ARG cc_start: 0.8493 (tpp80) cc_final: 0.7928 (tpt90) REVERT: B 861 MET cc_start: 0.8540 (ppp) cc_final: 0.7828 (ttt) REVERT: B 863 GLU cc_start: 0.7444 (mm-30) cc_final: 0.7122 (mt-10) REVERT: C 501 MET cc_start: 0.7682 (mtm) cc_final: 0.7404 (mtm) REVERT: C 534 MET cc_start: 0.8642 (ttm) cc_final: 0.8268 (ttp) REVERT: C 565 MET cc_start: 0.8576 (mmm) cc_final: 0.8334 (mmt) REVERT: C 698 LYS cc_start: 0.9353 (mmtt) cc_final: 0.8870 (mmtt) REVERT: C 755 ILE cc_start: 0.8717 (pt) cc_final: 0.8439 (mt) REVERT: C 761 SER cc_start: 0.8758 (t) cc_final: 0.8264 (m) REVERT: C 805 PRO cc_start: 0.8340 (Cg_exo) cc_final: 0.8100 (Cg_endo) REVERT: C 836 PHE cc_start: 0.8060 (m-80) cc_final: 0.7723 (m-10) REVERT: C 841 GLU cc_start: 0.7661 (mt-10) cc_final: 0.7291 (mm-30) REVERT: D 440 GLU cc_start: 0.8199 (tp30) cc_final: 0.7947 (tp30) REVERT: D 441 GLU cc_start: 0.8796 (mt-10) cc_final: 0.8141 (tt0) REVERT: D 564 TRP cc_start: 0.8758 (m100) cc_final: 0.8204 (m100) REVERT: D 572 LEU cc_start: 0.9234 (mm) cc_final: 0.8397 (mm) REVERT: D 576 CYS cc_start: 0.8575 (m) cc_final: 0.8132 (m) REVERT: D 612 PHE cc_start: 0.8321 (m-80) cc_final: 0.7855 (t80) REVERT: D 639 ILE cc_start: 0.9039 (tp) cc_final: 0.8782 (tp) REVERT: D 664 MET cc_start: 0.8663 (mtm) cc_final: 0.8458 (ptp) REVERT: D 778 ILE cc_start: 0.9264 (mt) cc_final: 0.9026 (mm) REVERT: D 800 ARG cc_start: 0.8457 (tpp80) cc_final: 0.8044 (tpt90) REVERT: D 861 MET cc_start: 0.8273 (ppp) cc_final: 0.7633 (ttt) outliers start: 18 outliers final: 18 residues processed: 215 average time/residue: 0.2100 time to fit residues: 70.3417 Evaluate side-chains 223 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 205 time to evaluate : 1.667 ------------------------------------------------------------------------------- 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 556 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 626 LEU Chi-restraints excluded: chain D residue 823 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 64 optimal weight: 0.6980 chunk 92 optimal weight: 0.8980 chunk 171 optimal weight: 0.7980 chunk 102 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 25 optimal weight: 6.9990 chunk 57 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 130 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 117 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3950 r_free = 0.3950 target = 0.138422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.099588 restraints weight = 70255.913| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 5.32 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3371 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3371 r_free = 0.3371 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3371 r_free = 0.3371 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3371 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.4645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14450 Z= 0.137 Angle : 0.673 10.188 19554 Z= 0.337 Chirality : 0.043 0.244 2172 Planarity : 0.005 0.055 2474 Dihedral : 5.158 42.445 1936 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.63 % Favored : 89.25 % Rotamer: Outliers : 1.74 % Allowed : 15.68 % 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: -0.82 (0.21), residues: 1774 helix: 1.00 (0.18), residues: 890 sheet: -2.56 (0.45), residues: 108 loop : -2.16 (0.23), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP A 589 HIS 0.007 0.001 HIS C 593 PHE 0.016 0.001 PHE A 533 TYR 0.016 0.001 TYR A 521 ARG 0.004 0.000 ARG C 583 Details of bonding type rmsd hydrogen bonds : bond 0.02974 ( 580) hydrogen bonds : angle 3.91966 ( 1706) SS BOND : bond 0.00039 ( 4) SS BOND : angle 0.48509 ( 8) covalent geometry : bond 0.00319 (14446) covalent geometry : angle 0.67321 (19546) ********************** 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 231 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 212 time to evaluate : 1.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 488 TYR cc_start: 0.8249 (m-80) cc_final: 0.7790 (m-80) REVERT: A 534 MET cc_start: 0.8583 (ttm) cc_final: 0.8296 (ttp) REVERT: A 565 MET cc_start: 0.8515 (mmm) cc_final: 0.8286 (mmt) REVERT: A 761 SER cc_start: 0.8844 (t) cc_final: 0.8406 (m) REVERT: A 836 PHE cc_start: 0.8121 (m-80) cc_final: 0.7740 (m-10) REVERT: A 841 GLU cc_start: 0.7506 (mt-10) cc_final: 0.7171 (mm-30) REVERT: A 861 MET cc_start: 0.8391 (mmp) cc_final: 0.7514 (mtm) REVERT: B 441 GLU cc_start: 0.8806 (mt-10) cc_final: 0.8320 (tt0) REVERT: B 443 TYR cc_start: 0.8082 (m-80) cc_final: 0.7575 (m-80) REVERT: B 572 LEU cc_start: 0.9246 (mm) cc_final: 0.8483 (mm) REVERT: B 576 CYS cc_start: 0.8547 (m) cc_final: 0.8105 (m) REVERT: B 584 PHE cc_start: 0.8272 (t80) cc_final: 0.7079 (m-10) REVERT: B 590 TYR cc_start: 0.7377 (p90) cc_final: 0.6783 (p90) REVERT: B 609 LEU cc_start: 0.8714 (tt) cc_final: 0.7953 (mt) REVERT: B 612 PHE cc_start: 0.8311 (m-80) cc_final: 0.8047 (t80) REVERT: B 709 MET cc_start: 0.8974 (mtt) cc_final: 0.8641 (mtt) REVERT: B 778 ILE cc_start: 0.9228 (mt) cc_final: 0.9024 (mm) REVERT: B 800 ARG cc_start: 0.8497 (tpp80) cc_final: 0.7906 (tpt90) REVERT: B 861 MET cc_start: 0.8531 (ppp) cc_final: 0.7845 (ttt) REVERT: B 863 GLU cc_start: 0.7486 (mm-30) cc_final: 0.6945 (tp30) REVERT: C 501 MET cc_start: 0.7732 (mtm) cc_final: 0.7457 (mtm) REVERT: C 534 MET cc_start: 0.8600 (ttm) cc_final: 0.8221 (ttp) REVERT: C 565 MET cc_start: 0.8558 (mmm) cc_final: 0.8324 (mmt) REVERT: C 698 LYS cc_start: 0.9354 (mmtt) cc_final: 0.8871 (mmtt) REVERT: C 761 SER cc_start: 0.8777 (t) cc_final: 0.8275 (m) REVERT: C 805 PRO cc_start: 0.8305 (Cg_exo) cc_final: 0.8061 (Cg_endo) REVERT: C 836 PHE cc_start: 0.8025 (m-80) cc_final: 0.7709 (m-10) REVERT: C 841 GLU cc_start: 0.7668 (mt-10) cc_final: 0.7307 (mm-30) REVERT: D 440 GLU cc_start: 0.8163 (tp30) cc_final: 0.7929 (tp30) REVERT: D 441 GLU cc_start: 0.8779 (mt-10) cc_final: 0.8127 (tt0) REVERT: D 564 TRP cc_start: 0.8784 (m100) cc_final: 0.8255 (m100) REVERT: D 572 LEU cc_start: 0.9239 (mm) cc_final: 0.8407 (mm) REVERT: D 576 CYS cc_start: 0.8579 (m) cc_final: 0.8152 (m) REVERT: D 612 PHE cc_start: 0.8324 (m-80) cc_final: 0.7860 (t80) REVERT: D 639 ILE cc_start: 0.9052 (tp) cc_final: 0.8790 (tp) REVERT: D 778 ILE cc_start: 0.9261 (mt) cc_final: 0.9049 (mm) REVERT: D 800 ARG cc_start: 0.8401 (tpp80) cc_final: 0.7975 (tpt90) REVERT: D 861 MET cc_start: 0.8349 (ppp) cc_final: 0.7739 (ttt) outliers start: 19 outliers final: 19 residues processed: 218 average time/residue: 0.2161 time to fit residues: 73.2192 Evaluate side-chains 223 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 204 time to evaluate : 1.498 ------------------------------------------------------------------------------- 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 556 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 626 LEU Chi-restraints excluded: chain D residue 810 LYS Chi-restraints excluded: chain D residue 823 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 158 optimal weight: 0.6980 chunk 112 optimal weight: 3.9990 chunk 38 optimal weight: 0.0010 chunk 21 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 64 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 139 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 overall best weight: 0.6586 ------------------------------------------------------------------------------- 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 = 0.3946 r_free = 0.3946 target = 0.138065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.099239 restraints weight = 56605.399| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 5.08 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3382 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3382 r_free = 0.3382 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3382 r_free = 0.3382 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3382 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.4743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14450 Z= 0.127 Angle : 0.668 10.442 19554 Z= 0.334 Chirality : 0.042 0.250 2172 Planarity : 0.005 0.071 2474 Dihedral : 5.105 43.454 1936 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.01 % Favored : 89.88 % Rotamer: Outliers : 1.74 % Allowed : 15.74 % Favored : 82.52 % 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: -0.75 (0.21), residues: 1774 helix: 1.05 (0.18), residues: 890 sheet: -2.47 (0.45), residues: 106 loop : -2.12 (0.23), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP A 589 HIS 0.006 0.001 HIS C 593 PHE 0.016 0.001 PHE D 584 TYR 0.015 0.001 TYR A 521 ARG 0.006 0.000 ARG C 800 Details of bonding type rmsd hydrogen bonds : bond 0.02971 ( 580) hydrogen bonds : angle 3.88452 ( 1706) SS BOND : bond 0.00041 ( 4) SS BOND : angle 0.45759 ( 8) covalent geometry : bond 0.00292 (14446) covalent geometry : angle 0.66835 (19546) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5993.53 seconds wall clock time: 105 minutes 2.87 seconds (6302.87 seconds total)