Starting phenix.real_space_refine on Thu Sep 18 04:46:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b35_44128/09_2025/9b35_44128.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b35_44128/09_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_44128/09_2025/9b35_44128.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b35_44128/09_2025/9b35_44128.map" model { file = "/net/cci-nas-00/data/ceres_data/9b35_44128/09_2025/9b35_44128.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b35_44128/09_2025/9b35_44128.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: C, D Time building chain proxies: 6.23, per 1000 atoms: 0.44 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: 1.08 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 1.2 microseconds 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: 0.47 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: 2.28 Time building geometry restraints manager: 1.51 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } 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: 1.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 17.440 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.430 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.010 0.001 ARG A 866 TYR 0.036 0.004 TYR B 488 PHE 0.041 0.003 PHE B 735 TRP 0.044 0.004 TRP A 799 HIS 0.022 0.003 HIS A 593 Details of bonding type rmsd covalent geometry : bond 0.00784 (14446) covalent geometry : angle 1.24465 (19546) SS BOND : bond 0.00096 ( 4) SS BOND : angle 1.19260 ( 8) hydrogen bonds : bond 0.28344 ( 580) hydrogen bonds : angle 10.36580 ( 1706) *********************** 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 : 0.576 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: 0.7780 (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: 0.8515 (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: 0.7415 (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: 0.7606 (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: 0.7828 (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: 0.1221 time to fit residues: 67.7109 Evaluate side-chains 217 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 217 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 596 ASN A 604 ASN A 802 ASN B 549 ASN B 604 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: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.138761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.100854 restraints weight = 60304.603| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 4.99 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3399 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3399 r_free = 0.3399 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 = 0.3399 r_free = 0.3399 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3399 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 14450 Z= 0.169 Angle : 0.763 8.249 19554 Z= 0.394 Chirality : 0.044 0.160 2172 Planarity : 0.006 0.053 2474 Dihedral : 6.491 45.330 1936 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.40 % Allowed : 11.54 % Favored : 88.07 % Rotamer: Outliers : 2.06 % Allowed : 10.52 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.56 (0.17), residues: 1774 helix: -1.71 (0.14), residues: 874 sheet: -2.92 (0.46), residues: 120 loop : -3.00 (0.20), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 583 TYR 0.020 0.002 TYR D 566 PHE 0.025 0.002 PHE B 476 TRP 0.021 0.002 TRP D 798 HIS 0.015 0.002 HIS C 593 Details of bonding type rmsd covalent geometry : bond 0.00379 (14446) covalent geometry : angle 0.76292 (19546) SS BOND : bond 0.00083 ( 4) SS BOND : angle 0.62999 ( 8) hydrogen bonds : bond 0.04309 ( 580) hydrogen bonds : angle 4.95425 ( 1706) *********************** 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 280 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 256 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 465 ASP cc_start: 0.8323 (t70) cc_final: 0.7718 (t0) REVERT: A 565 MET cc_start: 0.8476 (mmm) cc_final: 0.8205 (mmt) REVERT: A 635 ILE cc_start: 0.8813 (OUTLIER) cc_final: 0.8589 (mp) REVERT: A 794 MET cc_start: 0.7966 (mtp) cc_final: 0.7558 (mtp) REVERT: A 836 PHE cc_start: 0.7964 (m-80) cc_final: 0.7728 (m-10) REVERT: A 841 GLU cc_start: 0.7445 (mt-10) cc_final: 0.7195 (mt-10) REVERT: A 861 MET cc_start: 0.8498 (mmp) cc_final: 0.7865 (mtm) REVERT: A 866 ARG cc_start: 0.6898 (OUTLIER) cc_final: 0.6017 (tmm-80) REVERT: B 465 ASP cc_start: 0.8871 (m-30) cc_final: 0.8502 (m-30) REVERT: B 469 GLU cc_start: 0.8585 (mm-30) cc_final: 0.8080 (mm-30) REVERT: B 563 ILE cc_start: 0.9091 (mm) cc_final: 0.8867 (mt) REVERT: B 572 LEU cc_start: 0.9238 (mm) cc_final: 0.8379 (mm) REVERT: B 576 CYS cc_start: 0.8455 (m) cc_final: 0.7809 (m) REVERT: B 580 VAL cc_start: 0.9374 (t) cc_final: 0.8990 (m) REVERT: B 584 PHE cc_start: 0.7934 (t80) cc_final: 0.6866 (m-10) REVERT: B 590 TYR cc_start: 0.7683 (p90) cc_final: 0.7206 (p90) REVERT: B 609 LEU cc_start: 0.8934 (tt) cc_final: 0.8273 (mt) REVERT: B 612 PHE cc_start: 0.8518 (m-80) cc_final: 0.8116 (t80) REVERT: B 626 LEU cc_start: 0.8471 (mt) cc_final: 0.8099 (mt) REVERT: B 639 ILE cc_start: 0.9034 (tp) cc_final: 0.8770 (pt) REVERT: B 655 LEU cc_start: 0.8845 (tp) cc_final: 0.8608 (tp) REVERT: B 709 MET cc_start: 0.8931 (mtt) cc_final: 0.8584 (mtt) REVERT: B 800 ARG cc_start: 0.8280 (tpp80) cc_final: 0.7890 (mmm160) REVERT: C 565 MET cc_start: 0.8532 (mmm) cc_final: 0.8212 (mmt) REVERT: C 635 ILE cc_start: 0.8683 (OUTLIER) cc_final: 0.8448 (mp) REVERT: C 667 PRO cc_start: 0.9058 (Cg_exo) cc_final: 0.8648 (Cg_endo) REVERT: C 761 SER cc_start: 0.8803 (t) cc_final: 0.8338 (m) REVERT: C 805 PRO cc_start: 0.8274 (Cg_exo) cc_final: 0.7997 (Cg_endo) REVERT: C 841 GLU cc_start: 0.7530 (mt-10) cc_final: 0.7211 (mt-10) REVERT: D 469 GLU cc_start: 0.8465 (mm-30) cc_final: 0.8217 (mm-30) REVERT: D 535 THR cc_start: 0.9194 (OUTLIER) cc_final: 0.8972 (p) REVERT: D 556 LEU cc_start: 0.9096 (mm) cc_final: 0.8818 (mp) REVERT: D 572 LEU cc_start: 0.9240 (mm) cc_final: 0.8425 (mm) REVERT: D 576 CYS cc_start: 0.8412 (m) cc_final: 0.7979 (m) REVERT: D 590 TYR cc_start: 0.7653 (p90) cc_final: 0.7172 (p90) REVERT: D 627 MET cc_start: 0.8147 (tpp) cc_final: 0.7209 (tpp) REVERT: D 639 ILE cc_start: 0.9028 (tp) cc_final: 0.8748 (tp) REVERT: D 792 HIS cc_start: 0.8767 (t70) cc_final: 0.8514 (t-170) REVERT: D 815 LEU cc_start: 0.9121 (mt) cc_final: 0.8766 (mp) outliers start: 24 outliers final: 8 residues processed: 275 average time/residue: 0.1061 time to fit residues: 44.9646 Evaluate side-chains 223 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 211 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 591 ASN Chi-restraints excluded: chain B residue 725 ILE Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 635 ILE Chi-restraints excluded: chain D residue 444 VAL Chi-restraints excluded: chain D residue 535 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 67 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 chunk 118 optimal weight: 3.9990 chunk 90 optimal weight: 0.5980 chunk 114 optimal weight: 0.6980 chunk 140 optimal weight: 2.9990 chunk 175 optimal weight: 7.9990 chunk 110 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 = 0.3936 r_free = 0.3936 target = 0.137238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.098322 restraints weight = 72704.754| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 5.41 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: 3 | |-----------------------------------------------------------------------------| |-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: 3 | |-----------------------------------------------------------------------------| r_final: 0.3373 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14450 Z= 0.180 Angle : 0.729 8.346 19554 Z= 0.374 Chirality : 0.044 0.158 2172 Planarity : 0.006 0.053 2474 Dihedral : 6.003 41.949 1936 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.28 % Allowed : 11.88 % Favored : 87.84 % Rotamer: Outliers : 2.45 % Allowed : 12.00 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.53 (0.19), residues: 1774 helix: -0.64 (0.16), residues: 880 sheet: -2.72 (0.43), residues: 126 loop : -2.75 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 583 TYR 0.016 0.002 TYR D 566 PHE 0.022 0.002 PHE D 735 TRP 0.022 0.002 TRP D 706 HIS 0.016 0.002 HIS C 593 Details of bonding type rmsd covalent geometry : bond 0.00422 (14446) covalent geometry : angle 0.72911 (19546) SS BOND : bond 0.00022 ( 4) SS BOND : angle 0.53081 ( 8) hydrogen bonds : bond 0.03627 ( 580) hydrogen bonds : angle 4.47849 ( 1706) *********************** 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 263 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 233 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 488 TYR cc_start: 0.8213 (m-80) cc_final: 0.7712 (m-80) REVERT: A 565 MET cc_start: 0.8536 (mmm) cc_final: 0.8244 (mmt) REVERT: A 635 ILE cc_start: 0.8851 (OUTLIER) cc_final: 0.8595 (mp) REVERT: A 651 TYR cc_start: 0.8886 (t80) cc_final: 0.8667 (t80) REVERT: A 761 SER cc_start: 0.8854 (t) cc_final: 0.8296 (m) REVERT: A 836 PHE cc_start: 0.8020 (m-80) cc_final: 0.7675 (m-10) REVERT: A 841 GLU cc_start: 0.7485 (mt-10) cc_final: 0.7198 (mt-10) REVERT: A 861 MET cc_start: 0.8447 (mmp) cc_final: 0.7725 (mtm) REVERT: B 465 ASP cc_start: 0.8773 (m-30) cc_final: 0.8571 (m-30) REVERT: B 469 GLU cc_start: 0.8642 (mm-30) cc_final: 0.8184 (mm-30) REVERT: B 572 LEU cc_start: 0.9214 (mm) cc_final: 0.8403 (mm) REVERT: B 576 CYS cc_start: 0.8545 (m) cc_final: 0.8084 (m) REVERT: B 584 PHE cc_start: 0.7871 (t80) cc_final: 0.7029 (m-10) REVERT: B 590 TYR cc_start: 0.7609 (p90) cc_final: 0.6997 (p90) REVERT: B 609 LEU cc_start: 0.8803 (tt) cc_final: 0.8136 (mt) REVERT: B 612 PHE cc_start: 0.8511 (m-80) cc_final: 0.8153 (t80) REVERT: B 639 ILE cc_start: 0.9012 (tp) cc_final: 0.8709 (tp) REVERT: B 709 MET cc_start: 0.8959 (mtt) cc_final: 0.8641 (mtt) REVERT: C 501 MET cc_start: 0.7878 (mtm) cc_final: 0.7651 (mtm) REVERT: C 565 MET cc_start: 0.8544 (mmm) cc_final: 0.8313 (mmm) REVERT: C 635 ILE cc_start: 0.8841 (OUTLIER) cc_final: 0.8565 (mp) REVERT: C 698 LYS cc_start: 0.9342 (mmtt) cc_final: 0.8874 (mmtt) REVERT: C 761 SER cc_start: 0.8843 (t) cc_final: 0.8346 (m) REVERT: C 805 PRO cc_start: 0.8325 (Cg_exo) cc_final: 0.8020 (Cg_endo) REVERT: C 841 GLU cc_start: 0.7565 (mt-10) cc_final: 0.7238 (mt-10) REVERT: D 556 LEU cc_start: 0.9141 (mm) cc_final: 0.8849 (mp) REVERT: D 572 LEU cc_start: 0.9179 (mm) cc_final: 0.8394 (mm) REVERT: D 576 CYS cc_start: 0.8460 (m) cc_final: 0.7984 (m) REVERT: D 590 TYR cc_start: 0.7526 (p90) cc_final: 0.6788 (p90) REVERT: D 639 ILE cc_start: 0.9033 (tp) cc_final: 0.8750 (tp) REVERT: D 737 MET cc_start: 0.8369 (ptt) cc_final: 0.8162 (ptm) REVERT: D 792 HIS cc_start: 0.8749 (t70) cc_final: 0.8475 (t-170) outliers start: 30 outliers final: 18 residues processed: 248 average time/residue: 0.1094 time to fit residues: 41.6804 Evaluate side-chains 233 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 213 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 866 ARG Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 565 MET Chi-restraints excluded: chain B residue 591 ASN Chi-restraints excluded: chain B residue 725 ILE Chi-restraints excluded: chain B residue 831 LEU Chi-restraints excluded: chain C residue 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 84 optimal weight: 5.9990 chunk 116 optimal weight: 0.7980 chunk 151 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 138 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 104 optimal weight: 0.7980 chunk 134 optimal weight: 0.9990 chunk 50 optimal weight: 0.6980 chunk 87 optimal weight: 10.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3962 r_free = 0.3962 target = 0.139145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.101482 restraints weight = 76116.318| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 5.28 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3406 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3406 r_free = 0.3406 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3406 r_free = 0.3406 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3406 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.3556 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= 0.141 Angle : 0.680 8.151 19554 Z= 0.348 Chirality : 0.043 0.163 2172 Planarity : 0.005 0.053 2474 Dihedral : 5.675 41.009 1936 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.28 % Allowed : 11.43 % Favored : 88.29 % Rotamer: Outliers : 2.52 % Allowed : 12.45 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.87 (0.19), residues: 1774 helix: 0.04 (0.17), residues: 874 sheet: -2.63 (0.43), residues: 126 loop : -2.55 (0.22), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 583 TYR 0.022 0.002 TYR C 651 PHE 0.031 0.002 PHE D 584 TRP 0.015 0.002 TRP D 589 HIS 0.013 0.002 HIS A 593 Details of bonding type rmsd covalent geometry : bond 0.00326 (14446) covalent geometry : angle 0.68008 (19546) SS BOND : bond 0.00047 ( 4) SS BOND : angle 0.34700 ( 8) hydrogen bonds : bond 0.03238 ( 580) hydrogen bonds : angle 4.22906 ( 1706) *********************** 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 262 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 231 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 565 MET cc_start: 0.8496 (mmm) cc_final: 0.8218 (mmt) REVERT: A 635 ILE cc_start: 0.8855 (OUTLIER) cc_final: 0.8598 (mp) REVERT: A 651 TYR cc_start: 0.8760 (t80) cc_final: 0.8482 (t80) REVERT: A 761 SER cc_start: 0.8851 (t) cc_final: 0.8334 (m) REVERT: A 810 LYS cc_start: 0.8259 (mmtt) cc_final: 0.7933 (mmtm) REVERT: A 836 PHE cc_start: 0.8129 (m-80) cc_final: 0.7759 (m-10) REVERT: A 841 GLU cc_start: 0.7562 (mt-10) cc_final: 0.7312 (mt-10) REVERT: A 861 MET cc_start: 0.8427 (mmp) cc_final: 0.7738 (mtm) REVERT: A 866 ARG cc_start: 0.7286 (OUTLIER) cc_final: 0.6184 (tmm-80) REVERT: B 443 TYR cc_start: 0.8181 (m-80) cc_final: 0.7695 (m-80) REVERT: B 469 GLU cc_start: 0.8551 (mm-30) cc_final: 0.8315 (mm-30) REVERT: B 572 LEU cc_start: 0.9153 (mm) cc_final: 0.8359 (mm) REVERT: B 576 CYS cc_start: 0.8508 (m) cc_final: 0.7864 (m) REVERT: B 580 VAL cc_start: 0.9356 (t) cc_final: 0.9103 (m) REVERT: B 584 PHE cc_start: 0.7902 (t80) cc_final: 0.7009 (m-10) REVERT: B 590 TYR cc_start: 0.7462 (p90) cc_final: 0.6850 (p90) REVERT: B 609 LEU cc_start: 0.8710 (tt) cc_final: 0.8026 (mt) REVERT: B 612 PHE cc_start: 0.8372 (m-80) cc_final: 0.8090 (t80) REVERT: B 639 ILE cc_start: 0.8972 (tp) cc_final: 0.8675 (tp) REVERT: B 709 MET cc_start: 0.8976 (mtt) cc_final: 0.8659 (mtt) REVERT: B 800 ARG cc_start: 0.8522 (tpp80) cc_final: 0.8163 (ttp80) REVERT: C 501 MET cc_start: 0.7874 (mtm) cc_final: 0.7628 (mtm) REVERT: C 565 MET cc_start: 0.8500 (mmm) cc_final: 0.8238 (mmt) REVERT: C 589 TRP cc_start: 0.8270 (m100) cc_final: 0.8067 (m100) REVERT: C 635 ILE cc_start: 0.8821 (OUTLIER) cc_final: 0.8586 (mp) REVERT: C 651 TYR cc_start: 0.8634 (t80) cc_final: 0.8414 (t80) REVERT: C 698 LYS cc_start: 0.9360 (mmtt) cc_final: 0.8917 (mmtt) REVERT: C 761 SER cc_start: 0.8816 (t) cc_final: 0.8368 (m) REVERT: C 805 PRO cc_start: 0.8358 (Cg_exo) cc_final: 0.8072 (Cg_endo) REVERT: C 810 LYS cc_start: 0.8273 (mmtt) cc_final: 0.7787 (mmtp) REVERT: C 841 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7576 (mt-10) REVERT: D 572 LEU cc_start: 0.9160 (mm) cc_final: 0.8330 (mm) REVERT: D 576 CYS cc_start: 0.8444 (m) cc_final: 0.7976 (m) REVERT: D 590 TYR cc_start: 0.7731 (p90) cc_final: 0.7397 (p90) REVERT: D 612 PHE cc_start: 0.8359 (m-80) cc_final: 0.7939 (t80) REVERT: D 625 GLU cc_start: 0.8241 (pt0) cc_final: 0.7923 (pt0) REVERT: D 639 ILE cc_start: 0.9040 (tp) cc_final: 0.8770 (tp) outliers start: 31 outliers final: 18 residues processed: 250 average time/residue: 0.1105 time to fit residues: 42.5238 Evaluate side-chains 229 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 208 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 635 ILE Chi-restraints excluded: chain A residue 668 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 626 LEU Chi-restraints excluded: chain B residue 725 ILE Chi-restraints excluded: chain B residue 831 LEU Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 635 ILE Chi-restraints excluded: chain C residue 668 ILE Chi-restraints excluded: chain D residue 444 VAL Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 565 MET Chi-restraints excluded: chain D residue 831 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 130 optimal weight: 6.9990 chunk 126 optimal weight: 9.9990 chunk 39 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 134 optimal weight: 0.0370 chunk 54 optimal weight: 3.9990 chunk 112 optimal weight: 6.9990 chunk 106 optimal weight: 0.8980 chunk 114 optimal weight: 5.9990 chunk 2 optimal weight: 0.8980 overall best weight: 1.7662 ------------------------------------------------------------------------------- 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 = 0.3927 r_free = 0.3927 target = 0.136513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.098294 restraints weight = 63152.774| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 5.11 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3328 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3328 r_free = 0.3328 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3328 r_free = 0.3328 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3328 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.3768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 14450 Z= 0.219 Angle : 0.718 10.845 19554 Z= 0.367 Chirality : 0.045 0.139 2172 Planarity : 0.005 0.069 2474 Dihedral : 5.662 38.380 1936 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.28 % Allowed : 12.33 % Favored : 87.39 % Rotamer: Outliers : 2.58 % Allowed : 13.23 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.69 (0.20), residues: 1774 helix: 0.21 (0.17), residues: 876 sheet: -2.51 (0.41), residues: 140 loop : -2.48 (0.22), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 855 TYR 0.018 0.002 TYR C 651 PHE 0.023 0.002 PHE D 476 TRP 0.031 0.002 TRP A 589 HIS 0.011 0.002 HIS C 593 Details of bonding type rmsd covalent geometry : bond 0.00513 (14446) covalent geometry : angle 0.71830 (19546) SS BOND : bond 0.00086 ( 4) SS BOND : angle 0.38681 ( 8) hydrogen bonds : bond 0.03386 ( 580) hydrogen bonds : angle 4.25374 ( 1706) *********************** 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 248 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 216 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 565 MET cc_start: 0.8530 (mmm) cc_final: 0.8264 (mmt) REVERT: A 635 ILE cc_start: 0.8812 (OUTLIER) cc_final: 0.8513 (mp) REVERT: A 651 TYR cc_start: 0.8906 (t80) cc_final: 0.8562 (t80) REVERT: A 705 MET cc_start: 0.8890 (mmm) cc_final: 0.8293 (mmm) REVERT: A 810 LYS cc_start: 0.8248 (mmtt) cc_final: 0.7942 (mmtm) REVERT: A 836 PHE cc_start: 0.8309 (m-80) cc_final: 0.7778 (m-10) REVERT: A 841 GLU cc_start: 0.7580 (mt-10) cc_final: 0.7334 (mt-10) REVERT: A 861 MET cc_start: 0.8359 (mmp) cc_final: 0.7586 (mtm) REVERT: A 866 ARG cc_start: 0.7305 (OUTLIER) cc_final: 0.6352 (tmm-80) REVERT: B 443 TYR cc_start: 0.8238 (m-80) cc_final: 0.7776 (m-80) REVERT: B 572 LEU cc_start: 0.9100 (mm) cc_final: 0.8300 (mm) REVERT: B 576 CYS cc_start: 0.8507 (m) cc_final: 0.8032 (m) REVERT: B 584 PHE cc_start: 0.7984 (t80) cc_final: 0.7069 (m-10) REVERT: B 590 TYR cc_start: 0.7535 (p90) cc_final: 0.6955 (p90) REVERT: B 612 PHE cc_start: 0.8421 (m-80) cc_final: 0.8149 (t80) REVERT: B 639 ILE cc_start: 0.9078 (tp) cc_final: 0.8788 (tp) REVERT: B 709 MET cc_start: 0.8978 (mtt) cc_final: 0.8672 (mtt) REVERT: B 800 ARG cc_start: 0.8612 (tpp80) cc_final: 0.8048 (tpt90) REVERT: C 501 MET cc_start: 0.7889 (mtm) cc_final: 0.7654 (mtm) REVERT: C 565 MET cc_start: 0.8532 (mmm) cc_final: 0.8262 (mmt) REVERT: C 635 ILE cc_start: 0.8796 (OUTLIER) cc_final: 0.8535 (mp) REVERT: C 698 LYS cc_start: 0.9369 (mmtt) cc_final: 0.8862 (mmtm) REVERT: C 705 MET cc_start: 0.8733 (mmt) cc_final: 0.8395 (mmm) REVERT: C 761 SER cc_start: 0.8868 (t) cc_final: 0.8407 (m) REVERT: C 805 PRO cc_start: 0.8318 (Cg_exo) cc_final: 0.8094 (Cg_endo) REVERT: C 810 LYS cc_start: 0.8188 (mmtt) cc_final: 0.7714 (mmpt) REVERT: C 836 PHE cc_start: 0.8124 (m-80) cc_final: 0.7778 (m-10) REVERT: C 841 GLU cc_start: 0.7451 (mt-10) cc_final: 0.7149 (mt-10) REVERT: D 572 LEU cc_start: 0.9116 (mm) cc_final: 0.8297 (mm) REVERT: D 576 CYS cc_start: 0.8523 (m) cc_final: 0.8041 (m) REVERT: D 612 PHE cc_start: 0.8409 (m-80) cc_final: 0.7987 (t80) REVERT: D 625 GLU cc_start: 0.8226 (pt0) cc_final: 0.7997 (pt0) REVERT: D 639 ILE cc_start: 0.9067 (tp) cc_final: 0.8791 (tp) REVERT: D 861 MET cc_start: 0.8176 (ppp) cc_final: 0.7437 (ttt) outliers start: 32 outliers final: 19 residues processed: 233 average time/residue: 0.1154 time to fit residues: 41.1683 Evaluate side-chains 221 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 199 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 668 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 750 CYS Chi-restraints excluded: chain B residue 831 LEU 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 C residue 668 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 626 LEU Chi-restraints excluded: chain D residue 823 ILE Chi-restraints excluded: chain D residue 831 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 130 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 142 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 128 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 139 optimal weight: 0.2980 chunk 99 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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 = 0.3925 r_free = 0.3925 target = 0.138504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.097698 restraints weight = 68683.339| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 4.91 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3338 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3338 r_free = 0.3338 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3338 r_free = 0.3338 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3338 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.3981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14450 Z= 0.183 Angle : 0.703 11.026 19554 Z= 0.356 Chirality : 0.044 0.142 2172 Planarity : 0.005 0.070 2474 Dihedral : 5.579 37.177 1936 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.23 % Allowed : 12.10 % Favored : 87.67 % Rotamer: Outliers : 2.45 % Allowed : 14.00 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.48 (0.20), residues: 1774 helix: 0.43 (0.17), residues: 880 sheet: -2.45 (0.41), residues: 140 loop : -2.45 (0.22), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 458 TYR 0.032 0.002 TYR C 651 PHE 0.029 0.002 PHE D 584 TRP 0.025 0.002 TRP A 589 HIS 0.010 0.001 HIS A 593 Details of bonding type rmsd covalent geometry : bond 0.00434 (14446) covalent geometry : angle 0.70353 (19546) SS BOND : bond 0.00021 ( 4) SS BOND : angle 0.27379 ( 8) hydrogen bonds : bond 0.03278 ( 580) hydrogen bonds : angle 4.17829 ( 1706) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 212 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 565 MET cc_start: 0.8523 (mmm) cc_final: 0.8254 (mmt) REVERT: A 635 ILE cc_start: 0.8802 (OUTLIER) cc_final: 0.8569 (mp) REVERT: A 761 SER cc_start: 0.8826 (t) cc_final: 0.8321 (m) REVERT: A 810 LYS cc_start: 0.8272 (mmtt) cc_final: 0.7961 (mmtm) REVERT: A 836 PHE cc_start: 0.8457 (m-80) cc_final: 0.7908 (m-10) REVERT: A 841 GLU cc_start: 0.7728 (mt-10) cc_final: 0.7480 (mt-10) REVERT: A 861 MET cc_start: 0.8371 (mmp) cc_final: 0.7552 (mtm) REVERT: B 443 TYR cc_start: 0.8168 (m-80) cc_final: 0.7695 (m-80) REVERT: B 572 LEU cc_start: 0.9154 (mm) cc_final: 0.8456 (mm) REVERT: B 576 CYS cc_start: 0.8412 (m) cc_final: 0.8011 (m) REVERT: B 584 PHE cc_start: 0.7885 (t80) cc_final: 0.6993 (m-10) REVERT: B 590 TYR cc_start: 0.7337 (p90) cc_final: 0.6643 (p90) REVERT: B 609 LEU cc_start: 0.8822 (tt) cc_final: 0.8058 (mt) REVERT: B 612 PHE cc_start: 0.8411 (m-80) cc_final: 0.8160 (t80) REVERT: B 639 ILE cc_start: 0.9123 (tp) cc_final: 0.8836 (tp) REVERT: B 709 MET cc_start: 0.9036 (mtt) cc_final: 0.8745 (mtt) REVERT: B 800 ARG cc_start: 0.8528 (tpp80) cc_final: 0.8027 (tpt90) REVERT: C 501 MET cc_start: 0.7867 (mtm) cc_final: 0.7631 (mtm) REVERT: C 565 MET cc_start: 0.8544 (mmm) cc_final: 0.8265 (mmt) REVERT: C 761 SER cc_start: 0.8825 (t) cc_final: 0.8346 (m) REVERT: C 805 PRO cc_start: 0.8358 (Cg_exo) cc_final: 0.8064 (Cg_endo) REVERT: C 810 LYS cc_start: 0.8162 (mmtt) cc_final: 0.7689 (mmpt) REVERT: C 836 PHE cc_start: 0.8132 (m-80) cc_final: 0.7783 (m-10) REVERT: C 841 GLU cc_start: 0.7458 (mt-10) cc_final: 0.7188 (mt-10) REVERT: D 572 LEU cc_start: 0.9143 (mm) cc_final: 0.8331 (mm) REVERT: D 576 CYS cc_start: 0.8466 (m) cc_final: 0.8020 (m) REVERT: D 612 PHE cc_start: 0.8382 (m-80) cc_final: 0.7975 (t80) REVERT: D 625 GLU cc_start: 0.8108 (pt0) cc_final: 0.7907 (pt0) REVERT: D 639 ILE cc_start: 0.9096 (tp) cc_final: 0.8801 (tp) REVERT: D 709 MET cc_start: 0.9005 (mtt) cc_final: 0.8657 (mtt) REVERT: D 861 MET cc_start: 0.8512 (ppp) cc_final: 0.7727 (ttt) outliers start: 30 outliers final: 21 residues processed: 226 average time/residue: 0.1070 time to fit residues: 37.6635 Evaluate side-chains 224 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 202 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 571 CYS Chi-restraints excluded: chain A residue 635 ILE 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 750 CYS Chi-restraints excluded: chain B residue 823 ILE Chi-restraints excluded: chain B residue 831 LEU 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 668 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 626 LEU Chi-restraints excluded: chain D residue 823 ILE Chi-restraints excluded: chain D residue 831 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 74 optimal weight: 0.9980 chunk 99 optimal weight: 0.9990 chunk 16 optimal weight: 0.0570 chunk 53 optimal weight: 0.6980 chunk 151 optimal weight: 0.6980 chunk 25 optimal weight: 9.9990 chunk 162 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 114 optimal weight: 0.9990 chunk 46 optimal weight: 0.0370 chunk 10 optimal weight: 0.6980 overall best weight: 0.4376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 591 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.137238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.098437 restraints weight = 73261.908| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 5.41 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 = 0.08 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3380 r_free = 0.3380 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3380 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.4217 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= 0.121 Angle : 0.672 10.138 19554 Z= 0.338 Chirality : 0.042 0.148 2172 Planarity : 0.005 0.070 2474 Dihedral : 5.344 41.474 1936 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.11 % Allowed : 11.31 % Favored : 88.57 % Rotamer: Outliers : 1.74 % Allowed : 14.90 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.23 (0.20), residues: 1774 helix: 0.72 (0.18), residues: 892 sheet: -2.70 (0.45), residues: 108 loop : -2.46 (0.22), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 583 TYR 0.012 0.001 TYR C 542 PHE 0.022 0.001 PHE B 658 TRP 0.019 0.001 TRP A 589 HIS 0.009 0.001 HIS C 593 Details of bonding type rmsd covalent geometry : bond 0.00273 (14446) covalent geometry : angle 0.67236 (19546) SS BOND : bond 0.00044 ( 4) SS BOND : angle 0.28115 ( 8) hydrogen bonds : bond 0.03015 ( 580) hydrogen bonds : angle 4.02682 ( 1706) *********************** 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 252 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 233 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 565 MET cc_start: 0.8515 (mmm) cc_final: 0.8244 (mmt) REVERT: A 651 TYR cc_start: 0.8829 (t80) cc_final: 0.8610 (t80) REVERT: A 686 GLU cc_start: 0.6802 (tp30) cc_final: 0.6346 (tt0) REVERT: A 702 TYR cc_start: 0.9142 (m-10) cc_final: 0.8857 (m-80) REVERT: A 761 SER cc_start: 0.8842 (t) cc_final: 0.8334 (m) REVERT: A 810 LYS cc_start: 0.8269 (mmtt) cc_final: 0.7905 (mmtm) REVERT: A 836 PHE cc_start: 0.8208 (m-80) cc_final: 0.7792 (m-10) REVERT: A 841 GLU cc_start: 0.7423 (mt-10) cc_final: 0.6818 (mm-30) REVERT: A 861 MET cc_start: 0.8357 (mmp) cc_final: 0.7498 (mtm) REVERT: B 443 TYR cc_start: 0.7969 (m-80) cc_final: 0.7422 (m-80) REVERT: B 572 LEU cc_start: 0.9251 (mm) cc_final: 0.8573 (mm) REVERT: B 576 CYS cc_start: 0.8506 (m) cc_final: 0.8074 (m) REVERT: B 584 PHE cc_start: 0.8161 (t80) cc_final: 0.7008 (m-10) REVERT: B 590 TYR cc_start: 0.7276 (p90) cc_final: 0.6505 (p90) REVERT: B 609 LEU cc_start: 0.8746 (tt) cc_final: 0.7971 (mt) REVERT: B 612 PHE cc_start: 0.8358 (m-80) cc_final: 0.8105 (t80) REVERT: B 709 MET cc_start: 0.8959 (mtt) cc_final: 0.8623 (mtt) REVERT: B 800 ARG cc_start: 0.8543 (tpp80) cc_final: 0.7961 (tpt90) REVERT: C 501 MET cc_start: 0.7729 (mtm) cc_final: 0.7462 (mtm) REVERT: C 565 MET cc_start: 0.8560 (mmm) cc_final: 0.8328 (mmt) REVERT: C 626 LEU cc_start: 0.8588 (mt) cc_final: 0.8381 (mt) REVERT: C 698 LYS cc_start: 0.9472 (mmtt) cc_final: 0.8915 (mmtm) REVERT: C 761 SER cc_start: 0.8793 (t) cc_final: 0.8325 (m) REVERT: C 805 PRO cc_start: 0.8267 (Cg_exo) cc_final: 0.7963 (Cg_endo) REVERT: C 810 LYS cc_start: 0.8097 (mmtt) cc_final: 0.7647 (mmpt) REVERT: C 836 PHE cc_start: 0.8175 (m-80) cc_final: 0.7817 (m-10) REVERT: C 841 GLU cc_start: 0.7616 (mt-10) cc_final: 0.6954 (mm-30) REVERT: D 572 LEU cc_start: 0.9128 (mm) cc_final: 0.8290 (mm) REVERT: D 576 CYS cc_start: 0.8525 (m) cc_final: 0.8086 (m) REVERT: D 612 PHE cc_start: 0.8351 (m-80) cc_final: 0.7848 (t80) REVERT: D 639 ILE cc_start: 0.8997 (tp) cc_final: 0.8733 (tp) REVERT: D 861 MET cc_start: 0.8413 (ppp) cc_final: 0.7600 (ttt) outliers start: 19 outliers final: 15 residues processed: 242 average time/residue: 0.1040 time to fit residues: 39.3552 Evaluate side-chains 223 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 208 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 867 MET Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 565 MET 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 482 LEU Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 668 ILE Chi-restraints excluded: chain D residue 444 VAL Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 565 MET Chi-restraints excluded: chain D residue 831 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 11 optimal weight: 0.0670 chunk 142 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 135 optimal weight: 0.9980 chunk 140 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 16 optimal weight: 9.9990 chunk 172 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 98 optimal weight: 0.6980 chunk 133 optimal weight: 1.9990 overall best weight: 0.6718 ------------------------------------------------------------------------------- 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 = 0.3937 r_free = 0.3937 target = 0.137597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.099504 restraints weight = 70366.872| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 5.18 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3383 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3383 r_free = 0.3383 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3383 r_free = 0.3383 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3383 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.4343 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= 0.133 Angle : 0.678 10.287 19554 Z= 0.341 Chirality : 0.042 0.180 2172 Planarity : 0.005 0.071 2474 Dihedral : 5.279 40.912 1936 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.11 % Allowed : 11.43 % Favored : 88.46 % Rotamer: Outliers : 1.81 % Allowed : 15.16 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.10 (0.21), residues: 1774 helix: 0.81 (0.18), residues: 892 sheet: -2.68 (0.45), residues: 108 loop : -2.37 (0.23), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 583 TYR 0.012 0.001 TYR C 542 PHE 0.036 0.001 PHE B 476 TRP 0.040 0.002 TRP C 589 HIS 0.008 0.001 HIS C 593 Details of bonding type rmsd covalent geometry : bond 0.00306 (14446) covalent geometry : angle 0.67783 (19546) SS BOND : bond 0.00048 ( 4) SS BOND : angle 0.45754 ( 8) hydrogen bonds : bond 0.02944 ( 580) hydrogen bonds : angle 3.99199 ( 1706) *********************** 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 236 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 216 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 565 MET cc_start: 0.8495 (mmm) cc_final: 0.8231 (mmt) REVERT: A 651 TYR cc_start: 0.8828 (t80) cc_final: 0.8606 (t80) REVERT: A 761 SER cc_start: 0.8818 (t) cc_final: 0.8327 (m) REVERT: A 810 LYS cc_start: 0.8251 (mmtt) cc_final: 0.7629 (mmtm) REVERT: A 836 PHE cc_start: 0.8136 (m-80) cc_final: 0.7760 (m-10) REVERT: A 841 GLU cc_start: 0.7395 (mt-10) cc_final: 0.7008 (mm-30) REVERT: A 861 MET cc_start: 0.8360 (mmp) cc_final: 0.7463 (mtm) REVERT: B 443 TYR cc_start: 0.7989 (m-80) cc_final: 0.7458 (m-80) REVERT: B 572 LEU cc_start: 0.9246 (mm) cc_final: 0.8560 (mm) REVERT: B 576 CYS cc_start: 0.8444 (m) cc_final: 0.8037 (m) REVERT: B 584 PHE cc_start: 0.8174 (t80) cc_final: 0.7017 (m-10) REVERT: B 590 TYR cc_start: 0.7265 (p90) cc_final: 0.6520 (p90) REVERT: B 609 LEU cc_start: 0.8730 (tt) cc_final: 0.7980 (mt) REVERT: B 612 PHE cc_start: 0.8380 (m-80) cc_final: 0.8157 (t80) REVERT: B 709 MET cc_start: 0.8953 (mtt) cc_final: 0.8630 (mtt) REVERT: B 800 ARG cc_start: 0.8496 (tpp80) cc_final: 0.7932 (tpt90) REVERT: C 501 MET cc_start: 0.7817 (mtm) cc_final: 0.7540 (mtm) REVERT: C 565 MET cc_start: 0.8569 (mmm) cc_final: 0.8284 (mmt) REVERT: C 612 PHE cc_start: 0.8311 (m-10) cc_final: 0.8097 (m-80) REVERT: C 698 LYS cc_start: 0.9458 (mmtt) cc_final: 0.8906 (mmtm) REVERT: C 761 SER cc_start: 0.8792 (t) cc_final: 0.8325 (m) REVERT: C 805 PRO cc_start: 0.8298 (Cg_exo) cc_final: 0.7979 (Cg_endo) REVERT: C 810 LYS cc_start: 0.8082 (mmtt) cc_final: 0.7579 (mmpt) REVERT: C 836 PHE cc_start: 0.8136 (m-80) cc_final: 0.7763 (m-10) REVERT: C 841 GLU cc_start: 0.7562 (mt-10) cc_final: 0.6965 (mm-30) REVERT: D 572 LEU cc_start: 0.9104 (mm) cc_final: 0.8258 (mm) REVERT: D 576 CYS cc_start: 0.8544 (m) cc_final: 0.8086 (m) REVERT: D 612 PHE cc_start: 0.8335 (m-80) cc_final: 0.7857 (t80) REVERT: D 639 ILE cc_start: 0.8951 (tp) cc_final: 0.8670 (tp) REVERT: D 709 MET cc_start: 0.8835 (mtt) cc_final: 0.8580 (mtt) REVERT: D 861 MET cc_start: 0.8361 (ppp) cc_final: 0.7594 (ttt) outliers start: 20 outliers final: 18 residues processed: 224 average time/residue: 0.1065 time to fit residues: 37.3886 Evaluate side-chains 226 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 208 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 535 THR Chi-restraints excluded: chain B residue 565 MET 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 482 LEU Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 668 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 626 LEU Chi-restraints excluded: chain D residue 831 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 20 optimal weight: 4.9990 chunk 128 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 32 optimal weight: 0.4980 chunk 1 optimal weight: 3.9990 chunk 95 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 chunk 28 optimal weight: 6.9990 chunk 156 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3936 r_free = 0.3936 target = 0.137381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.098933 restraints weight = 64057.698| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 5.08 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3383 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3383 r_free = 0.3383 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3383 r_free = 0.3383 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3383 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.4448 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= 0.132 Angle : 0.685 10.029 19554 Z= 0.343 Chirality : 0.043 0.226 2172 Planarity : 0.005 0.072 2474 Dihedral : 5.231 41.195 1936 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.11 % Allowed : 11.03 % Favored : 88.86 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.01 (0.21), residues: 1774 helix: 0.88 (0.18), residues: 894 sheet: -2.67 (0.44), residues: 108 loop : -2.31 (0.23), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 583 TYR 0.019 0.001 TYR A 651 PHE 0.017 0.001 PHE B 658 TRP 0.033 0.002 TRP C 589 HIS 0.008 0.001 HIS C 593 Details of bonding type rmsd covalent geometry : bond 0.00306 (14446) covalent geometry : angle 0.68474 (19546) SS BOND : bond 0.00045 ( 4) SS BOND : angle 0.53833 ( 8) hydrogen bonds : bond 0.02965 ( 580) hydrogen bonds : angle 3.98739 ( 1706) *********************** 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 235 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 216 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 565 MET cc_start: 0.8472 (mmm) cc_final: 0.8196 (mmt) REVERT: A 589 TRP cc_start: 0.8058 (m100) cc_final: 0.7771 (m100) REVERT: A 761 SER cc_start: 0.8833 (t) cc_final: 0.8351 (m) REVERT: A 836 PHE cc_start: 0.8132 (m-80) cc_final: 0.7745 (m-10) REVERT: A 841 GLU cc_start: 0.7391 (mt-10) cc_final: 0.6930 (mm-30) REVERT: A 861 MET cc_start: 0.8387 (mmp) cc_final: 0.7512 (mtm) REVERT: B 443 TYR cc_start: 0.7982 (m-80) cc_final: 0.7467 (m-80) REVERT: B 572 LEU cc_start: 0.9242 (mm) cc_final: 0.8558 (mm) REVERT: B 576 CYS cc_start: 0.8472 (m) cc_final: 0.8060 (m) REVERT: B 584 PHE cc_start: 0.8171 (t80) cc_final: 0.7039 (m-10) REVERT: B 590 TYR cc_start: 0.7316 (p90) cc_final: 0.6758 (p90) REVERT: B 609 LEU cc_start: 0.8806 (tt) cc_final: 0.8026 (mt) REVERT: B 612 PHE cc_start: 0.8421 (m-80) cc_final: 0.8149 (t80) REVERT: B 709 MET cc_start: 0.8945 (mtt) cc_final: 0.8625 (mtt) REVERT: B 778 ILE cc_start: 0.9263 (mt) cc_final: 0.9005 (mm) REVERT: B 800 ARG cc_start: 0.8444 (tpp80) cc_final: 0.7868 (tpt90) REVERT: C 501 MET cc_start: 0.7790 (mtm) cc_final: 0.7525 (mtm) REVERT: C 565 MET cc_start: 0.8559 (mmm) cc_final: 0.8263 (mmt) REVERT: C 698 LYS cc_start: 0.9433 (mmtt) cc_final: 0.8924 (mmtt) REVERT: C 761 SER cc_start: 0.8794 (t) cc_final: 0.8329 (m) REVERT: C 805 PRO cc_start: 0.8310 (Cg_exo) cc_final: 0.7993 (Cg_endo) REVERT: C 810 LYS cc_start: 0.8083 (mmtt) cc_final: 0.7598 (mmpt) REVERT: C 836 PHE cc_start: 0.8129 (m-80) cc_final: 0.7753 (m-10) REVERT: C 841 GLU cc_start: 0.7526 (mt-10) cc_final: 0.6954 (mm-30) REVERT: D 572 LEU cc_start: 0.9197 (mm) cc_final: 0.8368 (mm) REVERT: D 576 CYS cc_start: 0.8526 (m) cc_final: 0.8060 (m) REVERT: D 612 PHE cc_start: 0.8356 (m-80) cc_final: 0.7839 (t80) REVERT: D 639 ILE cc_start: 0.8962 (tp) cc_final: 0.8677 (tp) REVERT: D 709 MET cc_start: 0.8865 (mtt) cc_final: 0.8515 (mtm) REVERT: D 800 ARG cc_start: 0.8397 (tpp80) cc_final: 0.7951 (tpt90) REVERT: D 861 MET cc_start: 0.8351 (ppp) cc_final: 0.7605 (ttt) outliers start: 19 outliers final: 18 residues processed: 222 average time/residue: 0.1049 time to fit residues: 36.8237 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 : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 535 THR Chi-restraints excluded: chain B residue 565 MET 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 482 LEU Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 668 ILE 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 831 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 98 optimal weight: 0.7980 chunk 155 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 170 optimal weight: 5.9990 chunk 70 optimal weight: 0.9980 chunk 75 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 138 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.3937 r_free = 0.3937 target = 0.137598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.099094 restraints weight = 71855.621| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 5.18 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3369 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3369 r_free = 0.3369 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 = 0.3369 r_free = 0.3369 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3369 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.4537 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= 0.145 Angle : 0.694 9.917 19554 Z= 0.348 Chirality : 0.043 0.176 2172 Planarity : 0.005 0.073 2474 Dihedral : 5.258 42.365 1936 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.11 % Allowed : 11.31 % Favored : 88.57 % Rotamer: Outliers : 1.81 % Allowed : 15.94 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.99 (0.21), residues: 1774 helix: 0.88 (0.18), residues: 894 sheet: -2.64 (0.45), residues: 108 loop : -2.29 (0.23), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 583 TYR 0.021 0.001 TYR A 702 PHE 0.015 0.001 PHE C 735 TRP 0.024 0.002 TRP C 589 HIS 0.007 0.001 HIS C 593 Details of bonding type rmsd covalent geometry : bond 0.00338 (14446) covalent geometry : angle 0.69428 (19546) SS BOND : bond 0.00035 ( 4) SS BOND : angle 0.46479 ( 8) hydrogen bonds : bond 0.03029 ( 580) hydrogen bonds : angle 3.99392 ( 1706) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 211 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 565 MET cc_start: 0.8468 (mmm) cc_final: 0.8197 (mmt) REVERT: A 761 SER cc_start: 0.8596 (t) cc_final: 0.8152 (m) REVERT: A 836 PHE cc_start: 0.8069 (m-80) cc_final: 0.7693 (m-10) REVERT: A 841 GLU cc_start: 0.7402 (mt-10) cc_final: 0.6956 (mm-30) REVERT: A 861 MET cc_start: 0.8446 (mmp) cc_final: 0.7572 (mtm) REVERT: B 443 TYR cc_start: 0.8094 (m-80) cc_final: 0.7627 (m-80) REVERT: B 572 LEU cc_start: 0.9251 (mm) cc_final: 0.8561 (mm) REVERT: B 576 CYS cc_start: 0.8439 (m) cc_final: 0.8041 (m) REVERT: B 584 PHE cc_start: 0.8206 (t80) cc_final: 0.7078 (m-10) REVERT: B 590 TYR cc_start: 0.7531 (p90) cc_final: 0.6975 (p90) REVERT: B 609 LEU cc_start: 0.8815 (tt) cc_final: 0.8046 (mt) REVERT: B 612 PHE cc_start: 0.8409 (m-80) cc_final: 0.8156 (t80) REVERT: B 627 MET cc_start: 0.8040 (tpp) cc_final: 0.7592 (tpp) REVERT: B 691 MET cc_start: 0.7418 (ptm) cc_final: 0.7137 (ttp) REVERT: B 709 MET cc_start: 0.8970 (mtt) cc_final: 0.8663 (mtt) REVERT: B 778 ILE cc_start: 0.9272 (mt) cc_final: 0.9029 (mm) REVERT: B 800 ARG cc_start: 0.8437 (tpp80) cc_final: 0.7937 (tpt90) REVERT: C 501 MET cc_start: 0.7828 (mtm) cc_final: 0.7564 (mtm) REVERT: C 565 MET cc_start: 0.8546 (mmm) cc_final: 0.8260 (mmt) REVERT: C 626 LEU cc_start: 0.8605 (mt) cc_final: 0.8376 (mt) REVERT: C 698 LYS cc_start: 0.9408 (mmtt) cc_final: 0.8825 (mmtm) REVERT: C 761 SER cc_start: 0.8772 (t) cc_final: 0.8307 (m) REVERT: C 805 PRO cc_start: 0.8259 (Cg_exo) cc_final: 0.7966 (Cg_endo) REVERT: C 810 LYS cc_start: 0.7993 (mmtt) cc_final: 0.7486 (mmpt) REVERT: C 836 PHE cc_start: 0.8112 (m-80) cc_final: 0.7756 (m-10) REVERT: C 841 GLU cc_start: 0.7537 (mt-10) cc_final: 0.6971 (mm-30) REVERT: D 572 LEU cc_start: 0.9215 (mm) cc_final: 0.8409 (mm) REVERT: D 576 CYS cc_start: 0.8534 (m) cc_final: 0.8082 (m) REVERT: D 612 PHE cc_start: 0.8338 (m-80) cc_final: 0.7847 (t80) REVERT: D 639 ILE cc_start: 0.8973 (tp) cc_final: 0.8695 (tp) REVERT: D 709 MET cc_start: 0.8906 (mtt) cc_final: 0.8569 (mtm) REVERT: D 778 ILE cc_start: 0.9293 (mt) cc_final: 0.9081 (mm) REVERT: D 800 ARG cc_start: 0.8388 (tpp80) cc_final: 0.7976 (tpt90) REVERT: D 861 MET cc_start: 0.8325 (ppp) cc_final: 0.7568 (ttt) outliers start: 20 outliers final: 19 residues processed: 218 average time/residue: 0.0993 time to fit residues: 34.3318 Evaluate side-chains 227 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 208 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 535 THR Chi-restraints excluded: chain B residue 565 MET 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 482 LEU Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 668 ILE 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 810 LYS Chi-restraints excluded: chain D residue 831 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 67 optimal weight: 0.1980 chunk 51 optimal weight: 0.8980 chunk 124 optimal weight: 0.8980 chunk 173 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 117 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 105 optimal weight: 7.9990 chunk 32 optimal weight: 0.3980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.138441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.099885 restraints weight = 75780.567| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 5.35 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3382 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3382 r_free = 0.3382 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3382 r_free = 0.3382 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3382 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.4616 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= 0.132 Angle : 0.687 9.925 19554 Z= 0.345 Chirality : 0.043 0.210 2172 Planarity : 0.005 0.073 2474 Dihedral : 5.210 39.813 1936 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.80 % Favored : 89.08 % Rotamer: Outliers : 1.87 % Allowed : 15.94 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.91 (0.21), residues: 1774 helix: 0.93 (0.18), residues: 894 sheet: -2.56 (0.44), residues: 106 loop : -2.24 (0.23), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 583 TYR 0.019 0.001 TYR A 702 PHE 0.020 0.001 PHE D 658 TRP 0.022 0.002 TRP C 589 HIS 0.006 0.001 HIS C 593 Details of bonding type rmsd covalent geometry : bond 0.00306 (14446) covalent geometry : angle 0.68661 (19546) SS BOND : bond 0.00030 ( 4) SS BOND : angle 0.54086 ( 8) hydrogen bonds : bond 0.02988 ( 580) hydrogen bonds : angle 3.98159 ( 1706) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3052.60 seconds wall clock time: 53 minutes 21.87 seconds (3201.87 seconds total)