Starting phenix.real_space_refine on Thu Aug 8 01:07:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wta_32773/08_2024/7wta_32773.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wta_32773/08_2024/7wta_32773.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wta_32773/08_2024/7wta_32773.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wta_32773/08_2024/7wta_32773.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wta_32773/08_2024/7wta_32773.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wta_32773/08_2024/7wta_32773.cif" } resolution = 3.9 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= 0.000 sd= 0.001 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 148 5.16 5 C 13396 2.51 5 N 3616 2.21 5 O 3920 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 691": "OE1" <-> "OE2" Residue "A GLU 1047": "OE1" <-> "OE2" Residue "D GLU 865": "OE1" <-> "OE2" Residue "D GLU 961": "OE1" <-> "OE2" Residue "D GLU 1097": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 21080 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 684, 5255 Classifications: {'peptide': 684} Link IDs: {'PTRANS': 45, 'TRANS': 638} Chain: "B" Number of atoms: 5255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 684, 5255 Classifications: {'peptide': 684} Link IDs: {'PTRANS': 45, 'TRANS': 638} Chain: "C" Number of atoms: 5255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 684, 5255 Classifications: {'peptide': 684} Link IDs: {'PTRANS': 45, 'TRANS': 638} Chain: "D" Number of atoms: 5255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 684, 5255 Classifications: {'peptide': 684} Link IDs: {'PTRANS': 45, 'TRANS': 638} Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Time building chain proxies: 12.89, per 1000 atoms: 0.61 Number of scatterers: 21080 At special positions: 0 Unit cell: (161.7, 147.4, 127.6, 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 148 16.00 O 3920 8.00 N 3616 7.00 C 13396 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 752 " - pdb=" SG CYS A 786 " distance=2.02 Simple disulfide: pdb=" SG CYS B 752 " - pdb=" SG CYS B 786 " distance=2.03 Simple disulfide: pdb=" SG CYS C 752 " - pdb=" SG CYS C 786 " distance=2.04 Simple disulfide: pdb=" SG CYS D 752 " - pdb=" SG CYS D 786 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 9.74 Conformation dependent library (CDL) restraints added in 3.9 seconds 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5032 Finding SS restraints... Secondary structure from input PDB file: 114 helices and 16 sheets defined 47.1% alpha, 11.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.59 Creating SS restraints... Processing helix chain 'A' and resid 496 through 511 Processing helix chain 'A' and resid 540 through 560 removed outlier: 4.208A pdb=" N ILE A 544 " --> pdb=" O GLY A 540 " (cutoff:3.500A) Proline residue: A 550 - end of helix Processing helix chain 'A' and resid 568 through 577 removed outlier: 3.511A pdb=" N ALA A 573 " --> pdb=" O THR A 569 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N HIS A 574 " --> pdb=" O PHE A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 598 removed outlier: 4.172A pdb=" N LEU A 587 " --> pdb=" O ARG A 583 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS A 589 " --> pdb=" O HIS A 585 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ILE A 590 " --> pdb=" O ASP A 586 " (cutoff:3.500A) Proline residue: A 592 - end of helix Processing helix chain 'A' and resid 608 through 618 removed outlier: 3.728A pdb=" N ASP A 613 " --> pdb=" O GLY A 609 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N VAL A 614 " --> pdb=" O ALA A 610 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N MET A 616 " --> pdb=" O PHE A 612 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE A 618 " --> pdb=" O VAL A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 634 removed outlier: 3.605A pdb=" N GLU A 632 " --> pdb=" O GLN A 628 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU A 633 " --> pdb=" O GLU A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 670 removed outlier: 3.711A pdb=" N VAL A 659 " --> pdb=" O PRO A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 697 Processing helix chain 'A' and resid 719 through 734 Processing helix chain 'A' and resid 748 through 761 Processing helix chain 'A' and resid 778 through 789 removed outlier: 3.535A pdb=" N ALA A 782 " --> pdb=" O ALA A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 817 Processing helix chain 'A' and resid 828 through 843 Processing helix chain 'A' and resid 844 through 846 No H-bonds generated for 'chain 'A' and resid 844 through 846' Processing helix chain 'A' and resid 849 through 853 removed outlier: 3.829A pdb=" N ALA A 852 " --> pdb=" O ASP A 849 " (cutoff:3.500A) Processing helix chain 'A' and resid 860 through 865 Processing helix chain 'A' and resid 870 through 881 Processing helix chain 'A' and resid 886 through 901 removed outlier: 4.002A pdb=" N LYS A 892 " --> pdb=" O LYS A 888 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR A 894 " --> pdb=" O VAL A 890 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N VAL A 895 " --> pdb=" O LYS A 891 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N GLU A 896 " --> pdb=" O LYS A 892 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LEU A 901 " --> pdb=" O ALA A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 907 through 925 Processing helix chain 'A' and resid 927 through 934 Processing helix chain 'A' and resid 941 through 949 Processing helix chain 'A' and resid 960 through 969 Processing helix chain 'A' and resid 977 through 982 Processing helix chain 'A' and resid 986 through 998 removed outlier: 3.735A pdb=" N LEU A 990 " --> pdb=" O ASP A 986 " (cutoff:3.500A) Processing helix chain 'A' and resid 1003 through 1013 Processing helix chain 'A' and resid 1013 through 1028 removed outlier: 3.667A pdb=" N PHE A1017 " --> pdb=" O TYR A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1034 through 1040 Processing helix chain 'B' and resid 496 through 510 Processing helix chain 'B' and resid 541 through 548 Processing helix chain 'B' and resid 549 through 560 Processing helix chain 'B' and resid 571 through 578 removed outlier: 4.195A pdb=" N GLN B 575 " --> pdb=" O ARG B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 588 removed outlier: 3.873A pdb=" N LEU B 587 " --> pdb=" O ARG B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 598 Processing helix chain 'B' and resid 608 through 610 No H-bonds generated for 'chain 'B' and resid 608 through 610' Processing helix chain 'B' and resid 611 through 617 Processing helix chain 'B' and resid 622 through 634 removed outlier: 3.661A pdb=" N ARG B 631 " --> pdb=" O LEU B 627 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N GLU B 632 " --> pdb=" O GLN B 628 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 669 Processing helix chain 'B' and resid 682 through 697 removed outlier: 3.614A pdb=" N MET B 686 " --> pdb=" O TYR B 682 " (cutoff:3.500A) Processing helix chain 'B' and resid 719 through 734 Processing helix chain 'B' and resid 748 through 763 removed outlier: 3.849A pdb=" N ARG B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 778 through 790 removed outlier: 3.678A pdb=" N ALA B 782 " --> pdb=" O ALA B 778 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLY B 790 " --> pdb=" O CYS B 786 " (cutoff:3.500A) Processing helix chain 'B' and resid 809 through 817 removed outlier: 3.701A pdb=" N LEU B 813 " --> pdb=" O SER B 809 " (cutoff:3.500A) Processing helix chain 'B' and resid 827 through 843 removed outlier: 3.966A pdb=" N VAL B 831 " --> pdb=" O PRO B 827 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASP B 833 " --> pdb=" O GLU B 829 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLY B 843 " --> pdb=" O GLU B 839 " (cutoff:3.500A) Processing helix chain 'B' and resid 844 through 846 No H-bonds generated for 'chain 'B' and resid 844 through 846' Processing helix chain 'B' and resid 849 through 853 Processing helix chain 'B' and resid 860 through 865 Processing helix chain 'B' and resid 870 through 881 Processing helix chain 'B' and resid 886 through 893 removed outlier: 3.699A pdb=" N VAL B 890 " --> pdb=" O LYS B 886 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS B 891 " --> pdb=" O PHE B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 893 through 902 Processing helix chain 'B' and resid 908 through 925 Processing helix chain 'B' and resid 927 through 934 removed outlier: 3.820A pdb=" N GLN B 934 " --> pdb=" O GLU B 930 " (cutoff:3.500A) Processing helix chain 'B' and resid 941 through 950 removed outlier: 3.667A pdb=" N GLY B 950 " --> pdb=" O GLU B 946 " (cutoff:3.500A) Processing helix chain 'B' and resid 960 through 969 removed outlier: 3.542A pdb=" N ARG B 964 " --> pdb=" O PRO B 960 " (cutoff:3.500A) Processing helix chain 'B' and resid 977 through 982 Processing helix chain 'B' and resid 987 through 999 Processing helix chain 'B' and resid 1003 through 1013 Processing helix chain 'B' and resid 1013 through 1028 removed outlier: 3.512A pdb=" N PHE B1017 " --> pdb=" O TYR B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1034 through 1040 Processing helix chain 'C' and resid 496 through 510 removed outlier: 3.798A pdb=" N LEU C 500 " --> pdb=" O ARG C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 541 through 548 Processing helix chain 'C' and resid 549 through 560 Processing helix chain 'C' and resid 571 through 578 removed outlier: 4.048A pdb=" N GLN C 575 " --> pdb=" O ARG C 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 590 through 598 Processing helix chain 'C' and resid 608 through 610 No H-bonds generated for 'chain 'C' and resid 608 through 610' Processing helix chain 'C' and resid 611 through 616 Processing helix chain 'C' and resid 622 through 632 removed outlier: 4.331A pdb=" N GLU C 632 " --> pdb=" O GLN C 628 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 669 Processing helix chain 'C' and resid 682 through 697 Processing helix chain 'C' and resid 719 through 734 Processing helix chain 'C' and resid 748 through 763 removed outlier: 3.541A pdb=" N ARG C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 778 through 790 removed outlier: 4.176A pdb=" N GLY C 790 " --> pdb=" O CYS C 786 " (cutoff:3.500A) Processing helix chain 'C' and resid 809 through 817 removed outlier: 3.787A pdb=" N LEU C 813 " --> pdb=" O SER C 809 " (cutoff:3.500A) Processing helix chain 'C' and resid 827 through 843 removed outlier: 3.828A pdb=" N VAL C 831 " --> pdb=" O PRO C 827 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLY C 843 " --> pdb=" O GLU C 839 " (cutoff:3.500A) Processing helix chain 'C' and resid 844 through 846 No H-bonds generated for 'chain 'C' and resid 844 through 846' Processing helix chain 'C' and resid 860 through 865 Processing helix chain 'C' and resid 867 through 869 No H-bonds generated for 'chain 'C' and resid 867 through 869' Processing helix chain 'C' and resid 870 through 882 Processing helix chain 'C' and resid 886 through 902 removed outlier: 4.177A pdb=" N VAL C 895 " --> pdb=" O LYS C 891 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N GLU C 896 " --> pdb=" O LYS C 892 " (cutoff:3.500A) Processing helix chain 'C' and resid 908 through 925 Processing helix chain 'C' and resid 927 through 934 Processing helix chain 'C' and resid 941 through 950 Processing helix chain 'C' and resid 960 through 969 removed outlier: 3.981A pdb=" N ARG C 964 " --> pdb=" O PRO C 960 " (cutoff:3.500A) Processing helix chain 'C' and resid 977 through 982 Processing helix chain 'C' and resid 987 through 999 removed outlier: 3.663A pdb=" N LYS C 992 " --> pdb=" O GLN C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1003 through 1013 Processing helix chain 'C' and resid 1013 through 1028 Processing helix chain 'C' and resid 1034 through 1040 Processing helix chain 'D' and resid 496 through 511 Processing helix chain 'D' and resid 541 through 548 removed outlier: 3.582A pdb=" N LEU D 545 " --> pdb=" O PHE D 541 " (cutoff:3.500A) Processing helix chain 'D' and resid 549 through 560 Processing helix chain 'D' and resid 571 through 578 Processing helix chain 'D' and resid 584 through 598 Proline residue: D 592 - end of helix Processing helix chain 'D' and resid 610 through 617 Processing helix chain 'D' and resid 622 through 634 removed outlier: 3.515A pdb=" N ARG D 626 " --> pdb=" O CYS D 622 " (cutoff:3.500A) Processing helix chain 'D' and resid 655 through 670 Processing helix chain 'D' and resid 682 through 697 Processing helix chain 'D' and resid 719 through 733 Processing helix chain 'D' and resid 748 through 761 Processing helix chain 'D' and resid 778 through 790 removed outlier: 3.655A pdb=" N ALA D 782 " --> pdb=" O ALA D 778 " (cutoff:3.500A) Processing helix chain 'D' and resid 809 through 817 removed outlier: 4.047A pdb=" N LEU D 813 " --> pdb=" O SER D 809 " (cutoff:3.500A) Processing helix chain 'D' and resid 827 through 845 removed outlier: 3.723A pdb=" N VAL D 831 " --> pdb=" O PRO D 827 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU D 844 " --> pdb=" O GLY D 840 " (cutoff:3.500A) Processing helix chain 'D' and resid 846 through 853 removed outlier: 3.911A pdb=" N ASP D 849 " --> pdb=" O ALA D 846 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N CYS D 850 " --> pdb=" O ALA D 847 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N THR D 851 " --> pdb=" O PHE D 848 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA D 852 " --> pdb=" O ASP D 849 " (cutoff:3.500A) Processing helix chain 'D' and resid 870 through 882 Processing helix chain 'D' and resid 883 through 885 No H-bonds generated for 'chain 'D' and resid 883 through 885' Processing helix chain 'D' and resid 886 through 901 removed outlier: 3.506A pdb=" N LYS D 892 " --> pdb=" O LYS D 888 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TYR D 894 " --> pdb=" O VAL D 890 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N VAL D 895 " --> pdb=" O LYS D 891 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N GLU D 896 " --> pdb=" O LYS D 892 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LEU D 901 " --> pdb=" O ALA D 897 " (cutoff:3.500A) Processing helix chain 'D' and resid 907 through 925 Processing helix chain 'D' and resid 927 through 934 Processing helix chain 'D' and resid 941 through 950 removed outlier: 3.705A pdb=" N VAL D 945 " --> pdb=" O PRO D 941 " (cutoff:3.500A) Processing helix chain 'D' and resid 960 through 969 Processing helix chain 'D' and resid 977 through 982 Processing helix chain 'D' and resid 988 through 998 Processing helix chain 'D' and resid 1003 through 1013 removed outlier: 3.846A pdb=" N VAL D1007 " --> pdb=" O THR D1003 " (cutoff:3.500A) Processing helix chain 'D' and resid 1013 through 1028 removed outlier: 3.627A pdb=" N PHE D1017 " --> pdb=" O TYR D1013 " (cutoff:3.500A) Processing helix chain 'D' and resid 1034 through 1040 Processing sheet with id=AA1, first strand: chain 'A' and resid 564 through 567 removed outlier: 7.288A pdb=" N LEU A 565 " --> pdb=" O SER A 603 " (cutoff:3.500A) removed outlier: 8.933A pdb=" N GLU A 605 " --> pdb=" O LEU A 565 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N ASP A 567 " --> pdb=" O GLU A 605 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N MET A 604 " --> pdb=" O GLN A 640 " (cutoff:3.500A) removed outlier: 8.480A pdb=" N LEU A 642 " --> pdb=" O MET A 604 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N PHE A 639 " --> pdb=" O VAL A 673 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N ARG A 675 " --> pdb=" O PHE A 639 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N MET A 641 " --> pdb=" O ARG A 675 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N PHE A 677 " --> pdb=" O MET A 641 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N LEU A 643 " --> pdb=" O PHE A 677 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N PHE A 674 " --> pdb=" O VAL A 699 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N VAL A 700 " --> pdb=" O ILE A 737 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N CYS A 739 " --> pdb=" O VAL A 700 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ALA A 702 " --> pdb=" O CYS A 739 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N LYS A 741 " --> pdb=" O ALA A 702 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ILE A 704 " --> pdb=" O LYS A 741 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N LEU A 738 " --> pdb=" O HIS A 769 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N HIS A 771 " --> pdb=" O LEU A 738 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ILE A 740 " --> pdb=" O HIS A 771 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LEU A 768 " --> pdb=" O VAL A 793 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N ASP A 795 " --> pdb=" O LEU A 768 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N ILE A 770 " --> pdb=" O ASP A 795 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N LEU A 564 " --> pdb=" O VAL A 794 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N VAL A 796 " --> pdb=" O LEU A 564 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N MET A 566 " --> pdb=" O VAL A 796 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1047 through 1050 removed outlier: 6.726A pdb=" N PHE A1077 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N VAL A1065 " --> pdb=" O GLN A1075 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N GLN A1075 " --> pdb=" O VAL A1065 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1111 through 1113 removed outlier: 4.010A pdb=" N LEU A1175 " --> pdb=" O ILE A1112 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N ILE A1174 " --> pdb=" O VAL A1160 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N VAL A1160 " --> pdb=" O ILE A1174 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLU A1176 " --> pdb=" O ARG A1158 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY A1155 " --> pdb=" O VAL A1131 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1146 through 1149 removed outlier: 3.587A pdb=" N THR A1147 " --> pdb=" O LEU A1140 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N CYS A1138 " --> pdb=" O VAL A1149 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASP A1122 " --> pdb=" O VAL A1139 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N SER A1141 " --> pdb=" O VAL A1120 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N VAL A1120 " --> pdb=" O SER A1141 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 564 through 567 removed outlier: 7.009A pdb=" N LEU B 565 " --> pdb=" O SER B 603 " (cutoff:3.500A) removed outlier: 8.402A pdb=" N GLU B 605 " --> pdb=" O LEU B 565 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N ASP B 567 " --> pdb=" O GLU B 605 " (cutoff:3.500A) removed outlier: 8.850A pdb=" N TRP B 607 " --> pdb=" O ASP B 567 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N MET B 604 " --> pdb=" O GLN B 640 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N LEU B 642 " --> pdb=" O MET B 604 " (cutoff:3.500A) removed outlier: 9.395A pdb=" N ASN B 606 " --> pdb=" O LEU B 642 " (cutoff:3.500A) removed outlier: 13.411A pdb=" N ARG B 644 " --> pdb=" O ASN B 606 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE B 674 " --> pdb=" O VAL B 699 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N VAL B 700 " --> pdb=" O ILE B 737 " (cutoff:3.500A) removed outlier: 8.443A pdb=" N CYS B 739 " --> pdb=" O VAL B 700 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ALA B 702 " --> pdb=" O CYS B 739 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N LYS B 741 " --> pdb=" O ALA B 702 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ILE B 704 " --> pdb=" O LYS B 741 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N LEU B 738 " --> pdb=" O HIS B 769 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N LEU B 768 " --> pdb=" O VAL B 793 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N ASP B 795 " --> pdb=" O LEU B 768 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N ILE B 770 " --> pdb=" O ASP B 795 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1047 through 1051 removed outlier: 6.851A pdb=" N PHE B1077 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N VAL B1065 " --> pdb=" O GLN B1075 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N GLN B1075 " --> pdb=" O VAL B1065 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 1112 through 1113 removed outlier: 6.824A pdb=" N ILE B1112 " --> pdb=" O ILE B1174 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N ILE B1174 " --> pdb=" O VAL B1160 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N VAL B1160 " --> pdb=" O ILE B1174 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N GLU B1176 " --> pdb=" O ARG B1158 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG B1158 " --> pdb=" O GLU B1176 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 1119 through 1123 removed outlier: 3.574A pdb=" N LYS B1119 " --> pdb=" O SER B1141 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL B1139 " --> pdb=" O ILE B1121 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ILE B1123 " --> pdb=" O LEU B1137 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N LEU B1137 " --> pdb=" O ILE B1123 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N CYS B1138 " --> pdb=" O VAL B1149 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 699 through 702 removed outlier: 6.689A pdb=" N MET C 604 " --> pdb=" O GLN C 640 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N LEU C 642 " --> pdb=" O MET C 604 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N LEU C 565 " --> pdb=" O SER C 603 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N GLU C 605 " --> pdb=" O LEU C 565 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N ASP C 567 " --> pdb=" O GLU C 605 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP C 795 " --> pdb=" O ILE C 770 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N THR C 772 " --> pdb=" O ASP C 795 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ILE C 704 " --> pdb=" O LYS C 741 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 1046 through 1051 removed outlier: 3.934A pdb=" N GLU C1046 " --> pdb=" O ALA C1062 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA C1062 " --> pdb=" O GLU C1046 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N PHE C1077 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N VAL C1065 " --> pdb=" O GLN C1075 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N GLN C1075 " --> pdb=" O VAL C1065 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 1111 through 1112 removed outlier: 3.949A pdb=" N LEU C1175 " --> pdb=" O ILE C1112 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N GLU C1176 " --> pdb=" O ARG C1158 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG C1158 " --> pdb=" O GLU C1176 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 1146 through 1151 removed outlier: 6.751A pdb=" N THR C1147 " --> pdb=" O VAL C1139 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N VAL C1139 " --> pdb=" O THR C1147 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL C1149 " --> pdb=" O LEU C1137 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLN C1135 " --> pdb=" O SER C1151 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N LEU C1137 " --> pdb=" O ILE C1123 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ILE C1123 " --> pdb=" O LEU C1137 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N VAL C1139 " --> pdb=" O ILE C1121 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER C1141 " --> pdb=" O LYS C1119 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS C1119 " --> pdb=" O SER C1141 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 564 through 567 removed outlier: 7.045A pdb=" N LEU D 564 " --> pdb=" O VAL D 794 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N VAL D 796 " --> pdb=" O LEU D 564 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N MET D 566 " --> pdb=" O VAL D 796 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N LEU D 768 " --> pdb=" O VAL D 793 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N ASP D 795 " --> pdb=" O LEU D 768 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N ILE D 770 " --> pdb=" O ASP D 795 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL D 700 " --> pdb=" O ILE D 737 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N CYS D 739 " --> pdb=" O VAL D 700 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N ALA D 702 " --> pdb=" O CYS D 739 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N LYS D 741 " --> pdb=" O ALA D 702 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N ILE D 704 " --> pdb=" O LYS D 741 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N PHE D 639 " --> pdb=" O VAL D 673 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N ARG D 675 " --> pdb=" O PHE D 639 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N MET D 641 " --> pdb=" O ARG D 675 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N PHE D 677 " --> pdb=" O MET D 641 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N LEU D 643 " --> pdb=" O PHE D 677 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N MET D 604 " --> pdb=" O GLN D 640 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N LEU D 642 " --> pdb=" O MET D 604 " (cutoff:3.500A) removed outlier: 9.304A pdb=" N ASN D 606 " --> pdb=" O LEU D 642 " (cutoff:3.500A) removed outlier: 13.836A pdb=" N ARG D 644 " --> pdb=" O ASN D 606 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 1047 through 1050 removed outlier: 6.510A pdb=" N PHE D1077 " --> pdb=" O LEU D1063 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 1111 through 1113 removed outlier: 7.968A pdb=" N ILE D1112 " --> pdb=" O ILE D1174 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE D1174 " --> pdb=" O ILE D1112 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N ILE D1174 " --> pdb=" O VAL D1160 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N VAL D1160 " --> pdb=" O ILE D1174 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N GLU D1176 " --> pdb=" O ARG D1158 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N THR D1156 " --> pdb=" O GLU D1178 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 1119 through 1123 removed outlier: 7.204A pdb=" N VAL D1139 " --> pdb=" O ILE D1121 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N ILE D1123 " --> pdb=" O LEU D1137 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N LEU D1137 " --> pdb=" O ILE D1123 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N CYS D1138 " --> pdb=" O VAL D1149 " (cutoff:3.500A) 882 hydrogen bonds defined for protein. 2601 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: 8.40 Time building geometry restraints manager: 10.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3570 1.31 - 1.43: 5335 1.43 - 1.56: 12365 1.56 - 1.69: 26 1.69 - 1.82: 260 Bond restraints: 21556 Sorted by residual: bond pdb=" C6 BTI A1900 " pdb=" S1 BTI A1900 " ideal model delta sigma weight residual 1.811 1.440 0.371 2.00e-02 2.50e+03 3.44e+02 bond pdb=" C6 BTI D1900 " pdb=" S1 BTI D1900 " ideal model delta sigma weight residual 1.811 1.442 0.369 2.00e-02 2.50e+03 3.40e+02 bond pdb=" C6 BTI C1900 " pdb=" S1 BTI C1900 " ideal model delta sigma weight residual 1.811 1.443 0.368 2.00e-02 2.50e+03 3.39e+02 bond pdb=" C6 BTI B1900 " pdb=" S1 BTI B1900 " ideal model delta sigma weight residual 1.811 1.443 0.368 2.00e-02 2.50e+03 3.38e+02 bond pdb=" C3 BTI B1900 " pdb=" N3 BTI B1900 " ideal model delta sigma weight residual 1.356 1.577 -0.221 2.00e-02 2.50e+03 1.22e+02 ... (remaining 21551 not shown) Histogram of bond angle deviations from ideal: 91.49 - 100.03: 22 100.03 - 108.56: 1357 108.56 - 117.09: 14239 117.09 - 125.62: 13288 125.62 - 134.16: 314 Bond angle restraints: 29220 Sorted by residual: angle pdb=" C10 BTI C1900 " pdb=" C11 BTI C1900 " pdb=" O11 BTI C1900 " ideal model delta sigma weight residual 125.49 91.49 34.00 3.00e+00 1.11e-01 1.28e+02 angle pdb=" C10 BTI B1900 " pdb=" C11 BTI B1900 " pdb=" O11 BTI B1900 " ideal model delta sigma weight residual 125.49 92.99 32.50 3.00e+00 1.11e-01 1.17e+02 angle pdb=" C10 BTI A1900 " pdb=" C11 BTI A1900 " pdb=" O11 BTI A1900 " ideal model delta sigma weight residual 125.49 99.42 26.07 3.00e+00 1.11e-01 7.55e+01 angle pdb=" C10 BTI D1900 " pdb=" C11 BTI D1900 " pdb=" O11 BTI D1900 " ideal model delta sigma weight residual 125.49 101.36 24.13 3.00e+00 1.11e-01 6.47e+01 angle pdb=" C2 BTI B1900 " pdb=" S1 BTI B1900 " pdb=" C6 BTI B1900 " ideal model delta sigma weight residual 89.29 106.58 -17.29 3.00e+00 1.11e-01 3.32e+01 ... (remaining 29215 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 11916 17.47 - 34.93: 1006 34.93 - 52.40: 179 52.40 - 69.86: 20 69.86 - 87.33: 15 Dihedral angle restraints: 13136 sinusoidal: 5300 harmonic: 7836 Sorted by residual: dihedral pdb=" CB CYS D 752 " pdb=" SG CYS D 752 " pdb=" SG CYS D 786 " pdb=" CB CYS D 786 " ideal model delta sinusoidal sigma weight residual 93.00 176.35 -83.35 1 1.00e+01 1.00e-02 8.49e+01 dihedral pdb=" CB CYS A 752 " pdb=" SG CYS A 752 " pdb=" SG CYS A 786 " pdb=" CB CYS A 786 " ideal model delta sinusoidal sigma weight residual 93.00 142.68 -49.68 1 1.00e+01 1.00e-02 3.39e+01 dihedral pdb=" CA CYS B 786 " pdb=" C CYS B 786 " pdb=" N ALA B 787 " pdb=" CA ALA B 787 " ideal model delta harmonic sigma weight residual 180.00 155.23 24.77 0 5.00e+00 4.00e-02 2.45e+01 ... (remaining 13133 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 2410 0.041 - 0.083: 614 0.083 - 0.124: 220 0.124 - 0.166: 15 0.166 - 0.207: 5 Chirality restraints: 3264 Sorted by residual: chirality pdb=" C5 BTI C1900 " pdb=" C4 BTI C1900 " pdb=" C6 BTI C1900 " pdb=" N3 BTI C1900 " both_signs ideal model delta sigma weight residual False 2.73 2.94 -0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" C5 BTI A1900 " pdb=" C4 BTI A1900 " pdb=" C6 BTI A1900 " pdb=" N3 BTI A1900 " both_signs ideal model delta sigma weight residual False 2.73 2.92 -0.19 2.00e-01 2.50e+01 8.94e-01 chirality pdb=" C4 BTI C1900 " pdb=" C2 BTI C1900 " pdb=" C5 BTI C1900 " pdb=" N2 BTI C1900 " both_signs ideal model delta sigma weight residual False 2.75 2.57 0.18 2.00e-01 2.50e+01 8.50e-01 ... (remaining 3261 not shown) Planarity restraints: 3828 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY D 535 " -0.055 5.00e-02 4.00e+02 8.35e-02 1.12e+01 pdb=" N PRO D 536 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO D 536 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO D 536 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN B 807 " 0.028 5.00e-02 4.00e+02 4.30e-02 2.96e+00 pdb=" N PRO B 808 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO B 808 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 808 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN D 807 " -0.027 5.00e-02 4.00e+02 4.07e-02 2.64e+00 pdb=" N PRO D 808 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO D 808 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO D 808 " -0.022 5.00e-02 4.00e+02 ... (remaining 3825 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1086 2.72 - 3.26: 23479 3.26 - 3.81: 37347 3.81 - 4.35: 43228 4.35 - 4.90: 70120 Nonbonded interactions: 175260 Sorted by model distance: nonbonded pdb=" O TYR B 593 " pdb=" ND2 ASN B 597 " model vdw 2.171 3.120 nonbonded pdb=" OD2 ASP A 613 " pdb=" OH TYR A 651 " model vdw 2.183 3.040 nonbonded pdb=" NE2 GLN A1075 " pdb=" OG SER A1086 " model vdw 2.185 3.120 nonbonded pdb=" OG SER D1066 " pdb=" O GLN D1075 " model vdw 2.186 3.040 nonbonded pdb=" OE1 GLU B 961 " pdb=" NH2 ARG B 964 " model vdw 2.188 3.120 ... (remaining 175255 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 4.880 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: 0.000 Extract box with map and model: 0.760 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 61.830 Find NCS groups from input model: 1.090 Set up NCS constraints: 0.100 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: 0.010 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.0000 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: