Starting phenix.real_space_refine on Thu Jun 12 17:12:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b35_44128/06_2025/9b35_44128.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b35_44128/06_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_44128/06_2025/9b35_44128.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b35_44128/06_2025/9b35_44128.map" model { file = "/net/cci-nas-00/data/ceres_data/9b35_44128/06_2025/9b35_44128.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b35_44128/06_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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 15.21, per 1000 atoms: 1.08 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: 3.17 Conformation dependent library (CDL) restraints added in 3.6 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: 1.50 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: 4.00 Time building geometry restraints manager: 3.83 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: 0.07 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'A' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.38 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.630 Check model and map are aligned: 0.100 Set scattering table: 0.150 Process input model: 42.650 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.080 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.040 ------------------------------------------------------------------------------- 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 : 1.731 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: 0.2805 time to fit residues: 154.0862 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 : 1.856 ------------------------------------------------------------------------------- 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 = 0.3975 r_free = 0.3975 target = 0.142312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.103383 restraints weight = 88730.593| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 5.94 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3398 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3398 r_free = 0.3398 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3398 r_free = 0.3398 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3398 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2771 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= 0.166 Angle : 0.760 8.499 19554 Z= 0.393 Chirality : 0.044 0.162 2172 Planarity : 0.006 0.053 2474 Dihedral : 6.362 45.689 1936 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.40 % Allowed : 11.71 % Favored : 87.90 % 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: -3.53 (0.17), residues: 1774 helix: -1.67 (0.14), residues: 876 sheet: -2.93 (0.45), 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 B 476 TYR 0.017 0.002 TYR D 566 ARG 0.007 0.001 ARG C 583 Details of bonding type rmsd hydrogen bonds : bond 0.03838 ( 580) hydrogen bonds : angle 4.82816 ( 1706) SS BOND : bond 0.00094 ( 4) SS BOND : angle 0.66392 ( 8) covalent geometry : bond 0.00373 (14446) covalent geometry : angle 0.75999 (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 287 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 263 time to evaluate : 1.765 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: 0.8186 (m-80) cc_final: 0.7779 (m-80) REVERT: A 534 MET cc_start: 0.8962 (ttm) cc_final: 0.8681 (ttp) REVERT: A 565 MET cc_start: 0.8525 (mmm) cc_final: 0.8245 (mmt) REVERT: A 635 ILE cc_start: 0.8885 (OUTLIER) cc_final: 0.8674 (mp) REVERT: A 761 SER cc_start: 0.8768 (t) cc_final: 0.8239 (m) REVERT: A 800 ARG cc_start: 0.7575 (ptp90) cc_final: 0.7359 (mtm110) REVERT: A 836 PHE cc_start: 0.7922 (m-80) cc_final: 0.7676 (m-10) REVERT: A 841 GLU cc_start: 0.7515 (mt-10) cc_final: 0.7219 (mt-10) REVERT: A 861 MET cc_start: 0.8435 (mmp) cc_final: 0.7829 (mtm) REVERT: A 866 ARG cc_start: 0.6822 (OUTLIER) cc_final: 0.6040 (tmm160) REVERT: B 465 ASP cc_start: 0.8840 (m-30) cc_final: 0.8571 (m-30) REVERT: B 469 GLU cc_start: 0.8560 (mm-30) cc_final: 0.8061 (mm-30) REVERT: B 535 THR cc_start: 0.9177 (OUTLIER) cc_final: 0.8946 (p) REVERT: B 563 ILE cc_start: 0.9102 (mm) cc_final: 0.8887 (mt) REVERT: B 572 LEU cc_start: 0.9249 (mm) cc_final: 0.8440 (mm) REVERT: B 576 CYS cc_start: 0.8529 (m) cc_final: 0.8111 (m) REVERT: B 584 PHE cc_start: 0.7859 (t80) cc_final: 0.6860 (m-10) REVERT: B 590 TYR cc_start: 0.7697 (p90) cc_final: 0.7235 (p90) REVERT: B 609 LEU cc_start: 0.8881 (tt) cc_final: 0.8303 (mt) REVERT: B 612 PHE cc_start: 0.8468 (m-80) cc_final: 0.8124 (t80) REVERT: B 626 LEU cc_start: 0.8442 (mt) cc_final: 0.8064 (mt) REVERT: B 639 ILE cc_start: 0.8989 (tp) cc_final: 0.8777 (pt) REVERT: B 655 LEU cc_start: 0.8843 (tp) cc_final: 0.8601 (tp) REVERT: B 709 MET cc_start: 0.8967 (mtt) cc_final: 0.8615 (mtt) REVERT: B 800 ARG cc_start: 0.8394 (tpp80) cc_final: 0.7661 (mmm160) REVERT: C 534 MET cc_start: 0.8317 (ttm) cc_final: 0.8110 (ttp) REVERT: C 565 MET cc_start: 0.8581 (mmm) cc_final: 0.8269 (mmt) REVERT: C 635 ILE cc_start: 0.8823 (OUTLIER) cc_final: 0.8595 (mp) REVERT: C 667 PRO cc_start: 0.8995 (Cg_exo) cc_final: 0.8555 (Cg_endo) REVERT: C 761 SER cc_start: 0.8751 (t) cc_final: 0.8315 (m) REVERT: C 805 PRO cc_start: 0.8194 (Cg_exo) cc_final: 0.7915 (Cg_endo) REVERT: C 841 GLU cc_start: 0.7786 (mt-10) cc_final: 0.7342 (mt-10) REVERT: C 867 MET cc_start: 0.5919 (mmp) cc_final: 0.5444 (mmp) REVERT: D 469 GLU cc_start: 0.8432 (mm-30) cc_final: 0.8209 (mm-30) REVERT: D 556 LEU cc_start: 0.9050 (mm) cc_final: 0.8761 (mp) REVERT: D 572 LEU cc_start: 0.9225 (mm) cc_final: 0.8445 (mm) REVERT: D 576 CYS cc_start: 0.8391 (m) cc_final: 0.8000 (m) REVERT: D 590 TYR cc_start: 0.7671 (p90) cc_final: 0.7225 (p90) REVERT: D 639 ILE cc_start: 0.8996 (tp) cc_final: 0.8747 (tp) REVERT: D 792 HIS cc_start: 0.8752 (t70) cc_final: 0.8475 (t-170) REVERT: D 800 ARG cc_start: 0.8463 (tpp80) cc_final: 0.7978 (mmm160) outliers start: 24 outliers final: 10 residues processed: 281 average time/residue: 0.2407 time to fit residues: 102.3214 Evaluate side-chains 222 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 208 time to evaluate : 1.778 ------------------------------------------------------------------------------- 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: 2.9990 chunk 156 optimal weight: 0.5980 chunk 92 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 173 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 168 optimal weight: 4.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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 = 0.3920 r_free = 0.3920 target = 0.135924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.098107 restraints weight = 69001.096| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 5.02 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3366 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3366 r_free = 0.3366 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3366 r_free = 0.3366 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3366 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.3272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 14450 Z= 0.201 Angle : 0.743 9.733 19554 Z= 0.380 Chirality : 0.045 0.164 2172 Planarity : 0.006 0.053 2474 Dihedral : 5.964 38.993 1936 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.28 % Allowed : 12.05 % Favored : 87.67 % Rotamer: Outliers : 2.97 % Allowed : 12.26 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.19), residues: 1774 helix: -0.61 (0.16), residues: 880 sheet: -2.59 (0.44), residues: 126 loop : -2.68 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 589 HIS 0.015 0.002 HIS C 593 PHE 0.024 0.002 PHE B 476 TYR 0.017 0.002 TYR D 566 ARG 0.007 0.001 ARG C 583 Details of bonding type rmsd hydrogen bonds : bond 0.03703 ( 580) hydrogen bonds : angle 4.49699 ( 1706) SS BOND : bond 0.00038 ( 4) SS BOND : angle 0.53649 ( 8) covalent geometry : bond 0.00472 (14446) covalent geometry : angle 0.74305 (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: 38 poor density : 222 time to evaluate : 1.602 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: 0.8837 (ttm) cc_final: 0.8595 (ttp) REVERT: A 565 MET cc_start: 0.8475 (mmm) cc_final: 0.8197 (mmt) REVERT: A 635 ILE cc_start: 0.8812 (OUTLIER) cc_final: 0.8572 (mp) REVERT: A 651 TYR cc_start: 0.8905 (t80) cc_final: 0.8674 (t80) REVERT: A 836 PHE cc_start: 0.8017 (m-80) cc_final: 0.7658 (m-10) REVERT: A 841 GLU cc_start: 0.7488 (mt-10) cc_final: 0.7205 (mt-10) REVERT: A 861 MET cc_start: 0.8376 (mmp) cc_final: 0.7702 (mtm) REVERT: B 465 ASP cc_start: 0.8772 (m-30) cc_final: 0.8528 (m-30) REVERT: B 469 GLU cc_start: 0.8656 (mm-30) cc_final: 0.8226 (mm-30) REVERT: B 572 LEU cc_start: 0.9215 (mm) cc_final: 0.8408 (mm) REVERT: B 576 CYS cc_start: 0.8517 (m) cc_final: 0.8029 (m) REVERT: B 584 PHE cc_start: 0.7917 (t80) cc_final: 0.7098 (m-10) REVERT: B 590 TYR cc_start: 0.7583 (p90) cc_final: 0.6969 (p90) REVERT: B 612 PHE cc_start: 0.8411 (m-80) cc_final: 0.8072 (t80) REVERT: B 639 ILE cc_start: 0.9023 (tp) cc_final: 0.8731 (tp) REVERT: B 709 MET cc_start: 0.9019 (mtt) cc_final: 0.8712 (mtt) REVERT: C 501 MET cc_start: 0.7864 (mtm) cc_final: 0.7653 (mtm) REVERT: C 534 MET cc_start: 0.8519 (ttm) cc_final: 0.8113 (ttp) REVERT: C 565 MET cc_start: 0.8539 (mmm) cc_final: 0.8256 (mmt) REVERT: C 635 ILE cc_start: 0.8767 (OUTLIER) cc_final: 0.8545 (mp) REVERT: C 698 LYS cc_start: 0.9347 (mmtt) cc_final: 0.8894 (mmtt) REVERT: C 761 SER cc_start: 0.8821 (t) cc_final: 0.8318 (m) REVERT: C 805 PRO cc_start: 0.8319 (Cg_exo) cc_final: 0.8033 (Cg_endo) REVERT: C 836 PHE cc_start: 0.8013 (m-80) cc_final: 0.7724 (m-10) REVERT: C 841 GLU cc_start: 0.7592 (mt-10) cc_final: 0.7281 (mt-10) REVERT: D 556 LEU cc_start: 0.9156 (mm) cc_final: 0.8877 (mp) REVERT: D 572 LEU cc_start: 0.9195 (mm) cc_final: 0.8408 (mm) REVERT: D 576 CYS cc_start: 0.8459 (m) cc_final: 0.7988 (m) REVERT: D 590 TYR cc_start: 0.7663 (p90) cc_final: 0.7063 (p90) REVERT: D 627 MET cc_start: 0.8190 (tpp) cc_final: 0.7153 (tpp) REVERT: D 639 ILE cc_start: 0.9033 (tp) cc_final: 0.8762 (tp) outliers start: 38 outliers final: 23 residues processed: 243 average time/residue: 0.2480 time to fit residues: 92.5525 Evaluate side-chains 230 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 205 time to evaluate : 1.563 ------------------------------------------------------------------------------- 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 520 THR Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 866 ARG Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 565 MET Chi-restraints excluded: chain B residue 580 VAL 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 580 VAL 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: 0.9980 chunk 104 optimal weight: 0.8980 chunk 148 optimal weight: 0.0870 chunk 60 optimal weight: 0.0870 chunk 64 optimal weight: 0.5980 chunk 53 optimal weight: 0.9980 chunk 152 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 174 optimal weight: 10.0000 chunk 160 optimal weight: 3.9990 chunk 86 optimal weight: 9.9990 overall best weight: 0.5336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 792 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.141539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.101523 restraints weight = 80285.095| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 5.20 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3383 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3383 r_free = 0.3383 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3383 r_free = 0.3383 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3383 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.3619 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= 0.129 Angle : 0.679 9.174 19554 Z= 0.346 Chirality : 0.043 0.168 2172 Planarity : 0.005 0.053 2474 Dihedral : 5.641 41.358 1936 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.86 % Favored : 88.91 % Rotamer: Outliers : 2.45 % Allowed : 13.23 % Favored : 84.32 % 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: -1.88 (0.19), residues: 1774 helix: 0.02 (0.17), residues: 874 sheet: -2.54 (0.43), residues: 126 loop : -2.54 (0.22), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 706 HIS 0.012 0.002 HIS A 593 PHE 0.028 0.001 PHE D 584 TYR 0.021 0.002 TYR C 651 ARG 0.007 0.001 ARG A 800 Details of bonding type rmsd hydrogen bonds : bond 0.03210 ( 580) hydrogen bonds : angle 4.19976 ( 1706) SS BOND : bond 0.00095 ( 4) SS BOND : angle 0.30594 ( 8) covalent geometry : bond 0.00291 (14446) covalent geometry : angle 0.67922 (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: 30 poor density : 233 time to evaluate : 1.815 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: 0.8644 (ttm) cc_final: 0.8293 (ttp) REVERT: A 565 MET cc_start: 0.8535 (mmm) cc_final: 0.8244 (mmt) REVERT: A 612 PHE cc_start: 0.8416 (m-10) cc_final: 0.8147 (m-80) REVERT: A 651 TYR cc_start: 0.8703 (t80) cc_final: 0.8416 (t80) REVERT: A 709 MET cc_start: 0.9017 (mtp) cc_final: 0.8656 (mpp) REVERT: A 761 SER cc_start: 0.8846 (t) cc_final: 0.8340 (m) REVERT: A 836 PHE cc_start: 0.8185 (m-80) cc_final: 0.7770 (m-10) REVERT: A 841 GLU cc_start: 0.7737 (mt-10) cc_final: 0.7468 (mt-10) REVERT: A 861 MET cc_start: 0.8409 (mmp) cc_final: 0.7736 (mtm) REVERT: B 443 TYR cc_start: 0.8124 (m-80) cc_final: 0.7637 (m-80) REVERT: B 572 LEU cc_start: 0.9142 (mm) cc_final: 0.8299 (mm) REVERT: B 576 CYS cc_start: 0.8473 (m) cc_final: 0.7798 (m) REVERT: B 580 VAL cc_start: 0.9363 (t) cc_final: 0.9106 (m) REVERT: B 584 PHE cc_start: 0.7903 (t80) cc_final: 0.7015 (m-10) REVERT: B 590 TYR cc_start: 0.7406 (p90) cc_final: 0.6805 (p90) REVERT: B 609 LEU cc_start: 0.8772 (tt) cc_final: 0.8074 (mt) REVERT: B 612 PHE cc_start: 0.8334 (m-80) cc_final: 0.7987 (t80) REVERT: B 639 ILE cc_start: 0.8998 (tp) cc_final: 0.8684 (tp) REVERT: B 709 MET cc_start: 0.8988 (mtt) cc_final: 0.8670 (mtt) REVERT: B 800 ARG cc_start: 0.8482 (tpp80) cc_final: 0.8177 (ttp80) REVERT: C 501 MET cc_start: 0.7747 (mtm) cc_final: 0.7501 (mtm) REVERT: C 534 MET cc_start: 0.8660 (ttm) cc_final: 0.8277 (ttp) REVERT: C 565 MET cc_start: 0.8532 (mmm) cc_final: 0.8258 (mmt) REVERT: C 698 LYS cc_start: 0.9388 (mmtt) cc_final: 0.8960 (mmtt) REVERT: C 761 SER cc_start: 0.8822 (t) cc_final: 0.8355 (m) REVERT: C 805 PRO cc_start: 0.8383 (Cg_exo) cc_final: 0.8170 (Cg_endo) REVERT: C 810 LYS cc_start: 0.8306 (mmtt) cc_final: 0.7804 (mmpt) REVERT: C 841 GLU cc_start: 0.7891 (mt-10) cc_final: 0.7611 (mt-10) REVERT: D 556 LEU cc_start: 0.9129 (mm) cc_final: 0.8860 (mp) REVERT: D 572 LEU cc_start: 0.9172 (mm) cc_final: 0.8334 (mm) REVERT: D 576 CYS cc_start: 0.8440 (m) cc_final: 0.7989 (m) REVERT: D 590 TYR cc_start: 0.8002 (p90) cc_final: 0.7526 (p90) REVERT: D 612 PHE cc_start: 0.8411 (m-80) cc_final: 0.7903 (t80) REVERT: D 625 GLU cc_start: 0.8119 (pt0) cc_final: 0.7806 (pt0) REVERT: D 639 ILE cc_start: 0.9044 (tp) cc_final: 0.8752 (tp) REVERT: D 800 ARG cc_start: 0.8467 (tpp80) cc_final: 0.8029 (tpt90) REVERT: D 861 MET cc_start: 0.8466 (ppp) cc_final: 0.7646 (ttt) outliers start: 30 outliers final: 16 residues processed: 251 average time/residue: 0.2604 time to fit residues: 100.7093 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 : 1.632 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 32 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 162 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 121 optimal weight: 0.0770 chunk 158 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 49 optimal weight: 0.6980 chunk 173 optimal weight: 1.9990 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.139596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.100340 restraints weight = 77927.533| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 5.51 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3380 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3380 r_free = 0.3380 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3380 r_free = 0.3380 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3380 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.3906 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= 0.133 Angle : 0.665 10.139 19554 Z= 0.337 Chirality : 0.042 0.145 2172 Planarity : 0.005 0.069 2474 Dihedral : 5.441 40.689 1936 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.28 % Allowed : 11.03 % Favored : 88.69 % Rotamer: Outliers : 2.13 % Allowed : 13.94 % Favored : 83.94 % 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: -1.49 (0.20), residues: 1774 helix: 0.41 (0.17), residues: 884 sheet: -2.65 (0.48), residues: 98 loop : -2.46 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 589 HIS 0.010 0.001 HIS C 593 PHE 0.021 0.001 PHE D 476 TYR 0.011 0.001 TYR A 542 ARG 0.005 0.001 ARG D 855 Details of bonding type rmsd hydrogen bonds : bond 0.03091 ( 580) hydrogen bonds : angle 4.02987 ( 1706) SS BOND : bond 0.00044 ( 4) SS BOND : angle 0.31300 ( 8) covalent geometry : bond 0.00308 (14446) covalent geometry : angle 0.66478 (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 250 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 225 time to evaluate : 1.725 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: 0.9038 (ttm) cc_final: 0.8719 (ttp) REVERT: A 565 MET cc_start: 0.8558 (mmm) cc_final: 0.8274 (mmt) REVERT: A 651 TYR cc_start: 0.8806 (t80) cc_final: 0.8468 (t80) REVERT: A 761 SER cc_start: 0.8893 (t) cc_final: 0.8368 (m) REVERT: A 810 LYS cc_start: 0.8282 (mmtt) cc_final: 0.7881 (mmtm) REVERT: A 836 PHE cc_start: 0.8059 (m-80) cc_final: 0.7722 (m-10) REVERT: A 841 GLU cc_start: 0.7696 (mt-10) cc_final: 0.7075 (mm-30) REVERT: A 861 MET cc_start: 0.8399 (mmp) cc_final: 0.7657 (mtm) REVERT: B 443 TYR cc_start: 0.8091 (m-80) cc_final: 0.7553 (m-80) REVERT: B 572 LEU cc_start: 0.9101 (mm) cc_final: 0.8258 (mm) REVERT: B 576 CYS cc_start: 0.8489 (m) cc_final: 0.8006 (m) REVERT: B 584 PHE cc_start: 0.7930 (t80) cc_final: 0.6871 (m-10) REVERT: B 590 TYR cc_start: 0.7354 (p90) cc_final: 0.6773 (p90) REVERT: B 612 PHE cc_start: 0.8400 (m-80) cc_final: 0.8086 (t80) REVERT: B 639 ILE cc_start: 0.9017 (tp) cc_final: 0.8775 (pt) REVERT: B 709 MET cc_start: 0.8951 (mtt) cc_final: 0.8605 (mtt) REVERT: B 800 ARG cc_start: 0.8592 (tpp80) cc_final: 0.7981 (tpt90) REVERT: B 861 MET cc_start: 0.8354 (ppp) cc_final: 0.7563 (ttt) REVERT: C 501 MET cc_start: 0.7872 (mtm) cc_final: 0.7630 (mtm) REVERT: C 534 MET cc_start: 0.8852 (ttm) cc_final: 0.8458 (ttp) REVERT: C 565 MET cc_start: 0.8584 (mmm) cc_final: 0.8298 (mmt) REVERT: C 612 PHE cc_start: 0.8423 (m-10) cc_final: 0.8160 (m-80) REVERT: C 698 LYS cc_start: 0.9415 (mmtt) cc_final: 0.8978 (mmtm) REVERT: C 709 MET cc_start: 0.9077 (mtp) cc_final: 0.8566 (mpp) REVERT: C 761 SER cc_start: 0.8821 (t) cc_final: 0.8340 (m) REVERT: C 805 PRO cc_start: 0.8383 (Cg_exo) cc_final: 0.8118 (Cg_endo) REVERT: C 810 LYS cc_start: 0.8138 (mmtt) cc_final: 0.7636 (mmpt) REVERT: C 836 PHE cc_start: 0.8056 (m-80) cc_final: 0.7759 (m-10) REVERT: C 841 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7039 (mm-30) REVERT: D 572 LEU cc_start: 0.9129 (mm) cc_final: 0.8333 (mm) REVERT: D 576 CYS cc_start: 0.8558 (m) cc_final: 0.8085 (m) REVERT: D 612 PHE cc_start: 0.8391 (m-80) cc_final: 0.7921 (t80) REVERT: D 625 GLU cc_start: 0.8101 (pt0) cc_final: 0.7881 (pt0) REVERT: D 639 ILE cc_start: 0.9065 (tp) cc_final: 0.8789 (tp) REVERT: D 800 ARG cc_start: 0.8476 (tpp80) cc_final: 0.8020 (tpt90) REVERT: D 861 MET cc_start: 0.8524 (ppp) cc_final: 0.7727 (ttt) outliers start: 25 outliers final: 18 residues processed: 237 average time/residue: 0.2459 time to fit residues: 88.4035 Evaluate side-chains 224 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 206 time to evaluate : 1.649 ------------------------------------------------------------------------------- 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 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 631 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 608 LEU Chi-restraints excluded: chain D residue 444 VAL Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 565 MET Chi-restraints excluded: chain D residue 626 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 157 optimal weight: 3.9990 chunk 119 optimal weight: 0.2980 chunk 160 optimal weight: 4.9990 chunk 66 optimal weight: 0.0050 chunk 37 optimal weight: 10.0000 chunk 106 optimal weight: 3.9990 chunk 104 optimal weight: 0.0970 chunk 125 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 85 optimal weight: 7.9990 chunk 79 optimal weight: 2.9990 overall best weight: 1.2796 ------------------------------------------------------------------------------- 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 = 0.3907 r_free = 0.3907 target = 0.135052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.096347 restraints weight = 72040.554| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 5.24 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3352 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3352 r_free = 0.3352 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3352 r_free = 0.3352 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3352 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.4102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14450 Z= 0.172 Angle : 0.685 10.096 19554 Z= 0.347 Chirality : 0.043 0.150 2172 Planarity : 0.005 0.071 2474 Dihedral : 5.431 37.804 1936 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.17 % Allowed : 11.54 % Favored : 88.29 % Rotamer: Outliers : 1.94 % Allowed : 14.32 % Favored : 83.74 % 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: -1.29 (0.20), residues: 1774 helix: 0.60 (0.17), residues: 876 sheet: -2.31 (0.43), residues: 130 loop : -2.37 (0.23), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 589 HIS 0.009 0.002 HIS A 593 PHE 0.028 0.002 PHE B 476 TYR 0.011 0.002 TYR C 521 ARG 0.004 0.001 ARG D 855 Details of bonding type rmsd hydrogen bonds : bond 0.03114 ( 580) hydrogen bonds : angle 4.04556 ( 1706) SS BOND : bond 0.00027 ( 4) SS BOND : angle 0.35167 ( 8) covalent geometry : bond 0.00405 (14446) covalent geometry : angle 0.68462 (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 235 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 213 time to evaluate : 1.550 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: 0.8686 (ttm) cc_final: 0.8415 (ttp) REVERT: A 565 MET cc_start: 0.8494 (mmm) cc_final: 0.8232 (mmt) REVERT: A 651 TYR cc_start: 0.8835 (t80) cc_final: 0.8417 (t80) REVERT: A 686 GLU cc_start: 0.6822 (tp30) cc_final: 0.6330 (tt0) REVERT: A 755 ILE cc_start: 0.9081 (mp) cc_final: 0.8784 (mp) REVERT: A 761 SER cc_start: 0.8819 (t) cc_final: 0.8304 (m) REVERT: A 810 LYS cc_start: 0.8261 (mmtt) cc_final: 0.7838 (mmtm) REVERT: A 836 PHE cc_start: 0.8165 (m-80) cc_final: 0.7760 (m-10) REVERT: A 841 GLU cc_start: 0.7597 (mt-10) cc_final: 0.6996 (mm-30) REVERT: A 861 MET cc_start: 0.8376 (mmp) cc_final: 0.7575 (mtm) REVERT: B 443 TYR cc_start: 0.8188 (m-80) cc_final: 0.7608 (m-80) REVERT: B 469 GLU cc_start: 0.8125 (mm-30) cc_final: 0.7885 (mm-30) REVERT: B 572 LEU cc_start: 0.9140 (mm) cc_final: 0.8296 (mm) REVERT: B 576 CYS cc_start: 0.8436 (m) cc_final: 0.8022 (m) REVERT: B 584 PHE cc_start: 0.7969 (t80) cc_final: 0.6863 (m-10) REVERT: B 590 TYR cc_start: 0.7292 (p90) cc_final: 0.6522 (p90) REVERT: B 609 LEU cc_start: 0.8949 (tt) cc_final: 0.8185 (mt) REVERT: B 612 PHE cc_start: 0.8385 (m-80) cc_final: 0.8116 (t80) REVERT: B 639 ILE cc_start: 0.8993 (tp) cc_final: 0.8706 (tp) REVERT: B 709 MET cc_start: 0.8994 (mtt) cc_final: 0.8677 (mtt) REVERT: B 778 ILE cc_start: 0.9308 (mt) cc_final: 0.9064 (mm) REVERT: B 800 ARG cc_start: 0.8571 (tpp80) cc_final: 0.7982 (tpt90) REVERT: B 861 MET cc_start: 0.8366 (ppp) cc_final: 0.7584 (ttt) REVERT: C 501 MET cc_start: 0.7807 (mtm) cc_final: 0.7575 (mtm) REVERT: C 534 MET cc_start: 0.8653 (ttm) cc_final: 0.8258 (ttp) REVERT: C 565 MET cc_start: 0.8547 (mmm) cc_final: 0.8268 (mmt) REVERT: C 589 TRP cc_start: 0.8314 (m100) cc_final: 0.8085 (m100) REVERT: C 612 PHE cc_start: 0.8443 (m-10) cc_final: 0.8182 (m-80) REVERT: C 698 LYS cc_start: 0.9380 (mmtt) cc_final: 0.8886 (mmtt) REVERT: C 761 SER cc_start: 0.8770 (t) cc_final: 0.8280 (m) REVERT: C 805 PRO cc_start: 0.8353 (Cg_exo) cc_final: 0.8090 (Cg_endo) REVERT: C 810 LYS cc_start: 0.8106 (mmtt) cc_final: 0.7629 (mmpt) REVERT: C 836 PHE cc_start: 0.8157 (m-80) cc_final: 0.7798 (m-10) REVERT: C 841 GLU cc_start: 0.7739 (mt-10) cc_final: 0.7030 (mm-30) REVERT: D 556 LEU cc_start: 0.9234 (mm) cc_final: 0.9009 (mp) REVERT: D 572 LEU cc_start: 0.9152 (mm) cc_final: 0.8297 (mm) REVERT: D 576 CYS cc_start: 0.8497 (m) cc_final: 0.8053 (m) REVERT: D 612 PHE cc_start: 0.8381 (m-80) cc_final: 0.7944 (t80) REVERT: D 639 ILE cc_start: 0.9017 (tp) cc_final: 0.8738 (tp) REVERT: D 861 MET cc_start: 0.8410 (ppp) cc_final: 0.7662 (ttt) outliers start: 22 outliers final: 18 residues processed: 221 average time/residue: 0.2363 time to fit residues: 80.0568 Evaluate side-chains 218 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 200 time to evaluate : 1.776 ------------------------------------------------------------------------------- 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 718 VAL 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 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 520 THR 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 Chi-restraints excluded: chain D residue 823 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 124 optimal weight: 0.9990 chunk 173 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 108 optimal weight: 2.9990 chunk 113 optimal weight: 0.4980 chunk 12 optimal weight: 0.7980 chunk 161 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 112 optimal weight: 4.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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 = 0.3928 r_free = 0.3928 target = 0.136498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.097657 restraints weight = 60467.253| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 5.25 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3362 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3362 r_free = 0.3362 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3362 r_free = 0.3362 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3362 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.4250 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= 0.136 Angle : 0.659 9.960 19554 Z= 0.334 Chirality : 0.042 0.155 2172 Planarity : 0.005 0.071 2474 Dihedral : 5.328 40.093 1936 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.11 % Allowed : 11.26 % Favored : 88.63 % Rotamer: Outliers : 1.94 % Allowed : 14.71 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.20), residues: 1774 helix: 0.71 (0.17), residues: 902 sheet: -2.60 (0.54), residues: 86 loop : -2.32 (0.22), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 589 HIS 0.008 0.001 HIS C 593 PHE 0.023 0.001 PHE D 476 TYR 0.010 0.001 TYR C 521 ARG 0.004 0.000 ARG A 583 Details of bonding type rmsd hydrogen bonds : bond 0.02983 ( 580) hydrogen bonds : angle 3.97685 ( 1706) SS BOND : bond 0.00034 ( 4) SS BOND : angle 0.32046 ( 8) covalent geometry : bond 0.00314 (14446) covalent geometry : angle 0.65890 (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 241 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 219 time to evaluate : 1.721 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: 0.8963 (ttm) cc_final: 0.8602 (ttp) REVERT: A 565 MET cc_start: 0.8473 (mmm) cc_final: 0.8215 (mmt) REVERT: A 709 MET cc_start: 0.9135 (mtp) cc_final: 0.8626 (mpp) REVERT: A 755 ILE cc_start: 0.9037 (mp) cc_final: 0.8805 (mp) REVERT: A 761 SER cc_start: 0.8855 (t) cc_final: 0.8331 (m) REVERT: A 810 LYS cc_start: 0.8217 (mmtt) cc_final: 0.7859 (mmtm) REVERT: A 836 PHE cc_start: 0.8140 (m-80) cc_final: 0.7742 (m-10) REVERT: A 841 GLU cc_start: 0.7562 (mt-10) cc_final: 0.7006 (mm-30) REVERT: A 861 MET cc_start: 0.8327 (mmp) cc_final: 0.7487 (mtm) REVERT: A 866 ARG cc_start: 0.7152 (OUTLIER) cc_final: 0.6389 (tmm160) REVERT: B 443 TYR cc_start: 0.8053 (m-80) cc_final: 0.7495 (m-80) REVERT: B 469 GLU cc_start: 0.8125 (mm-30) cc_final: 0.7877 (mm-30) REVERT: B 572 LEU cc_start: 0.9231 (mm) cc_final: 0.8499 (mm) REVERT: B 576 CYS cc_start: 0.8456 (m) cc_final: 0.8022 (m) REVERT: B 584 PHE cc_start: 0.8171 (t80) cc_final: 0.7020 (m-10) REVERT: B 590 TYR cc_start: 0.7170 (p90) cc_final: 0.6368 (p90) REVERT: B 609 LEU cc_start: 0.8734 (tt) cc_final: 0.7958 (mt) REVERT: B 612 PHE cc_start: 0.8391 (m-80) cc_final: 0.8108 (t80) REVERT: B 639 ILE cc_start: 0.8969 (tp) cc_final: 0.8676 (tp) REVERT: B 709 MET cc_start: 0.8963 (mtt) cc_final: 0.8635 (mtt) REVERT: B 778 ILE cc_start: 0.9302 (mt) cc_final: 0.9054 (mm) REVERT: B 800 ARG cc_start: 0.8544 (tpp80) cc_final: 0.7947 (tpt90) REVERT: B 861 MET cc_start: 0.8379 (ppp) cc_final: 0.7764 (ttt) REVERT: C 501 MET cc_start: 0.7821 (mtm) cc_final: 0.7572 (mtm) REVERT: C 534 MET cc_start: 0.8651 (ttm) cc_final: 0.8234 (ttp) REVERT: C 565 MET cc_start: 0.8576 (mmm) cc_final: 0.8297 (mmt) REVERT: C 698 LYS cc_start: 0.9397 (mmtt) cc_final: 0.8895 (mmtt) REVERT: C 709 MET cc_start: 0.9087 (mtp) cc_final: 0.8559 (mpp) REVERT: C 761 SER cc_start: 0.8780 (t) cc_final: 0.8291 (m) REVERT: C 805 PRO cc_start: 0.8310 (Cg_exo) cc_final: 0.8023 (Cg_endo) REVERT: C 810 LYS cc_start: 0.8119 (mmtt) cc_final: 0.7683 (mmpt) REVERT: C 836 PHE cc_start: 0.8156 (m-80) cc_final: 0.7779 (m-10) REVERT: C 841 GLU cc_start: 0.7601 (mt-10) cc_final: 0.6938 (mm-30) REVERT: D 572 LEU cc_start: 0.9110 (mm) cc_final: 0.8264 (mm) REVERT: D 576 CYS cc_start: 0.8540 (m) cc_final: 0.8057 (m) REVERT: D 612 PHE cc_start: 0.8339 (m-80) cc_final: 0.7874 (t80) REVERT: D 639 ILE cc_start: 0.8969 (tp) cc_final: 0.8690 (tp) REVERT: D 861 MET cc_start: 0.8324 (ppp) cc_final: 0.7628 (ttt) outliers start: 22 outliers final: 19 residues processed: 228 average time/residue: 0.2380 time to fit residues: 83.2468 Evaluate side-chains 223 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 203 time to evaluate : 1.597 ------------------------------------------------------------------------------- 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 A residue 866 ARG Chi-restraints excluded: chain A residue 867 MET Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 565 MET Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 823 ILE Chi-restraints excluded: chain B residue 831 LEU Chi-restraints excluded: chain C residue 458 ARG Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain D residue 444 VAL Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 565 MET Chi-restraints excluded: chain D residue 823 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 104 optimal weight: 0.5980 chunk 81 optimal weight: 10.0000 chunk 18 optimal weight: 4.9990 chunk 147 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 118 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- 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 = 0.3905 r_free = 0.3905 target = 0.134819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.096648 restraints weight = 61423.477| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 4.80 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3365 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3365 r_free = 0.3365 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3365 r_free = 0.3365 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3365 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.4335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14450 Z= 0.176 Angle : 0.690 10.168 19554 Z= 0.350 Chirality : 0.044 0.222 2172 Planarity : 0.005 0.071 2474 Dihedral : 5.375 38.696 1936 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.11 % Allowed : 11.82 % Favored : 88.07 % Rotamer: Outliers : 1.74 % Allowed : 15.29 % Favored : 82.97 % 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: -1.09 (0.20), residues: 1774 helix: 0.70 (0.17), residues: 902 sheet: -2.29 (0.52), residues: 96 loop : -2.30 (0.23), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 589 HIS 0.008 0.001 HIS C 593 PHE 0.029 0.002 PHE B 476 TYR 0.011 0.002 TYR C 521 ARG 0.004 0.000 ARG A 583 Details of bonding type rmsd hydrogen bonds : bond 0.03127 ( 580) hydrogen bonds : angle 4.04617 ( 1706) SS BOND : bond 0.00044 ( 4) SS BOND : angle 0.50606 ( 8) covalent geometry : bond 0.00412 (14446) covalent geometry : angle 0.69054 (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 226 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 207 time to evaluate : 1.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 534 MET cc_start: 0.8700 (ttm) cc_final: 0.8418 (ttp) REVERT: A 565 MET cc_start: 0.8479 (mmm) cc_final: 0.8216 (mmt) REVERT: A 651 TYR cc_start: 0.8836 (t80) cc_final: 0.8592 (t80) REVERT: A 709 MET cc_start: 0.9145 (mtp) cc_final: 0.8648 (mpp) REVERT: A 755 ILE cc_start: 0.9101 (mp) cc_final: 0.8869 (mp) REVERT: A 761 SER cc_start: 0.8822 (t) cc_final: 0.8312 (m) REVERT: A 810 LYS cc_start: 0.8213 (mmtt) cc_final: 0.7803 (mmtm) REVERT: A 836 PHE cc_start: 0.8289 (m-80) cc_final: 0.7799 (m-10) REVERT: A 841 GLU cc_start: 0.7554 (mt-10) cc_final: 0.7018 (mm-30) REVERT: A 861 MET cc_start: 0.8368 (mmp) cc_final: 0.7489 (mtm) REVERT: B 443 TYR cc_start: 0.8193 (m-80) cc_final: 0.7674 (m-80) REVERT: B 469 GLU cc_start: 0.8169 (mm-30) cc_final: 0.7907 (mm-30) REVERT: B 572 LEU cc_start: 0.9249 (mm) cc_final: 0.8494 (mm) REVERT: B 576 CYS cc_start: 0.8400 (m) cc_final: 0.7993 (m) REVERT: B 584 PHE cc_start: 0.8132 (t80) cc_final: 0.7052 (m-10) REVERT: B 590 TYR cc_start: 0.7241 (p90) cc_final: 0.6454 (p90) REVERT: B 609 LEU cc_start: 0.8748 (tt) cc_final: 0.7993 (mt) REVERT: B 612 PHE cc_start: 0.8365 (m-80) cc_final: 0.8110 (t80) REVERT: B 709 MET cc_start: 0.9014 (mtt) cc_final: 0.8700 (mtt) REVERT: B 778 ILE cc_start: 0.9289 (mt) cc_final: 0.9035 (mm) REVERT: B 800 ARG cc_start: 0.8519 (tpp80) cc_final: 0.7952 (tpt90) REVERT: B 861 MET cc_start: 0.8410 (ppp) cc_final: 0.7777 (ttt) REVERT: C 501 MET cc_start: 0.7780 (mtm) cc_final: 0.7532 (mtm) REVERT: C 534 MET cc_start: 0.8690 (ttm) cc_final: 0.8290 (ttp) REVERT: C 565 MET cc_start: 0.8551 (mmm) cc_final: 0.8280 (mmt) REVERT: C 589 TRP cc_start: 0.8295 (m100) cc_final: 0.8089 (m100) REVERT: C 698 LYS cc_start: 0.9387 (mmtt) cc_final: 0.8891 (mmtt) REVERT: C 709 MET cc_start: 0.9095 (mtp) cc_final: 0.8577 (mpp) REVERT: C 761 SER cc_start: 0.8759 (t) cc_final: 0.8265 (m) REVERT: C 805 PRO cc_start: 0.8271 (Cg_exo) cc_final: 0.7991 (Cg_endo) REVERT: C 810 LYS cc_start: 0.8167 (mmtt) cc_final: 0.7705 (mmpt) REVERT: C 836 PHE cc_start: 0.8145 (m-80) cc_final: 0.7750 (m-10) REVERT: C 841 GLU cc_start: 0.7649 (mt-10) cc_final: 0.6989 (mm-30) REVERT: D 441 GLU cc_start: 0.8643 (mt-10) cc_final: 0.8023 (tt0) REVERT: D 572 LEU cc_start: 0.9142 (mm) cc_final: 0.8253 (mm) REVERT: D 576 CYS cc_start: 0.8440 (m) cc_final: 0.8009 (m) REVERT: D 612 PHE cc_start: 0.8316 (m-80) cc_final: 0.7980 (t80) REVERT: D 639 ILE cc_start: 0.9054 (tp) cc_final: 0.8800 (tp) REVERT: D 861 MET cc_start: 0.8254 (ppp) cc_final: 0.7580 (ttt) outliers start: 19 outliers final: 18 residues processed: 214 average time/residue: 0.2313 time to fit residues: 77.0031 Evaluate side-chains 222 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 204 time to evaluate : 1.577 ------------------------------------------------------------------------------- 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 608 LEU 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 565 MET Chi-restraints excluded: chain B residue 580 VAL 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 D residue 444 VAL Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 565 MET Chi-restraints excluded: chain D residue 823 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 104 optimal weight: 0.4980 chunk 18 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 chunk 118 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 chunk 167 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 131 optimal weight: 6.9990 chunk 100 optimal weight: 0.9980 chunk 103 optimal weight: 0.7980 chunk 64 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 610 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.137846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.099742 restraints weight = 65849.503| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 4.99 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3376 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3376 r_free = 0.3376 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3376 r_free = 0.3376 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3376 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.4474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14450 Z= 0.129 Angle : 0.668 10.259 19554 Z= 0.338 Chirality : 0.042 0.209 2172 Planarity : 0.005 0.071 2474 Dihedral : 5.318 41.566 1936 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.86 % Favored : 89.03 % Rotamer: Outliers : 1.74 % Allowed : 15.55 % Favored : 82.71 % 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: -0.90 (0.21), residues: 1774 helix: 0.89 (0.18), residues: 902 sheet: -2.37 (0.51), residues: 96 loop : -2.24 (0.23), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 589 HIS 0.007 0.001 HIS C 593 PHE 0.018 0.001 PHE D 584 TYR 0.023 0.001 TYR A 702 ARG 0.004 0.000 ARG A 583 Details of bonding type rmsd hydrogen bonds : bond 0.03004 ( 580) hydrogen bonds : angle 3.98491 ( 1706) SS BOND : bond 0.00043 ( 4) SS BOND : angle 0.41486 ( 8) covalent geometry : bond 0.00294 (14446) covalent geometry : angle 0.66840 (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 231 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 212 time to evaluate : 1.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 534 MET cc_start: 0.8973 (ttm) cc_final: 0.8617 (ttp) REVERT: A 705 MET cc_start: 0.8879 (mtp) cc_final: 0.8678 (mtt) REVERT: A 709 MET cc_start: 0.9092 (mtp) cc_final: 0.8605 (mpp) REVERT: A 761 SER cc_start: 0.8781 (t) cc_final: 0.8370 (m) REVERT: A 836 PHE cc_start: 0.8250 (m-80) cc_final: 0.7792 (m-10) REVERT: A 841 GLU cc_start: 0.7456 (mt-10) cc_final: 0.6962 (mm-30) REVERT: A 861 MET cc_start: 0.8371 (mmp) cc_final: 0.7472 (mtm) REVERT: B 443 TYR cc_start: 0.7999 (m-80) cc_final: 0.7431 (m-80) REVERT: B 469 GLU cc_start: 0.8196 (mm-30) cc_final: 0.7963 (mm-30) REVERT: B 572 LEU cc_start: 0.9248 (mm) cc_final: 0.8536 (mm) REVERT: B 576 CYS cc_start: 0.8421 (m) cc_final: 0.8015 (m) REVERT: B 584 PHE cc_start: 0.8133 (t80) cc_final: 0.7020 (m-10) REVERT: B 590 TYR cc_start: 0.7214 (p90) cc_final: 0.6442 (p90) REVERT: B 609 LEU cc_start: 0.8723 (tt) cc_final: 0.7980 (mt) REVERT: B 612 PHE cc_start: 0.8321 (m-80) cc_final: 0.8111 (t80) REVERT: B 626 LEU cc_start: 0.8270 (tp) cc_final: 0.8014 (tp) REVERT: B 709 MET cc_start: 0.8982 (mtt) cc_final: 0.8652 (mtt) REVERT: B 778 ILE cc_start: 0.9268 (mt) cc_final: 0.9021 (mm) REVERT: B 800 ARG cc_start: 0.8495 (tpp80) cc_final: 0.7901 (tpt90) REVERT: B 861 MET cc_start: 0.8445 (ppp) cc_final: 0.7707 (ttt) REVERT: C 501 MET cc_start: 0.7711 (mtm) cc_final: 0.7449 (mtm) REVERT: C 534 MET cc_start: 0.8712 (ttm) cc_final: 0.8289 (ttp) REVERT: C 565 MET cc_start: 0.8554 (mmm) cc_final: 0.8326 (mmt) REVERT: C 589 TRP cc_start: 0.8121 (m100) cc_final: 0.7916 (m100) REVERT: C 612 PHE cc_start: 0.8330 (m-10) cc_final: 0.8122 (m-80) REVERT: C 698 LYS cc_start: 0.9380 (mmtt) cc_final: 0.8886 (mmtt) REVERT: C 709 MET cc_start: 0.9067 (mtp) cc_final: 0.8545 (mpp) REVERT: C 761 SER cc_start: 0.8786 (t) cc_final: 0.8292 (m) REVERT: C 805 PRO cc_start: 0.8299 (Cg_exo) cc_final: 0.8012 (Cg_endo) REVERT: C 810 LYS cc_start: 0.8111 (mmtt) cc_final: 0.7739 (mmpt) REVERT: C 836 PHE cc_start: 0.8121 (m-80) cc_final: 0.7723 (m-10) REVERT: C 841 GLU cc_start: 0.7544 (mt-10) cc_final: 0.6944 (mm-30) REVERT: D 441 GLU cc_start: 0.8682 (mt-10) cc_final: 0.8107 (tt0) REVERT: D 572 LEU cc_start: 0.9151 (mm) cc_final: 0.8347 (mm) REVERT: D 576 CYS cc_start: 0.8600 (m) cc_final: 0.8155 (m) REVERT: D 612 PHE cc_start: 0.8305 (m-80) cc_final: 0.7911 (t80) REVERT: D 639 ILE cc_start: 0.8970 (tp) cc_final: 0.8702 (tp) REVERT: D 792 HIS cc_start: 0.8794 (t70) cc_final: 0.8551 (t70) REVERT: D 861 MET cc_start: 0.8247 (ppp) cc_final: 0.7591 (ttt) outliers start: 19 outliers final: 19 residues processed: 219 average time/residue: 0.2313 time to fit residues: 79.2681 Evaluate side-chains 224 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 205 time to evaluate : 1.957 ------------------------------------------------------------------------------- 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 A residue 867 MET Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 565 MET Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 631 LEU 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 D residue 444 VAL Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 565 MET Chi-restraints excluded: chain D residue 823 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 64 optimal weight: 0.7980 chunk 92 optimal weight: 2.9990 chunk 171 optimal weight: 2.9990 chunk 102 optimal weight: 0.1980 chunk 12 optimal weight: 1.9990 chunk 25 optimal weight: 10.0000 chunk 57 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 130 optimal weight: 0.6980 chunk 3 optimal weight: 0.5980 chunk 117 optimal weight: 4.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.3935 r_free = 0.3935 target = 0.137483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.098722 restraints weight = 69887.240| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 5.21 r_work (final): 0.3373 ------------------------------------------------------------------------------- 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 = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3373 r_free = 0.3373 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3373 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.4567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14450 Z= 0.143 Angle : 0.682 10.067 19554 Z= 0.344 Chirality : 0.043 0.209 2172 Planarity : 0.005 0.073 2474 Dihedral : 5.321 41.892 1936 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.97 % Favored : 88.91 % Rotamer: Outliers : 1.94 % Allowed : 15.42 % Favored : 82.65 % 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: -0.84 (0.21), residues: 1774 helix: 0.90 (0.18), residues: 906 sheet: -2.33 (0.51), residues: 96 loop : -2.17 (0.23), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP A 589 HIS 0.007 0.001 HIS C 593 PHE 0.018 0.001 PHE D 584 TYR 0.019 0.001 TYR C 542 ARG 0.004 0.000 ARG C 583 Details of bonding type rmsd hydrogen bonds : bond 0.03009 ( 580) hydrogen bonds : angle 3.96409 ( 1706) SS BOND : bond 0.00045 ( 4) SS BOND : angle 0.48085 ( 8) covalent geometry : bond 0.00332 (14446) covalent geometry : angle 0.68235 (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 230 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 208 time to evaluate : 1.609 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: 0.8996 (ttm) cc_final: 0.8657 (ttp) REVERT: A 709 MET cc_start: 0.9052 (mtp) cc_final: 0.8540 (mpp) REVERT: A 761 SER cc_start: 0.8811 (t) cc_final: 0.8381 (m) REVERT: A 836 PHE cc_start: 0.8272 (m-80) cc_final: 0.7815 (m-10) REVERT: A 841 GLU cc_start: 0.7466 (mt-10) cc_final: 0.6987 (mm-30) REVERT: A 861 MET cc_start: 0.8406 (mmp) cc_final: 0.7528 (mtm) REVERT: B 443 TYR cc_start: 0.8066 (m-80) cc_final: 0.7514 (m-80) REVERT: B 469 GLU cc_start: 0.8213 (mm-30) cc_final: 0.7981 (mm-30) REVERT: B 572 LEU cc_start: 0.9246 (mm) cc_final: 0.8559 (mm) REVERT: B 576 CYS cc_start: 0.8489 (m) cc_final: 0.8077 (m) REVERT: B 584 PHE cc_start: 0.8190 (t80) cc_final: 0.7048 (m-10) REVERT: B 590 TYR cc_start: 0.7189 (p90) cc_final: 0.6434 (p90) REVERT: B 609 LEU cc_start: 0.8677 (tt) cc_final: 0.8023 (mt) REVERT: B 612 PHE cc_start: 0.8341 (m-80) cc_final: 0.8115 (t80) REVERT: B 626 LEU cc_start: 0.8316 (tp) cc_final: 0.8063 (tp) REVERT: B 709 MET cc_start: 0.8993 (mtt) cc_final: 0.8661 (mtt) REVERT: B 778 ILE cc_start: 0.9272 (mt) cc_final: 0.9033 (mm) REVERT: B 800 ARG cc_start: 0.8497 (tpp80) cc_final: 0.7897 (tpt90) REVERT: B 861 MET cc_start: 0.8515 (ppp) cc_final: 0.7810 (ttt) REVERT: C 501 MET cc_start: 0.7819 (mtm) cc_final: 0.7561 (mtm) REVERT: C 534 MET cc_start: 0.8587 (ttm) cc_final: 0.8153 (ttp) REVERT: C 565 MET cc_start: 0.8580 (mmm) cc_final: 0.8335 (mmt) REVERT: C 698 LYS cc_start: 0.9391 (mmtt) cc_final: 0.8895 (mmtt) REVERT: C 709 MET cc_start: 0.9105 (mtp) cc_final: 0.8576 (mpp) REVERT: C 761 SER cc_start: 0.8784 (t) cc_final: 0.8290 (m) REVERT: C 805 PRO cc_start: 0.8307 (Cg_exo) cc_final: 0.8049 (Cg_endo) REVERT: C 836 PHE cc_start: 0.8150 (m-80) cc_final: 0.7749 (m-10) REVERT: C 841 GLU cc_start: 0.7581 (mt-10) cc_final: 0.6978 (mm-30) REVERT: D 440 GLU cc_start: 0.8195 (tp30) cc_final: 0.7881 (tp30) REVERT: D 441 GLU cc_start: 0.8677 (mt-10) cc_final: 0.7978 (tt0) REVERT: D 564 TRP cc_start: 0.8764 (m100) cc_final: 0.8195 (m100) REVERT: D 572 LEU cc_start: 0.9160 (mm) cc_final: 0.8351 (mm) REVERT: D 576 CYS cc_start: 0.8580 (m) cc_final: 0.8143 (m) REVERT: D 612 PHE cc_start: 0.8337 (m-80) cc_final: 0.7871 (t80) REVERT: D 639 ILE cc_start: 0.8991 (tp) cc_final: 0.8716 (tp) REVERT: D 792 HIS cc_start: 0.8817 (t70) cc_final: 0.8563 (t70) REVERT: D 800 ARG cc_start: 0.8438 (tpp80) cc_final: 0.8017 (tpt90) REVERT: D 861 MET cc_start: 0.8349 (ppp) cc_final: 0.7765 (ttt) outliers start: 22 outliers final: 19 residues processed: 216 average time/residue: 0.2221 time to fit residues: 74.4133 Evaluate side-chains 220 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 201 time to evaluate : 1.594 ------------------------------------------------------------------------------- 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 867 MET Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 565 MET Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 823 ILE Chi-restraints excluded: chain B residue 831 LEU Chi-restraints excluded: chain C residue 458 ARG Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain D residue 444 VAL Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 565 MET Chi-restraints excluded: chain D residue 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: 1.9990 chunk 112 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 chunk 139 optimal weight: 0.4980 chunk 58 optimal weight: 0.9990 chunk 59 optimal weight: 4.9990 chunk 27 optimal weight: 8.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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 = 0.3909 r_free = 0.3909 target = 0.135212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.096913 restraints weight = 56149.171| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 4.74 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3367 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3367 r_free = 0.3367 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 = 0.3367 r_free = 0.3367 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3367 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.4597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 14450 Z= 0.172 Angle : 0.695 10.277 19554 Z= 0.350 Chirality : 0.044 0.204 2172 Planarity : 0.005 0.074 2474 Dihedral : 5.368 41.588 1936 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.11 % Allowed : 11.14 % Favored : 88.74 % Rotamer: Outliers : 1.74 % Allowed : 15.94 % Favored : 82.32 % 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: -0.86 (0.21), residues: 1774 helix: 0.89 (0.18), residues: 904 sheet: -2.30 (0.52), residues: 94 loop : -2.19 (0.23), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP C 589 HIS 0.007 0.001 HIS C 593 PHE 0.018 0.002 PHE D 584 TYR 0.017 0.002 TYR A 702 ARG 0.003 0.000 ARG A 583 Details of bonding type rmsd hydrogen bonds : bond 0.03116 ( 580) hydrogen bonds : angle 4.01049 ( 1706) SS BOND : bond 0.00047 ( 4) SS BOND : angle 0.50649 ( 8) covalent geometry : bond 0.00405 (14446) covalent geometry : angle 0.69483 (19546) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6859.65 seconds wall clock time: 120 minutes 39.15 seconds (7239.15 seconds total)