Starting phenix.real_space_refine on Thu Sep 26 21:14:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b35_44128/09_2024/9b35_44128.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b35_44128/09_2024/9b35_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b35_44128/09_2024/9b35_44128.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b35_44128/09_2024/9b35_44128.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b35_44128/09_2024/9b35_44128.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b35_44128/09_2024/9b35_44128.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 92 5.16 5 C 9102 2.51 5 N 2316 2.21 5 O 2622 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 14132 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3525 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 444, 3518 Classifications: {'peptide': 444} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 426} Conformer: "B" Number of residues, atoms: 444, 3518 Classifications: {'peptide': 444} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 426} bond proxies already assigned to first conformer: 3587 Chain: "B" Number of atoms: 3521 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 444, 3518 Classifications: {'peptide': 444} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 426} Conformer: "B" Number of residues, atoms: 444, 3518 Classifications: {'peptide': 444} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 426} bond proxies already assigned to first conformer: 3592 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Restraints were copied for chains: D, C Time building chain proxies: 15.37, per 1000 atoms: 1.09 Number of scatterers: 14132 At special positions: 0 Unit cell: (128.127, 87.6655, 140.265, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 92 16.00 O 2622 8.00 N 2316 7.00 C 9102 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 750 " - pdb=" SG CYS A 804 " distance=2.03 Simple disulfide: pdb=" SG CYS B 750 " - pdb=" SG CYS B 804 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.23 Conformation dependent library (CDL) restraints added in 3.4 seconds 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3308 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 16 sheets defined 51.1% alpha, 4.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.75 Creating SS restraints... Processing helix chain 'A' and resid 461 through 475 removed outlier: 3.558A pdb=" N GLU A 469 " --> pdb=" O ASP A 465 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR A 472 " --> pdb=" O ARG A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 507 removed outlier: 3.531A pdb=" N ASP A 507 " --> pdb=" O ARG A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 525 removed outlier: 3.886A pdb=" N LYS A 525 " --> pdb=" O TYR A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 557 removed outlier: 3.854A pdb=" N LEU A 556 " --> pdb=" O PHE A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 585 removed outlier: 3.952A pdb=" N SER A 575 " --> pdb=" O CYS A 571 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N CYS A 576 " --> pdb=" O LEU A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 620 removed outlier: 3.837A pdb=" N TRP A 613 " --> pdb=" O LEU A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 660 removed outlier: 3.591A pdb=" N ILE A 635 " --> pdb=" O LEU A 631 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N VAL A 636 " --> pdb=" O SER A 632 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA A 656 " --> pdb=" O THR A 652 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ALA A 657 " --> pdb=" O ALA A 653 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE A 658 " --> pdb=" O ASN A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 676 removed outlier: 4.080A pdb=" N LYS A 676 " --> pdb=" O ASP A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 697 removed outlier: 3.572A pdb=" N PHE A 694 " --> pdb=" O THR A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 710 Processing helix chain 'A' and resid 720 through 731 removed outlier: 3.972A pdb=" N VAL A 728 " --> pdb=" O GLY A 724 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 746 removed outlier: 3.821A pdb=" N PHE A 744 " --> pdb=" O THR A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 788 removed outlier: 4.080A pdb=" N LYS A 777 " --> pdb=" O PRO A 773 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE A 778 " --> pdb=" O TYR A 774 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU A 783 " --> pdb=" O THR A 779 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU A 785 " --> pdb=" O ALA A 781 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU A 788 " --> pdb=" O GLN A 784 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 800 removed outlier: 4.061A pdb=" N LYS A 795 " --> pdb=" O LEU A 791 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 820 removed outlier: 3.716A pdb=" N ASN A 819 " --> pdb=" O GLY A 816 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE A 820 " --> pdb=" O VAL A 817 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 816 through 820' Processing helix chain 'A' and resid 821 through 849 removed outlier: 3.650A pdb=" N ILE A 825 " --> pdb=" O GLY A 821 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N PHE A 836 " --> pdb=" O VAL A 832 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL A 837 " --> pdb=" O LEU A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 852 No H-bonds generated for 'chain 'A' and resid 850 through 852' Processing helix chain 'A' and resid 855 through 868 removed outlier: 3.899A pdb=" N ALA A 860 " --> pdb=" O SER A 856 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N MET A 861 " --> pdb=" O PHE A 857 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 457 No H-bonds generated for 'chain 'B' and resid 455 through 457' Processing helix chain 'B' and resid 461 through 474 Processing helix chain 'B' and resid 500 through 507 removed outlier: 3.704A pdb=" N GLU B 504 " --> pdb=" O GLY B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 525 removed outlier: 3.537A pdb=" N LYS B 525 " --> pdb=" O TYR B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 583 removed outlier: 3.884A pdb=" N LEU B 568 " --> pdb=" O TRP B 564 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N CYS B 576 " --> pdb=" O LEU B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 620 removed outlier: 3.833A pdb=" N PHE B 612 " --> pdb=" O LEU B 608 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TRP B 613 " --> pdb=" O LEU B 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 655 removed outlier: 3.654A pdb=" N ARG B 634 " --> pdb=" O ALA B 630 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL B 636 " --> pdb=" O SER B 632 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN B 654 " --> pdb=" O SER B 650 " (cutoff:3.500A) Processing helix chain 'B' and resid 670 through 676 removed outlier: 3.870A pdb=" N LEU B 674 " --> pdb=" O SER B 670 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA B 675 " --> pdb=" O ALA B 671 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 696 Processing helix chain 'B' and resid 699 through 712 removed outlier: 3.606A pdb=" N LYS B 704 " --> pdb=" O SER B 700 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N MET B 709 " --> pdb=" O MET B 705 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N SER B 711 " --> pdb=" O ALA B 707 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG B 712 " --> pdb=" O PHE B 708 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 716 Processing helix chain 'B' and resid 721 through 730 Processing helix chain 'B' and resid 739 through 749 removed outlier: 3.552A pdb=" N PHE B 744 " --> pdb=" O THR B 740 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLN B 747 " --> pdb=" O GLU B 743 " (cutoff:3.500A) Processing helix chain 'B' and resid 774 through 789 Processing helix chain 'B' and resid 789 through 800 Processing helix chain 'B' and resid 821 through 849 removed outlier: 3.562A pdb=" N ILE B 825 " --> pdb=" O GLY B 821 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL B 832 " --> pdb=" O ALA B 828 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASN B 849 " --> pdb=" O LYS B 845 " (cutoff:3.500A) Processing helix chain 'B' and resid 856 through 870 removed outlier: 3.635A pdb=" N MET B 867 " --> pdb=" O GLU B 863 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LYS B 870 " --> pdb=" O ARG B 866 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 475 removed outlier: 3.558A pdb=" N GLU C 469 " --> pdb=" O ASP C 465 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR C 472 " --> pdb=" O ARG C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 507 removed outlier: 3.532A pdb=" N ASP C 507 " --> pdb=" O ARG C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 525 removed outlier: 3.885A pdb=" N LYS C 525 " --> pdb=" O TYR C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 553 through 557 removed outlier: 3.854A pdb=" N LEU C 556 " --> pdb=" O PHE C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 562 through 585 removed outlier: 3.952A pdb=" N SER C 575 " --> pdb=" O CYS C 571 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N CYS C 576 " --> pdb=" O LEU C 572 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 620 removed outlier: 3.836A pdb=" N TRP C 613 " --> pdb=" O LEU C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 660 removed outlier: 3.592A pdb=" N ILE C 635 " --> pdb=" O LEU C 631 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N VAL C 636 " --> pdb=" O SER C 632 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA C 656 " --> pdb=" O THR C 652 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ALA C 657 " --> pdb=" O ALA C 653 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE C 658 " --> pdb=" O ASN C 654 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 676 removed outlier: 4.080A pdb=" N LYS C 676 " --> pdb=" O ASP C 672 " (cutoff:3.500A) Processing helix chain 'C' and resid 688 through 697 removed outlier: 3.573A pdb=" N PHE C 694 " --> pdb=" O THR C 690 " (cutoff:3.500A) Processing helix chain 'C' and resid 699 through 710 Processing helix chain 'C' and resid 720 through 731 removed outlier: 3.973A pdb=" N VAL C 728 " --> pdb=" O GLY C 724 " (cutoff:3.500A) Processing helix chain 'C' and resid 739 through 746 removed outlier: 3.822A pdb=" N PHE C 744 " --> pdb=" O THR C 740 " (cutoff:3.500A) Processing helix chain 'C' and resid 773 through 788 removed outlier: 4.080A pdb=" N LYS C 777 " --> pdb=" O PRO C 773 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE C 778 " --> pdb=" O TYR C 774 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU C 783 " --> pdb=" O THR C 779 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU C 785 " --> pdb=" O ALA C 781 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU C 788 " --> pdb=" O GLN C 784 " (cutoff:3.500A) Processing helix chain 'C' and resid 789 through 800 removed outlier: 4.060A pdb=" N LYS C 795 " --> pdb=" O LEU C 791 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 820 removed outlier: 3.716A pdb=" N ASN C 819 " --> pdb=" O GLY C 816 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE C 820 " --> pdb=" O VAL C 817 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 816 through 820' Processing helix chain 'C' and resid 821 through 849 removed outlier: 3.651A pdb=" N ILE C 825 " --> pdb=" O GLY C 821 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N PHE C 836 " --> pdb=" O VAL C 832 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL C 837 " --> pdb=" O LEU C 833 " (cutoff:3.500A) Processing helix chain 'C' and resid 850 through 852 No H-bonds generated for 'chain 'C' and resid 850 through 852' Processing helix chain 'C' and resid 855 through 868 removed outlier: 3.899A pdb=" N ALA C 860 " --> pdb=" O SER C 856 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N MET C 861 " --> pdb=" O PHE C 857 " (cutoff:3.500A) Processing helix chain 'D' and resid 455 through 457 No H-bonds generated for 'chain 'D' and resid 455 through 457' Processing helix chain 'D' and resid 461 through 474 Processing helix chain 'D' and resid 500 through 507 removed outlier: 3.704A pdb=" N GLU D 504 " --> pdb=" O GLY D 500 " (cutoff:3.500A) Processing helix chain 'D' and resid 520 through 525 removed outlier: 3.537A pdb=" N LYS D 525 " --> pdb=" O TYR D 521 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 583 removed outlier: 3.883A pdb=" N LEU D 568 " --> pdb=" O TRP D 564 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N CYS D 576 " --> pdb=" O LEU D 572 " (cutoff:3.500A) Processing helix chain 'D' and resid 607 through 620 removed outlier: 3.833A pdb=" N PHE D 612 " --> pdb=" O LEU D 608 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N TRP D 613 " --> pdb=" O LEU D 609 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 655 removed outlier: 3.654A pdb=" N ARG D 634 " --> pdb=" O ALA D 630 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL D 636 " --> pdb=" O SER D 632 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN D 654 " --> pdb=" O SER D 650 " (cutoff:3.500A) Processing helix chain 'D' and resid 670 through 676 removed outlier: 3.870A pdb=" N LEU D 674 " --> pdb=" O SER D 670 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA D 675 " --> pdb=" O ALA D 671 " (cutoff:3.500A) Processing helix chain 'D' and resid 688 through 696 Processing helix chain 'D' and resid 699 through 712 removed outlier: 3.605A pdb=" N LYS D 704 " --> pdb=" O SER D 700 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N MET D 709 " --> pdb=" O MET D 705 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N SER D 711 " --> pdb=" O ALA D 707 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG D 712 " --> pdb=" O PHE D 708 " (cutoff:3.500A) Processing helix chain 'D' and resid 712 through 716 Processing helix chain 'D' and resid 721 through 730 Processing helix chain 'D' and resid 739 through 749 removed outlier: 3.549A pdb=" N PHE D 744 " --> pdb=" O THR D 740 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLN D 747 " --> pdb=" O GLU D 743 " (cutoff:3.500A) Processing helix chain 'D' and resid 774 through 789 Processing helix chain 'D' and resid 789 through 800 Processing helix chain 'D' and resid 821 through 849 removed outlier: 3.561A pdb=" N ILE D 825 " --> pdb=" O GLY D 821 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL D 832 " --> pdb=" O ALA D 828 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASN D 849 " --> pdb=" O LYS D 845 " (cutoff:3.500A) Processing helix chain 'D' and resid 856 through 870 removed outlier: 3.635A pdb=" N MET D 867 " --> pdb=" O GLU D 863 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LYS D 870 " --> pdb=" O ARG D 866 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 445 through 446 Processing sheet with id=AA2, first strand: chain 'A' and resid 532 through 535 removed outlier: 6.590A pdb=" N TYR A 764 " --> pdb=" O PHE A 533 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 735 through 738 removed outlier: 3.694A pdb=" N ILE A 540 " --> pdb=" O ILE A 755 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 434 through 435 Processing sheet with id=AA5, first strand: chain 'B' and resid 445 through 446 Processing sheet with id=AA6, first strand: chain 'B' and resid 535 through 536 Processing sheet with id=AA7, first strand: chain 'B' and resid 717 through 718 removed outlier: 8.155A pdb=" N VAL B 718 " --> pdb=" O TYR B 682 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ALA B 684 " --> pdb=" O VAL B 718 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N GLU B 681 " --> pdb=" O ALA B 734 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N LEU B 736 " --> pdb=" O GLU B 681 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N GLY B 683 " --> pdb=" O LEU B 736 " (cutoff:3.500A) removed outlier: 8.536A pdb=" N GLU B 738 " --> pdb=" O GLY B 683 " (cutoff:3.500A) removed outlier: 10.349A pdb=" N VAL B 685 " --> pdb=" O GLU B 738 " (cutoff:3.500A) removed outlier: 8.684A pdb=" N TYR B 733 " --> pdb=" O ARG B 543 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N ARG B 543 " --> pdb=" O TYR B 733 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ILE B 540 " --> pdb=" O ILE B 755 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 548 through 549 removed outlier: 4.212A pdb=" N GLU B 662 " --> pdb=" O ASN B 549 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 445 through 446 Processing sheet with id=AB1, first strand: chain 'C' and resid 532 through 535 removed outlier: 6.591A pdb=" N TYR C 764 " --> pdb=" O PHE C 533 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 735 through 738 removed outlier: 3.694A pdb=" N ILE C 540 " --> pdb=" O ILE C 755 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 434 through 435 Processing sheet with id=AB4, first strand: chain 'D' and resid 445 through 446 Processing sheet with id=AB5, first strand: chain 'D' and resid 535 through 536 Processing sheet with id=AB6, first strand: chain 'D' and resid 717 through 718 removed outlier: 8.155A pdb=" N VAL D 718 " --> pdb=" O TYR D 682 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ALA D 684 " --> pdb=" O VAL D 718 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N GLU D 681 " --> pdb=" O ALA D 734 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N LEU D 736 " --> pdb=" O GLU D 681 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N GLY D 683 " --> pdb=" O LEU D 736 " (cutoff:3.500A) removed outlier: 8.534A pdb=" N GLU D 738 " --> pdb=" O GLY D 683 " (cutoff:3.500A) removed outlier: 10.350A pdb=" N VAL D 685 " --> pdb=" O GLU D 738 " (cutoff:3.500A) removed outlier: 8.683A pdb=" N TYR D 733 " --> pdb=" O ARG D 543 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N ARG D 543 " --> pdb=" O TYR D 733 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ILE D 540 " --> pdb=" O ILE D 755 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 548 through 549 removed outlier: 4.211A pdb=" N GLU D 662 " --> pdb=" O ASN D 549 " (cutoff:3.500A) 580 hydrogen bonds defined for protein. 1706 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.60 Time building geometry restraints manager: 3.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4425 1.34 - 1.46: 3140 1.46 - 1.58: 6729 1.58 - 1.70: 0 1.70 - 1.81: 152 Bond restraints: 14446 Sorted by residual: bond pdb=" C ASN C 557 " pdb=" N PRO C 558 " ideal model delta sigma weight residual 1.337 1.381 -0.045 1.11e-02 8.12e+03 1.63e+01 bond pdb=" C ASN A 557 " pdb=" N PRO A 558 " ideal model delta sigma weight residual 1.337 1.381 -0.044 1.11e-02 8.12e+03 1.59e+01 bond pdb=" C ASN B 557 " pdb=" N PRO B 558 " ideal model delta sigma weight residual 1.337 1.379 -0.043 1.11e-02 8.12e+03 1.49e+01 bond pdb=" C ASN D 557 " pdb=" N PRO D 558 " ideal model delta sigma weight residual 1.337 1.379 -0.043 1.11e-02 8.12e+03 1.48e+01 bond pdb=" C LEU B 626 " pdb=" N MET B 627 " ideal model delta sigma weight residual 1.332 1.290 0.042 1.40e-02 5.10e+03 9.21e+00 ... (remaining 14441 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 18332 2.33 - 4.66: 1002 4.66 - 6.99: 158 6.99 - 9.32: 42 9.32 - 11.65: 12 Bond angle restraints: 19546 Sorted by residual: angle pdb=" CA LYS C 676 " pdb=" C LYS C 676 " pdb=" N GLN C 677 " ideal model delta sigma weight residual 117.79 124.86 -7.07 1.22e+00 6.72e-01 3.36e+01 angle pdb=" CA LYS A 676 " pdb=" C LYS A 676 " pdb=" N GLN A 677 " ideal model delta sigma weight residual 117.79 124.83 -7.04 1.22e+00 6.72e-01 3.33e+01 angle pdb=" C ASP C 492 " pdb=" N ASP C 493 " pdb=" CA ASP C 493 " ideal model delta sigma weight residual 121.54 132.01 -10.47 1.91e+00 2.74e-01 3.00e+01 angle pdb=" C ASP A 492 " pdb=" N ASP A 493 " pdb=" CA ASP A 493 " ideal model delta sigma weight residual 121.54 131.89 -10.35 1.91e+00 2.74e-01 2.93e+01 angle pdb=" N LYS B 629 " pdb=" CA LYS B 629 " pdb=" C LYS B 629 " ideal model delta sigma weight residual 109.96 101.71 8.25 1.58e+00 4.01e-01 2.72e+01 ... (remaining 19541 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.39: 8215 17.39 - 34.79: 351 34.79 - 52.18: 64 52.18 - 69.57: 8 69.57 - 86.97: 6 Dihedral angle restraints: 8644 sinusoidal: 3484 harmonic: 5160 Sorted by residual: dihedral pdb=" CB CYS B 750 " pdb=" SG CYS B 750 " pdb=" SG CYS B 804 " pdb=" CB CYS B 804 " ideal model delta sinusoidal sigma weight residual 93.00 179.97 -86.97 1 1.00e+01 1.00e-02 9.09e+01 dihedral pdb=" CB CYS A 750 " pdb=" SG CYS A 750 " pdb=" SG CYS A 804 " pdb=" CB CYS A 804 " ideal model delta sinusoidal sigma weight residual -86.00 -162.20 76.20 1 1.00e+01 1.00e-02 7.31e+01 dihedral pdb=" CA ASP D 493 " pdb=" C ASP D 493 " pdb=" N VAL D 494 " pdb=" CA VAL D 494 " ideal model delta harmonic sigma weight residual -180.00 -145.47 -34.53 0 5.00e+00 4.00e-02 4.77e+01 ... (remaining 8641 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1730 0.069 - 0.138: 368 0.138 - 0.207: 58 0.207 - 0.276: 12 0.276 - 0.345: 4 Chirality restraints: 2172 Sorted by residual: chirality pdb=" CG LEU C 568 " pdb=" CB LEU C 568 " pdb=" CD1 LEU C 568 " pdb=" CD2 LEU C 568 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.34 2.00e-01 2.50e+01 2.97e+00 chirality pdb=" CG LEU A 568 " pdb=" CB LEU A 568 " pdb=" CD1 LEU A 568 " pdb=" CD2 LEU A 568 " both_signs ideal model delta sigma weight residual False -2.59 -2.25 -0.34 2.00e-01 2.50e+01 2.91e+00 chirality pdb=" CB ILE B 438 " pdb=" CA ILE B 438 " pdb=" CG1 ILE B 438 " pdb=" CG2 ILE B 438 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.63e+00 ... (remaining 2169 not shown) Planarity restraints: 2474 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP C 492 " 0.016 2.00e-02 2.50e+03 3.24e-02 1.05e+01 pdb=" C ASP C 492 " -0.056 2.00e-02 2.50e+03 pdb=" O ASP C 492 " 0.021 2.00e-02 2.50e+03 pdb=" N ASP C 493 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 492 " 0.016 2.00e-02 2.50e+03 3.23e-02 1.05e+01 pdb=" C ASP A 492 " -0.056 2.00e-02 2.50e+03 pdb=" O ASP A 492 " 0.021 2.00e-02 2.50e+03 pdb=" N ASP A 493 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG D 481 " -0.014 2.00e-02 2.50e+03 2.76e-02 7.62e+00 pdb=" C ARG D 481 " 0.048 2.00e-02 2.50e+03 pdb=" O ARG D 481 " -0.018 2.00e-02 2.50e+03 pdb=" N LEU D 482 " -0.016 2.00e-02 2.50e+03 ... (remaining 2471 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 160 2.60 - 3.18: 11897 3.18 - 3.75: 21599 3.75 - 4.33: 30493 4.33 - 4.90: 49336 Nonbonded interactions: 113485 Sorted by model distance: nonbonded pdb=" SG CYS D 750 " pdb=" SG CYS D 804 " model vdw 2.030 3.760 nonbonded pdb=" SG CYS C 750 " pdb=" SG CYS C 804 " model vdw 2.030 3.760 nonbonded pdb=" O ARG B 727 " pdb=" OG SER B 731 " model vdw 2.244 3.040 nonbonded pdb=" O ARG D 727 " pdb=" OG SER D 731 " model vdw 2.244 3.040 nonbonded pdb=" O LYS D 629 " pdb=" OG1 THR D 633 " model vdw 2.280 3.040 ... (remaining 113480 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 431 through 470 or resid 472 through 534 or resid 536 thro \ ugh 874 or resid 1001)) selection = (chain 'B' and (resid 431 through 470 or resid 472 through 534 or resid 536 thro \ ugh 874 or resid 1001)) selection = (chain 'C' and (resid 431 through 470 or resid 472 through 534 or resid 536 thro \ ugh 874 or resid 1001)) selection = (chain 'D' and (resid 431 through 470 or resid 472 through 534 or resid 536 thro \ ugh 874 or resid 1001)) } 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: 1.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 41.900 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.075 14446 Z= 0.505 Angle : 1.245 11.648 19546 Z= 0.728 Chirality : 0.060 0.345 2172 Planarity : 0.008 0.059 2474 Dihedral : 10.750 71.111 5330 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.90 % Allowed : 11.65 % Favored : 87.44 % Rotamer: Outliers : 0.65 % Allowed : 4.77 % Favored : 94.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.35 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.51 (0.14), residues: 1774 helix: -3.92 (0.09), residues: 858 sheet: -3.17 (0.37), residues: 164 loop : -3.26 (0.19), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.004 TRP A 799 HIS 0.022 0.003 HIS A 593 PHE 0.041 0.003 PHE B 735 TYR 0.036 0.004 TYR B 488 ARG 0.010 0.001 ARG A 866 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 378 time to evaluate : 1.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 465 ASP cc_start: 0.8006 (t70) cc_final: 0.7754 (t0) REVERT: A 565 MET cc_start: 0.8243 (mmm) cc_final: 0.7952 (mmt) REVERT: A 861 MET cc_start: 0.8239 (mmp) cc_final: 0.7781 (mtm) REVERT: B 465 ASP cc_start: 0.8494 (m-30) cc_final: 0.8232 (m-30) REVERT: B 469 GLU cc_start: 0.8373 (mm-30) cc_final: 0.8093 (mm-30) REVERT: B 572 LEU cc_start: 0.9141 (mm) cc_final: 0.8516 (mm) REVERT: B 576 CYS cc_start: 0.7820 (m) cc_final: 0.7434 (m) REVERT: B 580 VAL cc_start: 0.9300 (t) cc_final: 0.9075 (m) REVERT: B 584 PHE cc_start: 0.7503 (t80) cc_final: 0.6995 (m-10) REVERT: B 590 TYR cc_start: 0.7756 (p90) cc_final: 0.7276 (p90) REVERT: B 627 MET cc_start: 0.7846 (tpp) cc_final: 0.7416 (mmt) REVERT: B 639 ILE cc_start: 0.9186 (tp) cc_final: 0.8828 (pt) REVERT: B 655 LEU cc_start: 0.8641 (tp) cc_final: 0.8418 (tp) REVERT: B 792 HIS cc_start: 0.8346 (t70) cc_final: 0.7607 (t70) REVERT: B 861 MET cc_start: 0.7093 (ttt) cc_final: 0.6881 (ttt) REVERT: B 863 GLU cc_start: 0.7460 (mm-30) cc_final: 0.7035 (mt-10) REVERT: C 565 MET cc_start: 0.8134 (mmm) cc_final: 0.7929 (mmt) REVERT: C 639 ILE cc_start: 0.8799 (mm) cc_final: 0.8471 (tp) REVERT: C 761 SER cc_start: 0.8795 (t) cc_final: 0.8298 (m) REVERT: C 805 PRO cc_start: 0.8504 (Cg_exo) cc_final: 0.8269 (Cg_endo) REVERT: D 465 ASP cc_start: 0.8462 (m-30) cc_final: 0.8233 (m-30) REVERT: D 572 LEU cc_start: 0.9149 (mm) cc_final: 0.8552 (mm) REVERT: D 576 CYS cc_start: 0.7873 (m) cc_final: 0.7443 (m) REVERT: D 580 VAL cc_start: 0.9274 (t) cc_final: 0.9047 (m) REVERT: D 590 TYR cc_start: 0.7726 (p90) cc_final: 0.7227 (p90) REVERT: D 639 ILE cc_start: 0.9160 (tp) cc_final: 0.8832 (pt) REVERT: D 655 LEU cc_start: 0.8653 (tp) cc_final: 0.8444 (tp) REVERT: D 792 HIS cc_start: 0.8401 (t70) cc_final: 0.7830 (t70) REVERT: D 861 MET cc_start: 0.6936 (ttt) cc_final: 0.6722 (ttt) outliers start: 2 outliers final: 0 residues processed: 380 average time/residue: 0.2584 time to fit residues: 141.7504 Evaluate side-chains 215 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 215 time to evaluate : 1.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 6.9990 chunk 133 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 137 optimal weight: 0.5980 chunk 53 optimal weight: 0.8980 chunk 83 optimal weight: 0.9990 chunk 102 optimal weight: 0.7980 chunk 159 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 596 ASN A 604 ASN A 802 ASN B 549 ASN B 610 ASN B 792 HIS B 819 ASN C 596 ASN C 604 ASN C 802 ASN D 549 ASN D 604 ASN D 610 ASN D 819 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 14446 Z= 0.239 Angle : 0.768 8.453 19546 Z= 0.398 Chirality : 0.044 0.159 2172 Planarity : 0.006 0.053 2474 Dihedral : 6.438 44.776 1936 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.40 % Allowed : 11.76 % Favored : 87.84 % Rotamer: Outliers : 2.26 % Allowed : 10.00 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.46 (0.17), residues: 1774 helix: -1.61 (0.15), residues: 866 sheet: -2.95 (0.43), residues: 130 loop : -2.93 (0.20), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 798 HIS 0.015 0.002 HIS C 593 PHE 0.026 0.002 PHE B 476 TYR 0.022 0.002 TYR D 566 ARG 0.008 0.001 ARG C 583 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 260 time to evaluate : 1.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 534 MET cc_start: 0.8725 (ttm) cc_final: 0.8452 (ttp) REVERT: A 565 MET cc_start: 0.8218 (mmm) cc_final: 0.7991 (mmt) REVERT: A 635 ILE cc_start: 0.8885 (OUTLIER) cc_final: 0.8671 (mp) REVERT: A 668 ILE cc_start: 0.8703 (mm) cc_final: 0.8199 (pt) REVERT: A 836 PHE cc_start: 0.7870 (m-80) cc_final: 0.7646 (m-10) REVERT: A 841 GLU cc_start: 0.7353 (mt-10) cc_final: 0.7045 (mt-10) REVERT: A 861 MET cc_start: 0.8394 (mmp) cc_final: 0.7821 (mtm) REVERT: A 866 ARG cc_start: 0.6767 (OUTLIER) cc_final: 0.5921 (tmm-80) REVERT: B 465 ASP cc_start: 0.8508 (m-30) cc_final: 0.8265 (m-30) REVERT: B 469 GLU cc_start: 0.8234 (mm-30) cc_final: 0.7828 (mm-30) REVERT: B 572 LEU cc_start: 0.9089 (mm) cc_final: 0.8160 (mm) REVERT: B 576 CYS cc_start: 0.7713 (m) cc_final: 0.7272 (m) REVERT: B 580 VAL cc_start: 0.9372 (t) cc_final: 0.9116 (m) REVERT: B 584 PHE cc_start: 0.7450 (t80) cc_final: 0.6836 (m-10) REVERT: B 590 TYR cc_start: 0.7678 (p90) cc_final: 0.7337 (p90) REVERT: B 609 LEU cc_start: 0.8886 (tt) cc_final: 0.8387 (mt) REVERT: B 626 LEU cc_start: 0.8472 (mt) cc_final: 0.8245 (mt) REVERT: B 639 ILE cc_start: 0.9026 (tp) cc_final: 0.8812 (pt) REVERT: B 655 LEU cc_start: 0.8755 (tp) cc_final: 0.8517 (tp) REVERT: B 709 MET cc_start: 0.8964 (mtt) cc_final: 0.8651 (mtt) REVERT: B 792 HIS cc_start: 0.8376 (t-90) cc_final: 0.8169 (t-170) REVERT: C 565 MET cc_start: 0.8148 (mmm) cc_final: 0.7918 (mmt) REVERT: C 635 ILE cc_start: 0.8794 (OUTLIER) cc_final: 0.8556 (mp) REVERT: C 667 PRO cc_start: 0.9030 (Cg_exo) cc_final: 0.8689 (Cg_endo) REVERT: C 761 SER cc_start: 0.8715 (t) cc_final: 0.8286 (m) REVERT: C 805 PRO cc_start: 0.8426 (Cg_exo) cc_final: 0.7947 (Cg_endo) REVERT: C 841 GLU cc_start: 0.7387 (mt-10) cc_final: 0.6992 (mt-10) REVERT: D 535 THR cc_start: 0.9114 (OUTLIER) cc_final: 0.8904 (p) REVERT: D 556 LEU cc_start: 0.9093 (mm) cc_final: 0.8780 (mp) REVERT: D 572 LEU cc_start: 0.9128 (mm) cc_final: 0.8219 (mm) REVERT: D 576 CYS cc_start: 0.7786 (m) cc_final: 0.7536 (m) REVERT: D 590 TYR cc_start: 0.7627 (p90) cc_final: 0.7319 (p90) REVERT: D 627 MET cc_start: 0.8001 (tpp) cc_final: 0.7294 (tpp) REVERT: D 639 ILE cc_start: 0.9022 (tp) cc_final: 0.8754 (tp) REVERT: D 655 LEU cc_start: 0.8810 (tp) cc_final: 0.8602 (tp) REVERT: D 792 HIS cc_start: 0.8476 (t70) cc_final: 0.8273 (t-170) REVERT: D 800 ARG cc_start: 0.7983 (tpp80) cc_final: 0.7719 (mmm160) outliers start: 27 outliers final: 14 residues processed: 280 average time/residue: 0.2251 time to fit residues: 95.0387 Evaluate side-chains 224 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 206 time to evaluate : 1.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 458 ARG Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 866 ARG Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 591 ASN Chi-restraints excluded: chain B residue 725 ILE Chi-restraints excluded: chain C residue 458 ARG Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 575 SER Chi-restraints excluded: chain C residue 635 ILE Chi-restraints excluded: chain D residue 444 VAL Chi-restraints excluded: chain D residue 535 THR Chi-restraints excluded: chain D residue 770 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 88 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 133 optimal weight: 0.2980 chunk 108 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 160 optimal weight: 5.9990 chunk 172 optimal weight: 3.9990 chunk 142 optimal weight: 3.9990 chunk 158 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 128 optimal weight: 0.8980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 508 HIS B 604 ASN C 508 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.3247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14446 Z= 0.285 Angle : 0.730 8.570 19546 Z= 0.376 Chirality : 0.044 0.168 2172 Planarity : 0.006 0.053 2474 Dihedral : 5.994 39.345 1936 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.28 % Allowed : 11.82 % Favored : 87.90 % Rotamer: Outliers : 2.65 % Allowed : 11.94 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (0.19), residues: 1774 helix: -0.59 (0.16), residues: 880 sheet: -2.69 (0.44), residues: 126 loop : -2.73 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 706 HIS 0.016 0.002 HIS C 593 PHE 0.024 0.002 PHE B 476 TYR 0.020 0.002 TYR A 651 ARG 0.006 0.001 ARG C 583 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 231 time to evaluate : 1.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 534 MET cc_start: 0.8871 (ttm) cc_final: 0.8574 (ttp) REVERT: A 565 MET cc_start: 0.8239 (mmm) cc_final: 0.8011 (mmt) REVERT: A 635 ILE cc_start: 0.8930 (OUTLIER) cc_final: 0.8673 (mp) REVERT: A 651 TYR cc_start: 0.8852 (t80) cc_final: 0.8551 (t80) REVERT: A 668 ILE cc_start: 0.8666 (mm) cc_final: 0.8139 (pt) REVERT: A 755 ILE cc_start: 0.9133 (mp) cc_final: 0.8758 (mp) REVERT: A 810 LYS cc_start: 0.9177 (tmtm) cc_final: 0.8945 (mmtt) REVERT: A 836 PHE cc_start: 0.7930 (m-80) cc_final: 0.7589 (m-10) REVERT: A 841 GLU cc_start: 0.7377 (mt-10) cc_final: 0.7054 (mt-10) REVERT: A 861 MET cc_start: 0.8284 (mmp) cc_final: 0.7698 (mtm) REVERT: B 469 GLU cc_start: 0.8375 (mm-30) cc_final: 0.8132 (mm-30) REVERT: B 572 LEU cc_start: 0.9164 (mm) cc_final: 0.8236 (mm) REVERT: B 576 CYS cc_start: 0.7755 (m) cc_final: 0.7485 (m) REVERT: B 584 PHE cc_start: 0.7534 (t80) cc_final: 0.7070 (m-10) REVERT: B 590 TYR cc_start: 0.7638 (p90) cc_final: 0.7202 (p90) REVERT: B 609 LEU cc_start: 0.8858 (tt) cc_final: 0.8282 (mt) REVERT: B 639 ILE cc_start: 0.9063 (tp) cc_final: 0.8764 (tp) REVERT: B 655 LEU cc_start: 0.8917 (tp) cc_final: 0.8716 (tp) REVERT: B 709 MET cc_start: 0.8995 (mtt) cc_final: 0.8723 (mtt) REVERT: C 501 MET cc_start: 0.7721 (mtm) cc_final: 0.7497 (mtm) REVERT: C 635 ILE cc_start: 0.8832 (OUTLIER) cc_final: 0.8569 (mp) REVERT: C 698 LYS cc_start: 0.9328 (mmtt) cc_final: 0.8878 (mmtt) REVERT: C 761 SER cc_start: 0.8740 (t) cc_final: 0.8280 (m) REVERT: C 836 PHE cc_start: 0.7754 (m-80) cc_final: 0.7526 (m-10) REVERT: C 841 GLU cc_start: 0.7386 (mt-10) cc_final: 0.7038 (mt-10) REVERT: D 556 LEU cc_start: 0.9152 (mm) cc_final: 0.8813 (mp) REVERT: D 572 LEU cc_start: 0.9098 (mm) cc_final: 0.8236 (mm) REVERT: D 576 CYS cc_start: 0.7854 (m) cc_final: 0.7551 (m) REVERT: D 590 TYR cc_start: 0.7672 (p90) cc_final: 0.7268 (p90) REVERT: D 639 ILE cc_start: 0.9054 (tp) cc_final: 0.8761 (tp) REVERT: D 655 LEU cc_start: 0.8923 (tp) cc_final: 0.8710 (tp) outliers start: 33 outliers final: 20 residues processed: 247 average time/residue: 0.2307 time to fit residues: 86.9624 Evaluate side-chains 230 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 208 time to evaluate : 1.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 458 ARG Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 866 ARG Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 565 MET Chi-restraints excluded: chain B residue 591 ASN Chi-restraints excluded: chain B residue 725 ILE Chi-restraints excluded: chain B residue 831 LEU Chi-restraints excluded: chain C residue 458 ARG Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 571 CYS Chi-restraints excluded: chain C residue 635 ILE Chi-restraints excluded: chain D residue 444 VAL Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 565 MET Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain D residue 831 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 158 optimal weight: 1.9990 chunk 120 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 chunk 160 optimal weight: 0.7980 chunk 170 optimal weight: 6.9990 chunk 152 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 792 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.3581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14446 Z= 0.267 Angle : 0.707 9.772 19546 Z= 0.363 Chirality : 0.044 0.153 2172 Planarity : 0.005 0.054 2474 Dihedral : 5.757 38.811 1936 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.28 % Allowed : 11.65 % Favored : 88.07 % Rotamer: Outliers : 2.65 % Allowed : 12.90 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.19), residues: 1774 helix: -0.10 (0.17), residues: 874 sheet: -2.56 (0.43), residues: 126 loop : -2.59 (0.22), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 706 HIS 0.013 0.002 HIS A 593 PHE 0.031 0.002 PHE D 584 TYR 0.018 0.002 TYR A 651 ARG 0.011 0.001 ARG B 800 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 224 time to evaluate : 1.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 534 MET cc_start: 0.8904 (ttm) cc_final: 0.8590 (ttp) REVERT: A 565 MET cc_start: 0.8262 (mmm) cc_final: 0.8033 (mmt) REVERT: A 635 ILE cc_start: 0.8885 (OUTLIER) cc_final: 0.8612 (mp) REVERT: A 668 ILE cc_start: 0.8564 (mm) cc_final: 0.8185 (pt) REVERT: A 755 ILE cc_start: 0.9056 (mp) cc_final: 0.8689 (mp) REVERT: A 761 SER cc_start: 0.8724 (t) cc_final: 0.8239 (m) REVERT: A 810 LYS cc_start: 0.9169 (tmtm) cc_final: 0.8933 (mmtt) REVERT: A 836 PHE cc_start: 0.7928 (m-80) cc_final: 0.7600 (m-10) REVERT: A 841 GLU cc_start: 0.7474 (mt-10) cc_final: 0.7189 (mt-10) REVERT: A 861 MET cc_start: 0.8356 (mmp) cc_final: 0.7733 (mtm) REVERT: A 866 ARG cc_start: 0.7236 (OUTLIER) cc_final: 0.6150 (tmm-80) REVERT: B 443 TYR cc_start: 0.8161 (m-80) cc_final: 0.7715 (m-80) REVERT: B 469 GLU cc_start: 0.8353 (mm-30) cc_final: 0.8150 (mm-30) REVERT: B 572 LEU cc_start: 0.9151 (mm) cc_final: 0.8136 (mm) REVERT: B 576 CYS cc_start: 0.7735 (m) cc_final: 0.7263 (m) REVERT: B 580 VAL cc_start: 0.9364 (t) cc_final: 0.9103 (m) REVERT: B 584 PHE cc_start: 0.7564 (t80) cc_final: 0.7089 (m-10) REVERT: B 590 TYR cc_start: 0.7539 (p90) cc_final: 0.7116 (p90) REVERT: B 639 ILE cc_start: 0.9053 (tp) cc_final: 0.8757 (tp) REVERT: B 655 LEU cc_start: 0.8915 (tp) cc_final: 0.8697 (tp) REVERT: B 709 MET cc_start: 0.9007 (mtt) cc_final: 0.8741 (mtt) REVERT: C 501 MET cc_start: 0.7718 (mtm) cc_final: 0.7485 (mtm) REVERT: C 612 PHE cc_start: 0.8373 (m-10) cc_final: 0.8143 (m-80) REVERT: C 761 SER cc_start: 0.8706 (t) cc_final: 0.8275 (m) REVERT: C 836 PHE cc_start: 0.7853 (m-80) cc_final: 0.7586 (m-10) REVERT: C 841 GLU cc_start: 0.7309 (mt-10) cc_final: 0.6987 (mt-10) REVERT: D 572 LEU cc_start: 0.9082 (mm) cc_final: 0.8190 (mm) REVERT: D 576 CYS cc_start: 0.7873 (m) cc_final: 0.7550 (m) REVERT: D 612 PHE cc_start: 0.8248 (m-80) cc_final: 0.8004 (t80) REVERT: D 625 GLU cc_start: 0.7722 (pt0) cc_final: 0.7409 (pt0) REVERT: D 639 ILE cc_start: 0.9039 (tp) cc_final: 0.8743 (tp) REVERT: D 655 LEU cc_start: 0.8895 (tp) cc_final: 0.8694 (tp) REVERT: D 861 MET cc_start: 0.8358 (ppp) cc_final: 0.7479 (ttt) outliers start: 33 outliers final: 19 residues processed: 242 average time/residue: 0.2318 time to fit residues: 84.8517 Evaluate side-chains 228 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 207 time to evaluate : 1.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 458 ARG Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 866 ARG Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 565 MET Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 725 ILE 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 608 LEU Chi-restraints excluded: chain D residue 444 VAL Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 565 MET Chi-restraints excluded: chain D residue 580 VAL 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 96 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 126 optimal weight: 10.0000 chunk 70 optimal weight: 1.9990 chunk 145 optimal weight: 3.9990 chunk 117 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 86 optimal weight: 8.9990 chunk 152 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.3846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14446 Z= 0.262 Angle : 0.700 11.178 19546 Z= 0.357 Chirality : 0.044 0.152 2172 Planarity : 0.005 0.069 2474 Dihedral : 5.635 36.799 1936 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.28 % Allowed : 11.60 % Favored : 88.12 % Rotamer: Outliers : 2.52 % Allowed : 13.74 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.20), residues: 1774 helix: 0.17 (0.17), residues: 896 sheet: -2.48 (0.41), residues: 140 loop : -2.58 (0.22), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 799 HIS 0.011 0.002 HIS C 593 PHE 0.023 0.002 PHE D 476 TYR 0.012 0.002 TYR A 521 ARG 0.006 0.001 ARG B 800 *********************** 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 253 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 222 time to evaluate : 1.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 534 MET cc_start: 0.8909 (ttm) cc_final: 0.8561 (ttp) REVERT: A 565 MET cc_start: 0.8265 (mmm) cc_final: 0.8041 (mmt) REVERT: A 635 ILE cc_start: 0.8885 (OUTLIER) cc_final: 0.8613 (mp) REVERT: A 755 ILE cc_start: 0.9078 (mp) cc_final: 0.8820 (mp) REVERT: A 761 SER cc_start: 0.8713 (t) cc_final: 0.8236 (m) REVERT: A 810 LYS cc_start: 0.9157 (tmtm) cc_final: 0.8929 (mmtt) REVERT: A 836 PHE cc_start: 0.8200 (m-80) cc_final: 0.7679 (m-10) REVERT: A 841 GLU cc_start: 0.7603 (mt-10) cc_final: 0.7304 (mt-10) REVERT: A 861 MET cc_start: 0.8338 (mmp) cc_final: 0.7662 (mtm) REVERT: B 443 TYR cc_start: 0.8181 (m-80) cc_final: 0.7763 (m-80) REVERT: B 572 LEU cc_start: 0.9095 (mm) cc_final: 0.8012 (mm) REVERT: B 576 CYS cc_start: 0.7737 (m) cc_final: 0.7443 (m) REVERT: B 584 PHE cc_start: 0.7559 (t80) cc_final: 0.7055 (m-10) REVERT: B 590 TYR cc_start: 0.7624 (p90) cc_final: 0.7123 (p90) REVERT: B 609 LEU cc_start: 0.8783 (tt) cc_final: 0.8188 (mt) REVERT: B 625 GLU cc_start: 0.7697 (pt0) cc_final: 0.7422 (pt0) REVERT: B 639 ILE cc_start: 0.9082 (tp) cc_final: 0.8787 (tp) REVERT: B 655 LEU cc_start: 0.8915 (tp) cc_final: 0.8705 (tp) REVERT: B 861 MET cc_start: 0.8223 (ppp) cc_final: 0.7484 (ttt) REVERT: C 458 ARG cc_start: 0.7200 (OUTLIER) cc_final: 0.6958 (ptt-90) REVERT: C 501 MET cc_start: 0.7725 (mtm) cc_final: 0.7510 (mtm) REVERT: C 612 PHE cc_start: 0.8392 (m-10) cc_final: 0.8168 (m-80) REVERT: C 698 LYS cc_start: 0.9293 (mmtt) cc_final: 0.8870 (mmtt) REVERT: C 709 MET cc_start: 0.8901 (mtp) cc_final: 0.8498 (mpp) REVERT: C 761 SER cc_start: 0.8707 (t) cc_final: 0.8261 (m) REVERT: C 810 LYS cc_start: 0.8220 (mmtt) cc_final: 0.7741 (mmpt) REVERT: C 836 PHE cc_start: 0.7847 (m-80) cc_final: 0.7568 (m-10) REVERT: C 841 GLU cc_start: 0.7479 (mt-10) cc_final: 0.7123 (mt-10) REVERT: D 572 LEU cc_start: 0.9086 (mm) cc_final: 0.8196 (mm) REVERT: D 576 CYS cc_start: 0.7865 (m) cc_final: 0.7585 (m) REVERT: D 612 PHE cc_start: 0.8215 (m-80) cc_final: 0.7951 (t80) REVERT: D 639 ILE cc_start: 0.9069 (tp) cc_final: 0.8772 (tp) REVERT: D 655 LEU cc_start: 0.8909 (tp) cc_final: 0.8708 (tp) REVERT: D 709 MET cc_start: 0.8993 (mtt) cc_final: 0.8691 (mtt) REVERT: D 861 MET cc_start: 0.8442 (ppp) cc_final: 0.7611 (ttt) outliers start: 31 outliers final: 21 residues processed: 234 average time/residue: 0.2295 time to fit residues: 81.8616 Evaluate side-chains 235 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 212 time to evaluate : 1.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 458 ARG Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 571 CYS Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 565 MET Chi-restraints excluded: chain B residue 823 ILE Chi-restraints excluded: chain B residue 831 LEU Chi-restraints excluded: chain C residue 458 ARG Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 571 CYS Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain D residue 444 VAL Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 565 MET Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain D residue 750 CYS 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 153 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 99 optimal weight: 0.0570 chunk 41 optimal weight: 1.9990 chunk 170 optimal weight: 4.9990 chunk 141 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 56 optimal weight: 0.0370 chunk 89 optimal weight: 4.9990 chunk 164 optimal weight: 0.8980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.4107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14446 Z= 0.176 Angle : 0.660 10.189 19546 Z= 0.337 Chirality : 0.042 0.183 2172 Planarity : 0.005 0.070 2474 Dihedral : 5.429 39.149 1936 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.80 % Favored : 89.08 % Rotamer: Outliers : 1.94 % Allowed : 14.45 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.20), residues: 1774 helix: 0.53 (0.17), residues: 892 sheet: -2.50 (0.40), residues: 140 loop : -2.47 (0.23), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 706 HIS 0.009 0.002 HIS C 593 PHE 0.028 0.001 PHE D 584 TYR 0.012 0.001 TYR A 542 ARG 0.006 0.001 ARG B 800 *********************** 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 249 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 227 time to evaluate : 1.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 534 MET cc_start: 0.8887 (ttm) cc_final: 0.8530 (ttp) REVERT: A 565 MET cc_start: 0.8226 (mmm) cc_final: 0.8018 (mmt) REVERT: A 635 ILE cc_start: 0.8823 (OUTLIER) cc_final: 0.8598 (mp) REVERT: A 755 ILE cc_start: 0.9004 (mp) cc_final: 0.8753 (mp) REVERT: A 761 SER cc_start: 0.8705 (t) cc_final: 0.8248 (m) REVERT: A 810 LYS cc_start: 0.9150 (tmtm) cc_final: 0.8938 (mmtt) REVERT: A 836 PHE cc_start: 0.7984 (m-80) cc_final: 0.7611 (m-10) REVERT: A 841 GLU cc_start: 0.7428 (mt-10) cc_final: 0.6841 (mm-30) REVERT: A 861 MET cc_start: 0.8360 (mmp) cc_final: 0.7634 (mtm) REVERT: B 572 LEU cc_start: 0.9113 (mm) cc_final: 0.8043 (mm) REVERT: B 576 CYS cc_start: 0.7805 (m) cc_final: 0.7523 (m) REVERT: B 584 PHE cc_start: 0.7523 (t80) cc_final: 0.6875 (m-10) REVERT: B 590 TYR cc_start: 0.7362 (p90) cc_final: 0.6797 (p90) REVERT: B 609 LEU cc_start: 0.8695 (tt) cc_final: 0.8165 (mt) REVERT: B 639 ILE cc_start: 0.9007 (tp) cc_final: 0.8728 (tp) REVERT: B 655 LEU cc_start: 0.8899 (tp) cc_final: 0.8671 (tp) REVERT: B 861 MET cc_start: 0.8309 (ppp) cc_final: 0.7513 (ttt) REVERT: C 501 MET cc_start: 0.7701 (mtm) cc_final: 0.7452 (mtm) REVERT: C 612 PHE cc_start: 0.8381 (m-10) cc_final: 0.8156 (m-80) REVERT: C 668 ILE cc_start: 0.8711 (mm) cc_final: 0.8400 (pt) REVERT: C 698 LYS cc_start: 0.9378 (mmtt) cc_final: 0.8953 (mmtm) REVERT: C 709 MET cc_start: 0.8914 (mtp) cc_final: 0.8529 (mpp) REVERT: C 761 SER cc_start: 0.8692 (t) cc_final: 0.8264 (m) REVERT: C 810 LYS cc_start: 0.8194 (mmtt) cc_final: 0.7698 (mmpt) REVERT: C 836 PHE cc_start: 0.7804 (m-80) cc_final: 0.7537 (m-10) REVERT: C 841 GLU cc_start: 0.7405 (mt-10) cc_final: 0.6824 (mm-30) REVERT: D 572 LEU cc_start: 0.9074 (mm) cc_final: 0.8223 (mm) REVERT: D 576 CYS cc_start: 0.7859 (m) cc_final: 0.7578 (m) REVERT: D 612 PHE cc_start: 0.8180 (m-80) cc_final: 0.7860 (t80) REVERT: D 639 ILE cc_start: 0.9063 (tp) cc_final: 0.8794 (tp) REVERT: D 655 LEU cc_start: 0.8888 (tp) cc_final: 0.8680 (tp) REVERT: D 709 MET cc_start: 0.8919 (mtt) cc_final: 0.8589 (mtt) REVERT: D 861 MET cc_start: 0.8401 (ppp) cc_final: 0.7650 (ttt) outliers start: 22 outliers final: 16 residues processed: 236 average time/residue: 0.2503 time to fit residues: 89.3477 Evaluate side-chains 222 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 205 time to evaluate : 1.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 458 ARG Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 571 CYS Chi-restraints excluded: chain A residue 635 ILE 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 831 LEU Chi-restraints excluded: chain C residue 458 ARG Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain D residue 444 VAL Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 565 MET Chi-restraints excluded: chain D residue 831 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 19 optimal weight: 0.9990 chunk 97 optimal weight: 0.0570 chunk 124 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 143 optimal weight: 3.9990 chunk 95 optimal weight: 0.5980 chunk 169 optimal weight: 7.9990 chunk 106 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 104 optimal weight: 6.9990 overall best weight: 0.7102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 654 ASN ** D 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.4277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14446 Z= 0.194 Angle : 0.673 9.627 19546 Z= 0.343 Chirality : 0.042 0.230 2172 Planarity : 0.005 0.071 2474 Dihedral : 5.324 39.478 1936 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.17 % Allowed : 11.43 % Favored : 88.40 % Rotamer: Outliers : 1.94 % Allowed : 15.29 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.20), residues: 1774 helix: 0.76 (0.18), residues: 884 sheet: -2.48 (0.49), residues: 96 loop : -2.38 (0.22), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP C 589 HIS 0.009 0.001 HIS C 593 PHE 0.029 0.001 PHE B 476 TYR 0.010 0.001 TYR A 733 ARG 0.005 0.000 ARG B 800 *********************** 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 239 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 217 time to evaluate : 1.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 534 MET cc_start: 0.8916 (ttm) cc_final: 0.8571 (ttp) REVERT: A 565 MET cc_start: 0.8228 (mmm) cc_final: 0.8021 (mmt) REVERT: A 755 ILE cc_start: 0.8975 (mp) cc_final: 0.8725 (mp) REVERT: A 761 SER cc_start: 0.8716 (t) cc_final: 0.8244 (m) REVERT: A 810 LYS cc_start: 0.9155 (tmtm) cc_final: 0.8920 (mmtt) REVERT: A 836 PHE cc_start: 0.7914 (m-80) cc_final: 0.7573 (m-10) REVERT: A 841 GLU cc_start: 0.7312 (mt-10) cc_final: 0.6910 (mm-30) REVERT: A 861 MET cc_start: 0.8303 (mmp) cc_final: 0.7504 (mtm) REVERT: B 572 LEU cc_start: 0.9114 (mm) cc_final: 0.8048 (mm) REVERT: B 576 CYS cc_start: 0.7793 (m) cc_final: 0.7518 (m) REVERT: B 584 PHE cc_start: 0.7661 (t80) cc_final: 0.6937 (m-10) REVERT: B 590 TYR cc_start: 0.7381 (p90) cc_final: 0.6720 (p90) REVERT: B 639 ILE cc_start: 0.9007 (tp) cc_final: 0.8709 (tp) REVERT: B 655 LEU cc_start: 0.8917 (tp) cc_final: 0.8690 (tp) REVERT: B 861 MET cc_start: 0.8416 (ppp) cc_final: 0.7748 (ttt) REVERT: C 501 MET cc_start: 0.7709 (mtm) cc_final: 0.7453 (mtm) REVERT: C 612 PHE cc_start: 0.8375 (m-10) cc_final: 0.8155 (m-80) REVERT: C 668 ILE cc_start: 0.8656 (mm) cc_final: 0.8307 (pt) REVERT: C 698 LYS cc_start: 0.9351 (mmtt) cc_final: 0.8862 (mmtt) REVERT: C 709 MET cc_start: 0.8909 (mtp) cc_final: 0.8516 (mpp) REVERT: C 761 SER cc_start: 0.8693 (t) cc_final: 0.8252 (m) REVERT: C 810 LYS cc_start: 0.8159 (mmtt) cc_final: 0.7670 (mmpt) REVERT: C 836 PHE cc_start: 0.7818 (m-80) cc_final: 0.7531 (m-10) REVERT: C 841 GLU cc_start: 0.7344 (mt-10) cc_final: 0.6819 (mm-30) REVERT: D 572 LEU cc_start: 0.9063 (mm) cc_final: 0.8188 (mm) REVERT: D 576 CYS cc_start: 0.7871 (m) cc_final: 0.7594 (m) REVERT: D 612 PHE cc_start: 0.8206 (m-80) cc_final: 0.7866 (t80) REVERT: D 639 ILE cc_start: 0.9030 (tp) cc_final: 0.8733 (tp) REVERT: D 709 MET cc_start: 0.8924 (mtt) cc_final: 0.8603 (mtt) REVERT: D 861 MET cc_start: 0.8292 (ppp) cc_final: 0.7552 (ttt) outliers start: 22 outliers final: 18 residues processed: 226 average time/residue: 0.2160 time to fit residues: 76.1666 Evaluate side-chains 223 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 205 time to evaluate : 1.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 458 ARG Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 571 CYS Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 867 MET Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 565 MET 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 608 LEU Chi-restraints excluded: chain D residue 444 VAL Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 565 MET Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain D residue 823 ILE 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 67 optimal weight: 5.9990 chunk 101 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 107 optimal weight: 4.9990 chunk 115 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 133 optimal weight: 0.9980 chunk 154 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 610 ASN B 654 ASN D 654 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.4402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14446 Z= 0.211 Angle : 0.688 10.446 19546 Z= 0.350 Chirality : 0.043 0.214 2172 Planarity : 0.005 0.071 2474 Dihedral : 5.296 39.608 1936 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.11 % Allowed : 11.60 % Favored : 88.29 % Rotamer: Outliers : 1.81 % Allowed : 15.23 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.20), residues: 1774 helix: 0.81 (0.18), residues: 890 sheet: -2.67 (0.53), residues: 86 loop : -2.36 (0.22), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 589 HIS 0.008 0.001 HIS C 593 PHE 0.029 0.001 PHE B 476 TYR 0.010 0.001 TYR C 702 ARG 0.005 0.000 ARG C 458 *********************** 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 230 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 210 time to evaluate : 1.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 534 MET cc_start: 0.8919 (ttm) cc_final: 0.8578 (ttp) REVERT: A 565 MET cc_start: 0.8229 (mmm) cc_final: 0.8023 (mmt) REVERT: A 761 SER cc_start: 0.8716 (t) cc_final: 0.8230 (m) REVERT: A 836 PHE cc_start: 0.7915 (m-80) cc_final: 0.7566 (m-10) REVERT: A 841 GLU cc_start: 0.7287 (mt-10) cc_final: 0.6917 (mm-30) REVERT: A 861 MET cc_start: 0.8358 (mmp) cc_final: 0.7559 (mtm) REVERT: B 572 LEU cc_start: 0.9115 (mm) cc_final: 0.8049 (mm) REVERT: B 576 CYS cc_start: 0.7790 (m) cc_final: 0.7524 (m) REVERT: B 584 PHE cc_start: 0.7685 (t80) cc_final: 0.6960 (m-10) REVERT: B 590 TYR cc_start: 0.7463 (p90) cc_final: 0.6850 (p90) REVERT: B 609 LEU cc_start: 0.8679 (tt) cc_final: 0.7960 (mt) REVERT: B 626 LEU cc_start: 0.8212 (tp) cc_final: 0.8004 (tp) REVERT: B 639 ILE cc_start: 0.9009 (tp) cc_final: 0.8712 (tp) REVERT: B 655 LEU cc_start: 0.8926 (tp) cc_final: 0.8701 (tp) REVERT: B 800 ARG cc_start: 0.6526 (mmm160) cc_final: 0.5870 (tpt170) REVERT: B 861 MET cc_start: 0.8401 (ppp) cc_final: 0.7741 (ttt) REVERT: C 501 MET cc_start: 0.7715 (mtm) cc_final: 0.7460 (mtm) REVERT: C 612 PHE cc_start: 0.8347 (m-10) cc_final: 0.8144 (m-80) REVERT: C 668 ILE cc_start: 0.8637 (mm) cc_final: 0.8315 (pt) REVERT: C 698 LYS cc_start: 0.9360 (mmtt) cc_final: 0.8885 (mmtt) REVERT: C 709 MET cc_start: 0.8920 (mtp) cc_final: 0.8517 (mpp) REVERT: C 761 SER cc_start: 0.8699 (t) cc_final: 0.8248 (m) REVERT: C 810 LYS cc_start: 0.8139 (mmtt) cc_final: 0.7645 (mmpt) REVERT: C 836 PHE cc_start: 0.7836 (m-80) cc_final: 0.7528 (m-10) REVERT: C 841 GLU cc_start: 0.7317 (mt-10) cc_final: 0.6827 (mm-30) REVERT: D 572 LEU cc_start: 0.9200 (mm) cc_final: 0.8307 (mm) REVERT: D 576 CYS cc_start: 0.7879 (m) cc_final: 0.7598 (m) REVERT: D 612 PHE cc_start: 0.8191 (m-80) cc_final: 0.7856 (t80) REVERT: D 639 ILE cc_start: 0.9026 (tp) cc_final: 0.8733 (tp) REVERT: D 709 MET cc_start: 0.8913 (mtt) cc_final: 0.8606 (mtt) REVERT: D 861 MET cc_start: 0.8261 (ppp) cc_final: 0.7556 (ttt) outliers start: 20 outliers final: 20 residues processed: 215 average time/residue: 0.2318 time to fit residues: 77.8139 Evaluate side-chains 223 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 203 time to evaluate : 1.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 458 ARG Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 571 CYS Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 867 MET Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 565 MET Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 823 ILE Chi-restraints excluded: chain B residue 831 LEU Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 831 LEU Chi-restraints excluded: chain D residue 444 VAL Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 565 MET Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain D residue 823 ILE 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 162 optimal weight: 1.9990 chunk 148 optimal weight: 0.9980 chunk 158 optimal weight: 0.0030 chunk 95 optimal weight: 0.7980 chunk 68 optimal weight: 0.7980 chunk 124 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 142 optimal weight: 0.8980 chunk 149 optimal weight: 3.9990 chunk 157 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 654 ASN ** D 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.4539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14446 Z= 0.188 Angle : 0.681 12.312 19546 Z= 0.345 Chirality : 0.042 0.193 2172 Planarity : 0.005 0.072 2474 Dihedral : 5.225 41.047 1936 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.11 % Allowed : 11.14 % Favored : 88.74 % Rotamer: Outliers : 1.87 % Allowed : 15.48 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.21), residues: 1774 helix: 0.93 (0.18), residues: 892 sheet: -2.46 (0.49), residues: 96 loop : -2.31 (0.22), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 589 HIS 0.007 0.001 HIS C 593 PHE 0.019 0.001 PHE D 584 TYR 0.019 0.001 TYR A 702 ARG 0.004 0.000 ARG C 583 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 218 time to evaluate : 3.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 534 MET cc_start: 0.8920 (ttm) cc_final: 0.8568 (ttp) REVERT: A 761 SER cc_start: 0.8494 (t) cc_final: 0.8072 (m) REVERT: A 810 LYS cc_start: 0.8294 (mmtt) cc_final: 0.8008 (mmtm) REVERT: A 836 PHE cc_start: 0.7890 (m-80) cc_final: 0.7543 (m-10) REVERT: A 841 GLU cc_start: 0.7210 (mt-10) cc_final: 0.6800 (mm-30) REVERT: A 861 MET cc_start: 0.8389 (mmp) cc_final: 0.7590 (mtm) REVERT: B 469 GLU cc_start: 0.7552 (mm-30) cc_final: 0.7333 (mm-30) REVERT: B 572 LEU cc_start: 0.9116 (mm) cc_final: 0.8055 (mm) REVERT: B 576 CYS cc_start: 0.7774 (m) cc_final: 0.7506 (m) REVERT: B 584 PHE cc_start: 0.7693 (t80) cc_final: 0.7004 (m-10) REVERT: B 590 TYR cc_start: 0.7431 (p90) cc_final: 0.6825 (p90) REVERT: B 639 ILE cc_start: 0.9002 (tp) cc_final: 0.8711 (tp) REVERT: B 655 LEU cc_start: 0.8922 (tp) cc_final: 0.8692 (tp) REVERT: B 800 ARG cc_start: 0.6468 (mmm160) cc_final: 0.5838 (tpt170) REVERT: B 861 MET cc_start: 0.8531 (ppp) cc_final: 0.7862 (ttt) REVERT: C 501 MET cc_start: 0.7711 (mtm) cc_final: 0.7444 (mtm) REVERT: C 612 PHE cc_start: 0.8342 (m-10) cc_final: 0.8120 (m-80) REVERT: C 668 ILE cc_start: 0.8620 (mm) cc_final: 0.8317 (pt) REVERT: C 698 LYS cc_start: 0.9343 (mmtt) cc_final: 0.8868 (mmtt) REVERT: C 709 MET cc_start: 0.8927 (mtp) cc_final: 0.8516 (mpp) REVERT: C 761 SER cc_start: 0.8699 (t) cc_final: 0.8250 (m) REVERT: C 810 LYS cc_start: 0.8106 (mmtt) cc_final: 0.7629 (mmpt) REVERT: C 836 PHE cc_start: 0.7818 (m-80) cc_final: 0.7507 (m-10) REVERT: C 841 GLU cc_start: 0.7264 (mt-10) cc_final: 0.6812 (mm-30) REVERT: D 556 LEU cc_start: 0.9179 (mm) cc_final: 0.8930 (mp) REVERT: D 572 LEU cc_start: 0.9217 (mm) cc_final: 0.8355 (mm) REVERT: D 576 CYS cc_start: 0.7869 (m) cc_final: 0.7592 (m) REVERT: D 612 PHE cc_start: 0.8184 (m-80) cc_final: 0.7845 (t80) REVERT: D 639 ILE cc_start: 0.9014 (tp) cc_final: 0.8723 (tp) REVERT: D 709 MET cc_start: 0.8894 (mtt) cc_final: 0.8596 (mtt) REVERT: D 861 MET cc_start: 0.8239 (ppp) cc_final: 0.7575 (ttt) outliers start: 21 outliers final: 19 residues processed: 224 average time/residue: 0.2250 time to fit residues: 78.2507 Evaluate side-chains 230 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 211 time to evaluate : 1.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 458 ARG Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 867 MET Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 565 MET Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 823 ILE Chi-restraints excluded: chain B residue 831 LEU Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 831 LEU Chi-restraints excluded: chain D residue 444 VAL Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 565 MET Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain D residue 831 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 167 optimal weight: 0.9980 chunk 102 optimal weight: 3.9990 chunk 79 optimal weight: 0.8980 chunk 116 optimal weight: 8.9990 chunk 175 optimal weight: 0.9990 chunk 161 optimal weight: 0.7980 chunk 139 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 107 optimal weight: 0.0170 chunk 85 optimal weight: 0.0980 chunk 110 optimal weight: 0.8980 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.4687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14446 Z= 0.176 Angle : 0.678 10.446 19546 Z= 0.343 Chirality : 0.042 0.186 2172 Planarity : 0.005 0.055 2474 Dihedral : 5.180 42.276 1936 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.75 % Favored : 89.14 % Rotamer: Outliers : 2.00 % Allowed : 15.35 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.21), residues: 1774 helix: 1.06 (0.18), residues: 882 sheet: -2.41 (0.50), residues: 96 loop : -2.24 (0.23), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 589 HIS 0.007 0.001 HIS A 593 PHE 0.019 0.001 PHE D 658 TYR 0.019 0.001 TYR C 651 ARG 0.004 0.000 ARG C 583 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 221 time to evaluate : 1.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 534 MET cc_start: 0.8906 (ttm) cc_final: 0.8540 (ttp) REVERT: A 761 SER cc_start: 0.8516 (t) cc_final: 0.8085 (m) REVERT: A 810 LYS cc_start: 0.8318 (mmtt) cc_final: 0.8076 (mmtm) REVERT: A 836 PHE cc_start: 0.7869 (m-80) cc_final: 0.7527 (m-10) REVERT: A 861 MET cc_start: 0.8393 (mmp) cc_final: 0.7573 (mtm) REVERT: B 469 GLU cc_start: 0.7502 (mm-30) cc_final: 0.7301 (mm-30) REVERT: B 572 LEU cc_start: 0.9116 (mm) cc_final: 0.8063 (mm) REVERT: B 576 CYS cc_start: 0.7753 (m) cc_final: 0.7504 (m) REVERT: B 584 PHE cc_start: 0.7715 (t80) cc_final: 0.6987 (m-10) REVERT: B 590 TYR cc_start: 0.7422 (p90) cc_final: 0.6833 (p90) REVERT: B 639 ILE cc_start: 0.9047 (tp) cc_final: 0.8769 (tp) REVERT: B 655 LEU cc_start: 0.8909 (tp) cc_final: 0.8699 (tp) REVERT: B 800 ARG cc_start: 0.6142 (mmm160) cc_final: 0.5391 (tpt170) REVERT: B 861 MET cc_start: 0.8522 (ppp) cc_final: 0.7861 (ttt) REVERT: C 501 MET cc_start: 0.7701 (mtm) cc_final: 0.7461 (mtm) REVERT: C 612 PHE cc_start: 0.8340 (m-10) cc_final: 0.8123 (m-80) REVERT: C 668 ILE cc_start: 0.8682 (mm) cc_final: 0.8271 (pt) REVERT: C 698 LYS cc_start: 0.9338 (mmtt) cc_final: 0.8862 (mmtt) REVERT: C 709 MET cc_start: 0.8869 (mtp) cc_final: 0.8502 (mpp) REVERT: C 761 SER cc_start: 0.8697 (t) cc_final: 0.8234 (m) REVERT: C 810 LYS cc_start: 0.8069 (mmtt) cc_final: 0.7603 (mmpt) REVERT: C 836 PHE cc_start: 0.7780 (m-80) cc_final: 0.7455 (m-10) REVERT: C 841 GLU cc_start: 0.7378 (mt-10) cc_final: 0.7146 (mm-30) REVERT: D 556 LEU cc_start: 0.9106 (mm) cc_final: 0.8753 (mp) REVERT: D 564 TRP cc_start: 0.8893 (m100) cc_final: 0.8578 (m100) REVERT: D 572 LEU cc_start: 0.9201 (mm) cc_final: 0.8333 (mm) REVERT: D 576 CYS cc_start: 0.7946 (m) cc_final: 0.7645 (m) REVERT: D 612 PHE cc_start: 0.8181 (m-80) cc_final: 0.7820 (t80) REVERT: D 639 ILE cc_start: 0.9010 (tp) cc_final: 0.8721 (tp) REVERT: D 709 MET cc_start: 0.8877 (mtt) cc_final: 0.8579 (mtt) REVERT: D 861 MET cc_start: 0.8228 (ppp) cc_final: 0.7574 (ttt) outliers start: 23 outliers final: 19 residues processed: 226 average time/residue: 0.2242 time to fit residues: 78.3746 Evaluate side-chains 229 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 210 time to evaluate : 1.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 458 ARG Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 867 MET Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 445 LEU 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 831 LEU Chi-restraints excluded: chain D residue 444 VAL Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain D residue 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 148 optimal weight: 0.0670 chunk 42 optimal weight: 2.9990 chunk 128 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 139 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 143 optimal weight: 3.9990 chunk 17 optimal weight: 0.0670 chunk 25 optimal weight: 7.9990 chunk 122 optimal weight: 0.5980 overall best weight: 0.5056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 654 ASN ** D 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.138908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.101127 restraints weight = 60889.217| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 4.81 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3417 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3417 r_free = 0.3417 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3417 r_free = 0.3417 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3417 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.4799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14446 Z= 0.174 Angle : 0.671 10.615 19546 Z= 0.340 Chirality : 0.042 0.185 2172 Planarity : 0.005 0.071 2474 Dihedral : 5.179 42.775 1936 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.75 % Favored : 89.14 % Rotamer: Outliers : 1.74 % Allowed : 16.00 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.21), residues: 1774 helix: 1.12 (0.18), residues: 880 sheet: -2.25 (0.50), residues: 94 loop : -2.21 (0.23), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 589 HIS 0.006 0.001 HIS C 593 PHE 0.018 0.001 PHE D 584 TYR 0.016 0.001 TYR C 542 ARG 0.011 0.001 ARG C 800 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2955.94 seconds wall clock time: 53 minutes 53.41 seconds (3233.41 seconds total)