Starting phenix.real_space_refine on Tue Jun 24 08:24:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wch_32422/06_2025/7wch_32422_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wch_32422/06_2025/7wch_32422.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wch_32422/06_2025/7wch_32422.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wch_32422/06_2025/7wch_32422.map" model { file = "/net/cci-nas-00/data/ceres_data/7wch_32422/06_2025/7wch_32422_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wch_32422/06_2025/7wch_32422_neut.cif" } resolution = 3.19 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= 0.065 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 135 5.16 5 C 17995 2.51 5 N 4766 2.21 5 O 5423 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 73 residue(s): 1.63s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 28319 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 7683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 999, 7683 Classifications: {'peptide': 999} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 53, 'TRANS': 945} Chain breaks: 9 Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 3, 'PHE:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 69 Chain: "B" Number of atoms: 7736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 7736 Classifications: {'peptide': 1002} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 53, 'TRANS': 948} Chain breaks: 9 Unresolved non-hydrogen bonds: 88 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 57 Chain: "D" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 927 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "E" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 822 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 8, 'TRANS': 98} Chain: "G" Number of atoms: 7653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 991, 7653 Classifications: {'peptide': 991} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 53, 'TRANS': 937} Chain breaks: 10 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 3, 'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 45 Chain: "H" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 927 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "L" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 822 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 8, 'TRANS': 98} Chain: "M" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 927 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "N" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 822 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 8, 'TRANS': 98} Time building chain proxies: 18.50, per 1000 atoms: 0.65 Number of scatterers: 28319 At special positions: 0 Unit cell: (163.08, 204.12, 152.28, 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 135 16.00 O 5423 8.00 N 4766 7.00 C 17995 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=46, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.02 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.06 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.28 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.02 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=1.91 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=1.41 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.06 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=1.97 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.87 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.05 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 101 " - pdb=" SG CYS D 106 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 89 " distance=2.04 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 166 " distance=2.03 Simple disulfide: pdb=" SG CYS G 291 " - pdb=" SG CYS G 301 " distance=2.02 Simple disulfide: pdb=" SG CYS G 336 " - pdb=" SG CYS G 361 " distance=1.05 Simple disulfide: pdb=" SG CYS G 379 " - pdb=" SG CYS G 432 " distance=2.06 Simple disulfide: pdb=" SG CYS G 391 " - pdb=" SG CYS G 525 " distance=2.89 Simple disulfide: pdb=" SG CYS G 480 " - pdb=" SG CYS G 488 " distance=2.03 Simple disulfide: pdb=" SG CYS G 538 " - pdb=" SG CYS G 590 " distance=2.04 Simple disulfide: pdb=" SG CYS G 662 " - pdb=" SG CYS G 671 " distance=2.03 Simple disulfide: pdb=" SG CYS G 738 " - pdb=" SG CYS G 760 " distance=2.02 Simple disulfide: pdb=" SG CYS G 743 " - pdb=" SG CYS G 749 " distance=2.03 Simple disulfide: pdb=" SG CYS G1032 " - pdb=" SG CYS G1043 " distance=2.02 Simple disulfide: pdb=" SG CYS G1082 " - pdb=" SG CYS G1126 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 101 " - pdb=" SG CYS H 106 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.04 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 96 " distance=2.03 Simple disulfide: pdb=" SG CYS M 101 " - pdb=" SG CYS M 106 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 89 " distance=2.04 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 9.30 Conformation dependent library (CDL) restraints added in 5.1 seconds 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6854 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 70 sheets defined 19.5% alpha, 26.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.84 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 386 through 390 removed outlier: 3.747A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 386 through 390' Processing helix chain 'A' and resid 405 through 408 removed outlier: 3.956A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 405 through 408' Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.657A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 752 through 757 Processing helix chain 'A' and resid 761 through 783 removed outlier: 3.552A pdb=" N ARG A 765 " --> pdb=" O THR A 761 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.715A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 936 removed outlier: 3.546A pdb=" N LYS A 933 " --> pdb=" O SER A 929 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 955 removed outlier: 3.697A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 964 Processing helix chain 'A' and resid 976 through 983 removed outlier: 3.803A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 990 through 1032 removed outlier: 3.599A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLN A1002 " --> pdb=" O THR A 998 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 removed outlier: 3.545A pdb=" N LEU B 303 " --> pdb=" O THR B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.604A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 408 removed outlier: 3.956A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 405 through 408' Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.655A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.554A pdb=" N TYR B 741 " --> pdb=" O ASP B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 754 removed outlier: 4.080A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.847A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.559A pdb=" N ALA B 890 " --> pdb=" O THR B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 removed outlier: 3.675A pdb=" N TYR B 904 " --> pdb=" O MET B 900 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 917 removed outlier: 4.242A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 912 through 917' Processing helix chain 'B' and resid 919 through 939 removed outlier: 3.771A pdb=" N SER B 939 " --> pdb=" O GLN B 935 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 964 removed outlier: 4.134A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N THR B 961 " --> pdb=" O GLN B 957 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 983 removed outlier: 3.645A pdb=" N ARG B 983 " --> pdb=" O ASP B 979 " (cutoff:3.500A) Processing helix chain 'B' and resid 991 through 1032 removed outlier: 3.512A pdb=" N LEU B1024 " --> pdb=" O ALA B1020 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 removed outlier: 3.521A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 91 removed outlier: 4.090A pdb=" N THR D 91 " --> pdb=" O SER D 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 33 removed outlier: 3.841A pdb=" N SER E 32 " --> pdb=" O VAL E 29 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU E 33 " --> pdb=" O ARG E 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 29 through 33' Processing helix chain 'E' and resid 80 through 84 removed outlier: 3.635A pdb=" N PHE E 84 " --> pdb=" O PRO E 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 294 through 304 Processing helix chain 'G' and resid 365 through 370 Processing helix chain 'G' and resid 386 through 390 removed outlier: 3.745A pdb=" N ASP G 389 " --> pdb=" O LYS G 386 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU G 390 " --> pdb=" O LEU G 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 386 through 390' Processing helix chain 'G' and resid 405 through 408 removed outlier: 3.956A pdb=" N ARG G 408 " --> pdb=" O ASP G 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 405 through 408' Processing helix chain 'G' and resid 417 through 422 Processing helix chain 'G' and resid 438 through 443 removed outlier: 3.656A pdb=" N SER G 443 " --> pdb=" O ASN G 439 " (cutoff:3.500A) Processing helix chain 'G' and resid 737 through 744 Processing helix chain 'G' and resid 746 through 754 Processing helix chain 'G' and resid 755 through 757 No H-bonds generated for 'chain 'G' and resid 755 through 757' Processing helix chain 'G' and resid 758 through 783 removed outlier: 3.835A pdb=" N ASP G 775 " --> pdb=" O ALA G 771 " (cutoff:3.500A) Processing helix chain 'G' and resid 811 through 815 removed outlier: 4.190A pdb=" N LYS G 814 " --> pdb=" O LYS G 811 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ARG G 815 " --> pdb=" O PRO G 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 811 through 815' Processing helix chain 'G' and resid 816 through 825 Processing helix chain 'G' and resid 866 through 885 removed outlier: 3.525A pdb=" N GLN G 872 " --> pdb=" O GLU G 868 " (cutoff:3.500A) Processing helix chain 'G' and resid 897 through 908 Processing helix chain 'G' and resid 913 through 918 removed outlier: 3.562A pdb=" N TYR G 917 " --> pdb=" O GLN G 913 " (cutoff:3.500A) Processing helix chain 'G' and resid 919 through 940 removed outlier: 3.520A pdb=" N LYS G 933 " --> pdb=" O SER G 929 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ILE G 934 " --> pdb=" O ALA G 930 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLN G 935 " --> pdb=" O ILE G 931 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASP G 936 " --> pdb=" O GLY G 932 " (cutoff:3.500A) Processing helix chain 'G' and resid 945 through 965 removed outlier: 4.091A pdb=" N VAL G 951 " --> pdb=" O LYS G 947 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL G 952 " --> pdb=" O LEU G 948 " (cutoff:3.500A) Processing helix chain 'G' and resid 977 through 982 removed outlier: 3.706A pdb=" N LEU G 981 " --> pdb=" O LEU G 977 " (cutoff:3.500A) Processing helix chain 'G' and resid 988 through 1032 removed outlier: 3.788A pdb=" N GLN G 992 " --> pdb=" O GLU G 988 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N ASP G 994 " --> pdb=" O GLU G 990 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA G1016 " --> pdb=" O LEU G1012 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLU G1017 " --> pdb=" O ILE G1013 " (cutoff:3.500A) Processing helix chain 'G' and resid 1141 through 1145 removed outlier: 3.721A pdb=" N LEU G1145 " --> pdb=" O GLN G1142 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 4.090A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 29 through 33 removed outlier: 3.840A pdb=" N SER L 32 " --> pdb=" O VAL L 29 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU L 33 " --> pdb=" O ARG L 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 29 through 33' Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.634A pdb=" N PHE L 84 " --> pdb=" O PRO L 81 " (cutoff:3.500A) Processing helix chain 'M' and resid 87 through 91 removed outlier: 4.089A pdb=" N THR M 91 " --> pdb=" O SER M 88 " (cutoff:3.500A) Processing helix chain 'N' and resid 29 through 33 removed outlier: 3.838A pdb=" N SER N 32 " --> pdb=" O VAL N 29 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU N 33 " --> pdb=" O ARG N 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 29 through 33' Processing helix chain 'N' and resid 80 through 84 removed outlier: 3.635A pdb=" N PHE N 84 " --> pdb=" O PRO N 81 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.550A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.358A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 9.436A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.318A pdb=" N PHE A 43 " --> pdb=" O ARG G 567 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N GLY G 566 " --> pdb=" O ASP G 574 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 7.346A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.417A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ASN A 122 " --> pdb=" O ASN A 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 317 removed outlier: 6.977A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 357 through 358 removed outlier: 3.634A pdb=" N GLY A 431 " --> pdb=" O TYR A 380 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TYR A 380 " --> pdb=" O GLY A 431 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL A 433 " --> pdb=" O LYS A 378 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.686A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 542 through 543 Processing sheet with id=AB2, first strand: chain 'A' and resid 551 through 554 Processing sheet with id=AB3, first strand: chain 'A' and resid 565 through 566 removed outlier: 6.740A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.147A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 701 through 704 removed outlier: 3.508A pdb=" N LYS B 790 " --> pdb=" O ASN A 703 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 712 through 714 Processing sheet with id=AB7, first strand: chain 'A' and resid 719 through 728 removed outlier: 7.000A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.211A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 788 through 789 removed outlier: 5.627A pdb=" N ILE A 788 " --> pdb=" O ASN G 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.321A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC3, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.551A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 9.470A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 47 through 55 removed outlier: 7.305A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.638A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 317 removed outlier: 6.576A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 325 through 328 removed outlier: 4.090A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N PHE B 565 " --> pdb=" O PHE G 43 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 357 through 358 removed outlier: 3.633A pdb=" N GLY B 431 " --> pdb=" O TYR B 380 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TYR B 380 " --> pdb=" O GLY B 431 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL B 433 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.630A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD2, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD3, first strand: chain 'B' and resid 665 through 667 removed outlier: 6.687A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.454A pdb=" N ALA B 701 " --> pdb=" O ILE G 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'B' and resid 713 through 728 removed outlier: 6.625A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.309A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1076 through 1078 removed outlier: 3.781A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.572A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 3 through 6 Processing sheet with id=AE1, first strand: chain 'D' and resid 3 through 6 Processing sheet with id=AE2, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.593A pdb=" N GLU D 10 " --> pdb=" O MET D 118 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL D 52 " --> pdb=" O ASN D 57 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASN D 57 " --> pdb=" O VAL D 52 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 4 through 6 Processing sheet with id=AE4, first strand: chain 'E' and resid 11 through 12 removed outlier: 5.772A pdb=" N LEU E 11 " --> pdb=" O GLU E 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'E' and resid 19 through 21 removed outlier: 3.594A pdb=" N ALA E 19 " --> pdb=" O ILE E 76 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 54 through 55 removed outlier: 6.494A pdb=" N TRP E 36 " --> pdb=" O LEU E 48 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL E 86 " --> pdb=" O GLN E 39 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 28 through 30 removed outlier: 8.103A pdb=" N ASN G 61 " --> pdb=" O TYR G 269 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N TYR G 269 " --> pdb=" O ASN G 61 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLU G 96 " --> pdb=" O ASN G 188 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASN G 188 " --> pdb=" O GLU G 96 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N PHE G 201 " --> pdb=" O ASP G 228 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ASP G 228 " --> pdb=" O PHE G 201 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ILE G 203 " --> pdb=" O LEU G 226 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N HIS G 207 " --> pdb=" O ALA G 222 " (cutoff:3.500A) removed outlier: 9.234A pdb=" N ALA G 222 " --> pdb=" O HIS G 207 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N VAL G 36 " --> pdb=" O LEU G 223 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 47 through 55 removed outlier: 3.503A pdb=" N ASP G 53 " --> pdb=" O ARG G 273 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASP G 287 " --> pdb=" O LYS G 278 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 84 through 85 removed outlier: 3.932A pdb=" N GLY G 103 " --> pdb=" O LEU G 241 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N GLU G 132 " --> pdb=" O CYS G 166 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N CYS G 166 " --> pdb=" O GLU G 132 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 311 through 319 removed outlier: 6.690A pdb=" N VAL G 595 " --> pdb=" O THR G 315 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N ASN G 317 " --> pdb=" O GLY G 593 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N GLY G 593 " --> pdb=" O ASN G 317 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N GLY G 594 " --> pdb=" O GLN G 613 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'G' and resid 324 through 325 removed outlier: 6.547A pdb=" N GLU G 324 " --> pdb=" O ASN G 540 " (cutoff:3.500A) removed outlier: 8.644A pdb=" N ASN G 542 " --> pdb=" O GLU G 324 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'G' and resid 357 through 358 removed outlier: 3.633A pdb=" N GLY G 431 " --> pdb=" O TYR G 380 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TYR G 380 " --> pdb=" O GLY G 431 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL G 433 " --> pdb=" O LYS G 378 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LYS G 378 " --> pdb=" O VAL G 433 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'G' and resid 361 through 362 removed outlier: 6.871A pdb=" N CYS G 361 " --> pdb=" O CYS G 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'G' and resid 452 through 454 Processing sheet with id=AF6, first strand: chain 'G' and resid 473 through 474 Processing sheet with id=AF7, first strand: chain 'G' and resid 654 through 655 removed outlier: 6.563A pdb=" N ILE G 670 " --> pdb=" O ILE G 666 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'G' and resid 711 through 728 removed outlier: 7.023A pdb=" N GLN G1071 " --> pdb=" O THR G 716 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N PHE G 718 " --> pdb=" O PRO G1069 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ILE G 720 " --> pdb=" O TYR G1067 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N TYR G1067 " --> pdb=" O ILE G 720 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N VAL G 722 " --> pdb=" O VAL G1065 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL G1065 " --> pdb=" O VAL G 722 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N THR G 724 " --> pdb=" O LEU G1063 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU G1063 " --> pdb=" O THR G 724 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ILE G 726 " --> pdb=" O VAL G1061 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL G1061 " --> pdb=" O ILE G 726 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N GLY G1059 " --> pdb=" O PRO G 728 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N GLY G1059 " --> pdb=" O SER G1055 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N SER G1055 " --> pdb=" O GLY G1059 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL G1061 " --> pdb=" O PRO G1053 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N LEU G1063 " --> pdb=" O SER G1051 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N SER G1051 " --> pdb=" O LEU G1063 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N VAL G1065 " --> pdb=" O LEU G1049 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'G' and resid 711 through 728 removed outlier: 7.023A pdb=" N GLN G1071 " --> pdb=" O THR G 716 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N PHE G 718 " --> pdb=" O PRO G1069 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ILE G 720 " --> pdb=" O TYR G1067 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N TYR G1067 " --> pdb=" O ILE G 720 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N VAL G 722 " --> pdb=" O VAL G1065 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL G1065 " --> pdb=" O VAL G 722 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N THR G 724 " --> pdb=" O LEU G1063 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU G1063 " --> pdb=" O THR G 724 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ILE G 726 " --> pdb=" O VAL G1061 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL G1061 " --> pdb=" O ILE G 726 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N GLY G1059 " --> pdb=" O PRO G 728 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR G1076 " --> pdb=" O SER G1097 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA G1078 " --> pdb=" O PHE G1095 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N PHE G1095 " --> pdb=" O ALA G1078 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'G' and resid 733 through 736 removed outlier: 4.224A pdb=" N LYS G 733 " --> pdb=" O LEU G 861 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'G' and resid 1120 through 1122 Processing sheet with id=AG3, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AG4, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AG5, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.594A pdb=" N GLU H 10 " --> pdb=" O MET H 118 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AG7, first strand: chain 'L' and resid 11 through 12 removed outlier: 5.772A pdb=" N LEU L 11 " --> pdb=" O GLU L 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG7 Processing sheet with id=AG8, first strand: chain 'L' and resid 19 through 21 removed outlier: 3.595A pdb=" N ALA L 19 " --> pdb=" O ILE L 76 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'L' and resid 54 through 55 removed outlier: 6.494A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL L 86 " --> pdb=" O GLN L 39 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'M' and resid 3 through 6 Processing sheet with id=AH2, first strand: chain 'M' and resid 3 through 6 Processing sheet with id=AH3, first strand: chain 'M' and resid 10 through 12 removed outlier: 3.595A pdb=" N GLU M 10 " --> pdb=" O MET M 118 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY M 49 " --> pdb=" O TRP M 36 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL M 52 " --> pdb=" O ASN M 57 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASN M 57 " --> pdb=" O VAL M 52 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'N' and resid 4 through 6 Processing sheet with id=AH5, first strand: chain 'N' and resid 11 through 12 removed outlier: 5.773A pdb=" N LEU N 11 " --> pdb=" O GLU N 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH5 Processing sheet with id=AH6, first strand: chain 'N' and resid 19 through 21 removed outlier: 3.594A pdb=" N ALA N 19 " --> pdb=" O ILE N 76 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'N' and resid 54 through 55 removed outlier: 6.493A pdb=" N TRP N 36 " --> pdb=" O LEU N 48 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL N 86 " --> pdb=" O GLN N 39 " (cutoff:3.500A) 990 hydrogen bonds defined for protein. 2664 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: 14.14 Time building geometry restraints manager: 10.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.11 - 1.28: 4665 1.28 - 1.44: 8159 1.44 - 1.60: 15954 1.60 - 1.76: 29 1.76 - 1.93: 142 Bond restraints: 28949 Sorted by residual: bond pdb=" CA HIS L 92 " pdb=" C HIS L 92 " ideal model delta sigma weight residual 1.526 1.376 0.151 1.11e-02 8.12e+03 1.85e+02 bond pdb=" CA HIS N 92 " pdb=" C HIS N 92 " ideal model delta sigma weight residual 1.526 1.376 0.150 1.11e-02 8.12e+03 1.84e+02 bond pdb=" CA HIS E 92 " pdb=" C HIS E 92 " ideal model delta sigma weight residual 1.526 1.376 0.150 1.11e-02 8.12e+03 1.83e+02 bond pdb=" C GLU A1072 " pdb=" O GLU A1072 " ideal model delta sigma weight residual 1.233 1.114 0.119 1.32e-02 5.74e+03 8.09e+01 bond pdb=" C THR A1076 " pdb=" O THR A1076 " ideal model delta sigma weight residual 1.235 1.122 0.114 1.28e-02 6.10e+03 7.88e+01 ... (remaining 28944 not shown) Histogram of bond angle deviations from ideal: 0.00 - 12.05: 39377 12.05 - 24.09: 21 24.09 - 36.14: 1 36.14 - 48.18: 3 48.18 - 60.23: 2 Bond angle restraints: 39404 Sorted by residual: angle pdb=" C PHE A 329 " pdb=" N PRO A 330 " pdb=" CD PRO A 330 " ideal model delta sigma weight residual 125.00 64.77 60.23 4.10e+00 5.95e-02 2.16e+02 angle pdb=" C GLY A 526 " pdb=" N PRO A 527 " pdb=" CD PRO A 527 " ideal model delta sigma weight residual 125.00 66.10 58.90 4.10e+00 5.95e-02 2.06e+02 angle pdb=" C ASN A 334 " pdb=" N LEU A 335 " pdb=" CA LEU A 335 " ideal model delta sigma weight residual 121.42 103.86 17.56 1.43e+00 4.89e-01 1.51e+02 angle pdb=" C PRO L 96 " pdb=" N PRO L 97 " pdb=" CD PRO L 97 " ideal model delta sigma weight residual 125.00 78.82 46.18 4.10e+00 5.95e-02 1.27e+02 angle pdb=" C PRO N 96 " pdb=" N PRO N 97 " pdb=" CD PRO N 97 " ideal model delta sigma weight residual 125.00 78.83 46.17 4.10e+00 5.95e-02 1.27e+02 ... (remaining 39399 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 15531 17.98 - 35.96: 1394 35.96 - 53.94: 242 53.94 - 71.93: 61 71.93 - 89.91: 34 Dihedral angle restraints: 17262 sinusoidal: 6622 harmonic: 10640 Sorted by residual: dihedral pdb=" CA SER E 7 " pdb=" C SER E 7 " pdb=" N PRO E 8 " pdb=" CA PRO E 8 " ideal model delta harmonic sigma weight residual -180.00 -121.82 -58.18 0 5.00e+00 4.00e-02 1.35e+02 dihedral pdb=" CA SER N 7 " pdb=" C SER N 7 " pdb=" N PRO N 8 " pdb=" CA PRO N 8 " ideal model delta harmonic sigma weight residual -180.00 -121.83 -58.17 0 5.00e+00 4.00e-02 1.35e+02 dihedral pdb=" CA SER L 7 " pdb=" C SER L 7 " pdb=" N PRO L 8 " pdb=" CA PRO L 8 " ideal model delta harmonic sigma weight residual -180.00 -121.84 -58.16 0 5.00e+00 4.00e-02 1.35e+02 ... (remaining 17259 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.227: 4423 0.227 - 0.455: 65 0.455 - 0.682: 7 0.682 - 0.909: 1 0.909 - 1.137: 1 Chirality restraints: 4497 Sorted by residual: chirality pdb=" CA CYS A 617 " pdb=" N CYS A 617 " pdb=" C CYS A 617 " pdb=" CB CYS A 617 " both_signs ideal model delta sigma weight residual False 2.51 1.37 1.14 2.00e-01 2.50e+01 3.23e+01 chirality pdb=" CA THR G 333 " pdb=" N THR G 333 " pdb=" C THR G 333 " pdb=" CB THR G 333 " both_signs ideal model delta sigma weight residual False 2.53 1.84 0.68 2.00e-01 2.50e+01 1.17e+01 chirality pdb=" CG LEU G 821 " pdb=" CB LEU G 821 " pdb=" CD1 LEU G 821 " pdb=" CD2 LEU G 821 " both_signs ideal model delta sigma weight residual False -2.59 -1.95 -0.64 2.00e-01 2.50e+01 1.01e+01 ... (remaining 4494 not shown) Planarity restraints: 5109 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO G 330 " 0.053 2.00e-02 2.50e+03 1.23e-01 1.50e+02 pdb=" C PRO G 330 " -0.211 2.00e-02 2.50e+03 pdb=" O PRO G 330 " 0.087 2.00e-02 2.50e+03 pdb=" N ASN G 331 " 0.071 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 526 " 0.183 5.00e-02 4.00e+02 2.56e-01 1.05e+02 pdb=" N PRO A 527 " -0.434 5.00e-02 4.00e+02 pdb=" CA PRO A 527 " 0.190 5.00e-02 4.00e+02 pdb=" CD PRO A 527 " 0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO N 96 " -0.157 5.00e-02 4.00e+02 2.35e-01 8.82e+01 pdb=" N PRO N 97 " 0.402 5.00e-02 4.00e+02 pdb=" CA PRO N 97 " -0.166 5.00e-02 4.00e+02 pdb=" CD PRO N 97 " -0.080 5.00e-02 4.00e+02 ... (remaining 5106 not shown) Histogram of nonbonded interaction distances: 1.33 - 2.04: 13 2.04 - 2.76: 5132 2.76 - 3.47: 37582 3.47 - 4.19: 67944 4.19 - 4.90: 121092 Nonbonded interactions: 231763 Sorted by model distance: nonbonded pdb=" OD1 ASN B 334 " pdb=" CA CYS B 361 " model vdw 1.327 3.470 nonbonded pdb=" SG CYS A 336 " pdb=" O VAL A 362 " model vdw 1.527 3.400 nonbonded pdb=" CG PRO A 330 " pdb=" CA GLN A 580 " model vdw 1.668 3.870 nonbonded pdb=" OD1 ASN B 334 " pdb=" CB CYS B 361 " model vdw 1.680 3.440 nonbonded pdb=" O PHE A 392 " pdb=" CG2 VAL A 524 " model vdw 1.783 3.460 ... (remaining 231758 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 27 through 59 or (resid 60 and (name N or name CA or name \ C or name O or name CB )) or resid 61 through 66 or resid 81 through 187 or (res \ id 188 and (name N or name CA or name C or name O or name CB )) or resid 189 thr \ ough 209 or resid 217 through 243 or resid 264 through 280 or (resid 281 and (na \ me N or name CA or name C or name O or name CB )) or resid 282 through 327 or re \ sid 330 through 1146)) selection = (chain 'B' and (resid 27 through 66 or resid 81 through 101 or (resid 102 and (n \ ame N or name CA or name C or name O or name CB )) or resid 103 through 128 or ( \ resid 129 and (name N or name CA or name C or name O or name CB )) or resid 130 \ through 187 or (resid 188 and (name N or name CA or name C or name O or name CB \ )) or resid 189 or (resid 190 and (name N or name CA or name C or name O or name \ CB )) or resid 191 through 194 or (resid 195 through 198 and (name N or name CA \ or name C or name O or name CB )) or resid 199 through 209 or resid 217 through \ 236 or (resid 237 and (name N or name CA or name C or name O or name CB )) or r \ esid 238 or (resid 239 and (name N or name CA or name C or name O or name CB )) \ or resid 240 through 243 or resid 264 through 327 or resid 330 through 620 or re \ sid 641 through 1146)) selection = (chain 'G' and (resid 27 through 95 or resid 99 through 128 or (resid 129 and (n \ ame N or name CA or name C or name O or name CB )) or resid 130 through 140 or r \ esid 158 through 175 or (resid 176 through 188 and (name N or name CA or name C \ or name O or name CB )) or resid 189 or (resid 190 and (name N or name CA or nam \ e C or name O or name CB )) or resid 191 through 195 or (resid 196 through 198 a \ nd (name N or name CA or name C or name O or name CB )) or resid 199 through 236 \ or (resid 237 and (name N or name CA or name C or name O or name CB )) or resid \ 238 or (resid 239 and (name N or name CA or name C or name O or name CB )) or r \ esid 240 through 289 or (resid 290 and (name N or name CA or name C or name O or \ name CB )) or resid 291 through 620 or resid 641 through 1146)) } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'M' } ncs_group { reference = chain 'E' selection = chain 'L' selection = chain 'N' } 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 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: 6.430 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: 0.030 Extract box with map and model: 1.270 Check model and map are aligned: 0.220 Set scattering table: 0.300 Process input model: 72.500 Find NCS groups from input model: 1.490 Set up NCS constraints: 0.140 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 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 : 0.018 0.985 28996 Z= 0.856 Angle : 1.533 60.229 39496 Z= 0.785 Chirality : 0.084 1.137 4497 Planarity : 0.012 0.256 5109 Dihedral : 14.506 89.907 10270 Min Nonbonded Distance : 1.327 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 1.05 % Allowed : 7.83 % Favored : 91.12 % Rotamer: Outliers : 0.93 % Allowed : 1.15 % Favored : 97.92 % Cbeta Deviations : 0.44 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.67 % 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: -2.89 (0.12), residues: 3602 helix: -2.21 (0.16), residues: 647 sheet: -0.97 (0.17), residues: 950 loop : -2.35 (0.12), residues: 2005 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.004 TRP A 886 HIS 0.012 0.003 HIS N 92 PHE 0.107 0.004 PHE A 906 TYR 0.059 0.003 TYR A 904 ARG 0.026 0.002 ARG B 190 Details of bonding type rmsd hydrogen bonds : bond 0.18115 ( 961) hydrogen bonds : angle 8.85173 ( 2664) SS BOND : bond 0.25022 ( 46) SS BOND : angle 10.81057 ( 92) covalent geometry : bond 0.01474 (28949) covalent geometry : angle 1.44354 (39404) Misc. bond : bond 0.19036 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 3198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 496 time to evaluate : 2.960 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 191 GLU cc_start: 0.6672 (mt-10) cc_final: 0.6031 (mt-10) REVERT: A 211 ASN cc_start: 0.6115 (m-40) cc_final: 0.5793 (p0) REVERT: A 369 TYR cc_start: 0.5554 (t80) cc_final: 0.5302 (t80) REVERT: A 537 LYS cc_start: 0.8862 (mtmt) cc_final: 0.8574 (mptt) REVERT: A 902 MET cc_start: 0.8306 (tpp) cc_final: 0.7868 (tpt) REVERT: B 29 THR cc_start: 0.6515 (m) cc_final: 0.6131 (p) REVERT: B 85 PRO cc_start: 0.8134 (Cg_exo) cc_final: 0.7154 (Cg_endo) REVERT: B 246 ARG cc_start: 0.5442 (pmt170) cc_final: 0.4915 (mmt180) REVERT: B 387 LEU cc_start: 0.7923 (OUTLIER) cc_final: 0.7557 (pp) REVERT: B 646 ARG cc_start: 0.8170 (mmm-85) cc_final: 0.7968 (tpm170) REVERT: B 902 MET cc_start: 0.8749 (tpt) cc_final: 0.8473 (tpt) REVERT: B 1117 THR cc_start: 0.9111 (m) cc_final: 0.8910 (p) outliers start: 29 outliers final: 15 residues processed: 520 average time/residue: 0.3877 time to fit residues: 320.0875 Evaluate side-chains 280 residues out of total 3198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 264 time to evaluate : 2.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 330 PRO Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain G residue 335 LEU Chi-restraints excluded: chain N residue 95 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 307 optimal weight: 0.9980 chunk 275 optimal weight: 0.6980 chunk 153 optimal weight: 2.9990 chunk 94 optimal weight: 0.7980 chunk 186 optimal weight: 0.7980 chunk 147 optimal weight: 2.9990 chunk 285 optimal weight: 0.9990 chunk 110 optimal weight: 6.9990 chunk 173 optimal weight: 0.7980 chunk 212 optimal weight: 1.9990 chunk 330 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 GLN A 613 GLN A 901 GLN A 969 ASN B 282 ASN ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B1002 GLN B1135 ASN ** D 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 91 GLN G 955 ASN G1071 GLN L 39 GLN ** L 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 91 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.150913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.099772 restraints weight = 56596.495| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.88 r_work: 0.3282 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 28996 Z= 0.161 Angle : 0.724 16.463 39496 Z= 0.379 Chirality : 0.049 0.333 4497 Planarity : 0.008 0.167 5109 Dihedral : 6.586 58.304 3945 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.39 % Allowed : 6.19 % Favored : 93.42 % Rotamer: Outliers : 1.95 % Allowed : 9.00 % Favored : 89.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.67 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.13), residues: 3602 helix: -0.75 (0.19), residues: 655 sheet: -0.71 (0.16), residues: 970 loop : -2.09 (0.13), residues: 1977 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 353 HIS 0.008 0.001 HIS E 92 PHE 0.023 0.002 PHE A 906 TYR 0.021 0.001 TYR M 80 ARG 0.010 0.001 ARG H 67 Details of bonding type rmsd hydrogen bonds : bond 0.03750 ( 961) hydrogen bonds : angle 6.20861 ( 2664) SS BOND : bond 0.00543 ( 46) SS BOND : angle 2.04389 ( 92) covalent geometry : bond 0.00369 (28949) covalent geometry : angle 0.71838 (39404) Misc. bond : bond 0.00376 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 3198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 316 time to evaluate : 3.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7457 (tt0) REVERT: A 211 ASN cc_start: 0.6537 (m-40) cc_final: 0.5959 (p0) REVERT: A 347 PHE cc_start: 0.7210 (m-10) cc_final: 0.6906 (m-80) REVERT: A 537 LYS cc_start: 0.9115 (mtmt) cc_final: 0.8888 (mptt) REVERT: A 582 LEU cc_start: 0.8668 (tt) cc_final: 0.8411 (mt) REVERT: A 740 MET cc_start: 0.8583 (ttt) cc_final: 0.8372 (ttm) REVERT: B 29 THR cc_start: 0.6803 (m) cc_final: 0.6343 (p) REVERT: B 246 ARG cc_start: 0.5756 (pmt170) cc_final: 0.5123 (mmt180) REVERT: B 353 TRP cc_start: 0.7619 (p-90) cc_final: 0.7413 (p-90) REVERT: B 390 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.7626 (mt) REVERT: B 497 PHE cc_start: 0.5971 (m-10) cc_final: 0.5595 (m-80) REVERT: B 646 ARG cc_start: 0.8999 (mmm-85) cc_final: 0.8489 (tpm170) REVERT: B 745 ASP cc_start: 0.8144 (p0) cc_final: 0.7926 (p0) REVERT: D 2 MET cc_start: 0.3983 (mmp) cc_final: 0.2983 (mtm) REVERT: D 81 LEU cc_start: 0.6154 (tt) cc_final: 0.5952 (tt) REVERT: E 4 LEU cc_start: 0.1941 (OUTLIER) cc_final: 0.1630 (tp) REVERT: E 95 SER cc_start: 0.7960 (OUTLIER) cc_final: 0.7741 (t) REVERT: G 347 PHE cc_start: 0.7325 (OUTLIER) cc_final: 0.6829 (t80) REVERT: G 453 TYR cc_start: 0.6897 (p90) cc_final: 0.6361 (p90) REVERT: G 512 VAL cc_start: 0.8381 (t) cc_final: 0.8111 (p) REVERT: G 987 PRO cc_start: 0.8826 (Cg_exo) cc_final: 0.8427 (Cg_endo) REVERT: H 2 MET cc_start: 0.7513 (ptm) cc_final: 0.6417 (mpp) REVERT: H 73 ASP cc_start: 0.6908 (t0) cc_final: 0.6326 (p0) REVERT: H 110 PHE cc_start: 0.3669 (m-80) cc_final: 0.3088 (m-80) REVERT: L 36 TRP cc_start: 0.4901 (m100) cc_final: 0.3772 (m100) REVERT: M 118 MET cc_start: 0.5595 (mmt) cc_final: 0.4950 (mmt) outliers start: 61 outliers final: 27 residues processed: 361 average time/residue: 0.3812 time to fit residues: 227.0364 Evaluate side-chains 272 residues out of total 3198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 241 time to evaluate : 3.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 1142 GLN Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 36 TRP Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain G residue 240 THR Chi-restraints excluded: chain G residue 335 LEU Chi-restraints excluded: chain G residue 347 PHE Chi-restraints excluded: chain G residue 393 THR Chi-restraints excluded: chain G residue 859 THR Chi-restraints excluded: chain G residue 997 ILE Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 97 PRO Chi-restraints excluded: chain M residue 2 MET Chi-restraints excluded: chain M residue 52 VAL Chi-restraints excluded: chain N residue 97 PRO Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 242 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 141 optimal weight: 10.0000 chunk 206 optimal weight: 7.9990 chunk 345 optimal weight: 20.0000 chunk 124 optimal weight: 6.9990 chunk 305 optimal weight: 2.9990 chunk 154 optimal weight: 1.9990 chunk 9 optimal weight: 9.9990 chunk 69 optimal weight: 0.0570 chunk 120 optimal weight: 2.9990 overall best weight: 2.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 440 ASN B 487 ASN ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1058 HIS ** D 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 ASN ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 563 GLN G 955 ASN L 39 GLN N 90 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.145702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.094228 restraints weight = 56706.222| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.63 r_work: 0.3191 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.153 28996 Z= 0.248 Angle : 0.719 12.199 39496 Z= 0.376 Chirality : 0.050 0.302 4497 Planarity : 0.007 0.159 5109 Dihedral : 5.928 59.114 3928 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.72 % Favored : 92.98 % Rotamer: Outliers : 2.71 % Allowed : 11.24 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.67 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.13), residues: 3602 helix: -0.06 (0.20), residues: 633 sheet: -0.67 (0.16), residues: 968 loop : -2.08 (0.13), residues: 2001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 50 HIS 0.004 0.001 HIS A1088 PHE 0.024 0.002 PHE A 898 TYR 0.020 0.002 TYR A1067 ARG 0.006 0.001 ARG B 646 Details of bonding type rmsd hydrogen bonds : bond 0.03772 ( 961) hydrogen bonds : angle 5.79695 ( 2664) SS BOND : bond 0.00618 ( 46) SS BOND : angle 2.14301 ( 92) covalent geometry : bond 0.00575 (28949) covalent geometry : angle 0.71273 (39404) Misc. bond : bond 0.00245 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 3198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 256 time to evaluate : 3.111 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 191 GLU cc_start: 0.8219 (mt-10) cc_final: 0.7565 (mt-10) REVERT: A 211 ASN cc_start: 0.6330 (m-40) cc_final: 0.5822 (p0) REVERT: A 537 LYS cc_start: 0.9210 (mtmt) cc_final: 0.8957 (mptt) REVERT: A 582 LEU cc_start: 0.8758 (tt) cc_final: 0.8531 (mt) REVERT: A 740 MET cc_start: 0.8733 (ttt) cc_final: 0.8517 (ttm) REVERT: B 239 GLN cc_start: 0.6477 (mm110) cc_final: 0.5792 (tp40) REVERT: B 246 ARG cc_start: 0.5812 (pmt170) cc_final: 0.5094 (mmt180) REVERT: B 353 TRP cc_start: 0.7989 (p-90) cc_final: 0.7673 (p-90) REVERT: B 390 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7634 (mt) REVERT: B 497 PHE cc_start: 0.5912 (m-10) cc_final: 0.5511 (m-80) REVERT: B 745 ASP cc_start: 0.8098 (p0) cc_final: 0.7891 (p0) REVERT: B 858 LEU cc_start: 0.9317 (OUTLIER) cc_final: 0.8875 (pp) REVERT: D 2 MET cc_start: 0.3962 (mmp) cc_final: 0.3064 (mtm) REVERT: E 4 LEU cc_start: 0.2432 (OUTLIER) cc_final: 0.2206 (tp) REVERT: G 242 LEU cc_start: 0.7772 (OUTLIER) cc_final: 0.7517 (mt) REVERT: G 274 THR cc_start: 0.9108 (OUTLIER) cc_final: 0.8898 (p) REVERT: G 347 PHE cc_start: 0.7400 (OUTLIER) cc_final: 0.6882 (t80) REVERT: G 453 TYR cc_start: 0.6759 (p90) cc_final: 0.6142 (p90) REVERT: G 512 VAL cc_start: 0.8316 (t) cc_final: 0.8068 (p) REVERT: G 855 PHE cc_start: 0.7331 (OUTLIER) cc_final: 0.7008 (t80) REVERT: H 2 MET cc_start: 0.7742 (ptm) cc_final: 0.6020 (mmp) REVERT: H 3 GLN cc_start: 0.6966 (mp10) cc_final: 0.6682 (pp30) REVERT: H 73 ASP cc_start: 0.6890 (t0) cc_final: 0.6218 (p0) REVERT: L 34 LEU cc_start: 0.4689 (OUTLIER) cc_final: 0.4361 (mp) REVERT: L 36 TRP cc_start: 0.4859 (m100) cc_final: 0.4017 (m100) outliers start: 85 outliers final: 52 residues processed: 325 average time/residue: 0.3658 time to fit residues: 197.6422 Evaluate side-chains 275 residues out of total 3198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 215 time to evaluate : 2.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1082 CYS Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1142 GLN Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 36 TRP Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain G residue 240 THR Chi-restraints excluded: chain G residue 242 LEU Chi-restraints excluded: chain G residue 274 THR Chi-restraints excluded: chain G residue 332 ILE Chi-restraints excluded: chain G residue 335 LEU Chi-restraints excluded: chain G residue 347 PHE Chi-restraints excluded: chain G residue 393 THR Chi-restraints excluded: chain G residue 534 VAL Chi-restraints excluded: chain G residue 615 VAL Chi-restraints excluded: chain G residue 738 CYS Chi-restraints excluded: chain G residue 855 PHE Chi-restraints excluded: chain G residue 859 THR Chi-restraints excluded: chain G residue 977 LEU Chi-restraints excluded: chain G residue 997 ILE Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 97 PRO Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain M residue 52 VAL Chi-restraints excluded: chain M residue 74 MET Chi-restraints excluded: chain N residue 97 PRO Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 188 optimal weight: 0.8980 chunk 147 optimal weight: 5.9990 chunk 113 optimal weight: 9.9990 chunk 21 optimal weight: 0.6980 chunk 174 optimal weight: 0.6980 chunk 61 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 68 optimal weight: 0.8980 chunk 216 optimal weight: 0.0980 chunk 331 optimal weight: 5.9990 chunk 175 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 440 ASN A 493 GLN A 907 ASN ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 38 GLN G 125 ASN ** G 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 950 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.147519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.096490 restraints weight = 56978.722| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.73 r_work: 0.3225 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 28996 Z= 0.125 Angle : 0.625 10.783 39496 Z= 0.325 Chirality : 0.046 0.277 4497 Planarity : 0.006 0.150 5109 Dihedral : 5.486 56.931 3927 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.75 % Favored : 94.00 % Rotamer: Outliers : 2.46 % Allowed : 12.93 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.07 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.14), residues: 3602 helix: 0.32 (0.21), residues: 641 sheet: -0.43 (0.17), residues: 954 loop : -1.99 (0.13), residues: 2007 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 353 HIS 0.002 0.001 HIS B 207 PHE 0.017 0.001 PHE B 168 TYR 0.017 0.001 TYR A1067 ARG 0.011 0.000 ARG H 38 Details of bonding type rmsd hydrogen bonds : bond 0.03181 ( 961) hydrogen bonds : angle 5.49646 ( 2664) SS BOND : bond 0.00417 ( 46) SS BOND : angle 1.73325 ( 92) covalent geometry : bond 0.00287 (28949) covalent geometry : angle 0.62049 (39404) Misc. bond : bond 0.00191 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 3198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 254 time to evaluate : 3.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 ASN cc_start: 0.6365 (m-40) cc_final: 0.5826 (p0) REVERT: A 537 LYS cc_start: 0.9129 (mtmt) cc_final: 0.8871 (mptt) REVERT: A 740 MET cc_start: 0.8667 (ttt) cc_final: 0.8447 (ttm) REVERT: A 823 PHE cc_start: 0.8350 (m-80) cc_final: 0.8140 (m-80) REVERT: A 1041 ASP cc_start: 0.8470 (t0) cc_final: 0.8266 (t0) REVERT: B 239 GLN cc_start: 0.6436 (mm110) cc_final: 0.5727 (tp40) REVERT: B 246 ARG cc_start: 0.5833 (pmt170) cc_final: 0.5112 (mmt180) REVERT: B 335 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8445 (mm) REVERT: B 353 TRP cc_start: 0.7779 (p-90) cc_final: 0.7539 (p-90) REVERT: B 434 ILE cc_start: 0.8280 (OUTLIER) cc_final: 0.7949 (mp) REVERT: B 497 PHE cc_start: 0.6004 (m-10) cc_final: 0.5583 (m-80) REVERT: B 858 LEU cc_start: 0.9347 (OUTLIER) cc_final: 0.8917 (pp) REVERT: D 2 MET cc_start: 0.3995 (mmp) cc_final: 0.3143 (mtm) REVERT: E 4 LEU cc_start: 0.2522 (OUTLIER) cc_final: 0.2289 (tp) REVERT: G 242 LEU cc_start: 0.7831 (mp) cc_final: 0.7588 (mt) REVERT: G 347 PHE cc_start: 0.7392 (OUTLIER) cc_final: 0.6718 (t80) REVERT: G 374 PHE cc_start: 0.6770 (m-10) cc_final: 0.6308 (m-10) REVERT: G 453 TYR cc_start: 0.6920 (p90) cc_final: 0.6571 (p90) REVERT: G 855 PHE cc_start: 0.7146 (OUTLIER) cc_final: 0.6540 (t80) REVERT: H 2 MET cc_start: 0.7732 (ptm) cc_final: 0.5963 (mmp) REVERT: H 3 GLN cc_start: 0.7122 (mp10) cc_final: 0.6531 (pp30) REVERT: H 23 LYS cc_start: 0.7680 (tptp) cc_final: 0.7352 (mptt) REVERT: H 38 ARG cc_start: 0.5125 (OUTLIER) cc_final: 0.4862 (ttt180) REVERT: H 73 ASP cc_start: 0.7220 (t0) cc_final: 0.6782 (p0) REVERT: H 118 MET cc_start: 0.7864 (tpp) cc_final: 0.6762 (pmm) REVERT: L 36 TRP cc_start: 0.5316 (m100) cc_final: 0.4149 (m100) REVERT: M 80 TYR cc_start: 0.6979 (m-10) cc_final: 0.6726 (m-80) outliers start: 77 outliers final: 42 residues processed: 314 average time/residue: 0.3642 time to fit residues: 190.8815 Evaluate side-chains 267 residues out of total 3198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 218 time to evaluate : 2.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1082 CYS Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1142 GLN Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain G residue 240 THR Chi-restraints excluded: chain G residue 347 PHE Chi-restraints excluded: chain G residue 393 THR Chi-restraints excluded: chain G residue 432 CYS Chi-restraints excluded: chain G residue 534 VAL Chi-restraints excluded: chain G residue 855 PHE Chi-restraints excluded: chain G residue 977 LEU Chi-restraints excluded: chain G residue 997 ILE Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 12 LYS Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 110 PHE Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 97 PRO Chi-restraints excluded: chain M residue 74 MET Chi-restraints excluded: chain M residue 75 SER Chi-restraints excluded: chain M residue 105 THR Chi-restraints excluded: chain N residue 97 PRO Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 19 optimal weight: 4.9990 chunk 221 optimal weight: 7.9990 chunk 137 optimal weight: 0.9990 chunk 296 optimal weight: 0.7980 chunk 278 optimal weight: 0.0870 chunk 283 optimal weight: 0.0470 chunk 243 optimal weight: 4.9990 chunk 176 optimal weight: 2.9990 chunk 345 optimal weight: 10.0000 chunk 162 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 overall best weight: 0.7860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 440 ASN ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 102 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.146952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.096719 restraints weight = 56615.839| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.81 r_work: 0.3185 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 28996 Z= 0.131 Angle : 0.615 10.717 39496 Z= 0.319 Chirality : 0.046 0.272 4497 Planarity : 0.006 0.145 5109 Dihedral : 5.247 57.529 3925 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.89 % Favored : 93.86 % Rotamer: Outliers : 2.55 % Allowed : 13.79 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.07 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.14), residues: 3602 helix: 0.56 (0.21), residues: 639 sheet: -0.49 (0.16), residues: 983 loop : -1.91 (0.13), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 36 HIS 0.002 0.001 HIS B 207 PHE 0.016 0.001 PHE A 906 TYR 0.018 0.001 TYR G 453 ARG 0.004 0.000 ARG H 44 Details of bonding type rmsd hydrogen bonds : bond 0.03126 ( 961) hydrogen bonds : angle 5.36543 ( 2664) SS BOND : bond 0.00518 ( 46) SS BOND : angle 1.95038 ( 92) covalent geometry : bond 0.00306 (28949) covalent geometry : angle 0.60834 (39404) Misc. bond : bond 0.00141 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 3198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 244 time to evaluate : 3.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 ASN cc_start: 0.6269 (m-40) cc_final: 0.5933 (p0) REVERT: A 342 PHE cc_start: 0.8794 (m-80) cc_final: 0.8555 (m-80) REVERT: A 440 ASN cc_start: 0.8648 (t160) cc_final: 0.8352 (m110) REVERT: A 740 MET cc_start: 0.8471 (ttt) cc_final: 0.8254 (ttm) REVERT: B 239 GLN cc_start: 0.6365 (mm110) cc_final: 0.5708 (tp40) REVERT: B 246 ARG cc_start: 0.5698 (pmt170) cc_final: 0.5036 (mmt180) REVERT: B 335 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8484 (mm) REVERT: B 353 TRP cc_start: 0.7730 (p-90) cc_final: 0.7480 (p-90) REVERT: B 434 ILE cc_start: 0.8257 (OUTLIER) cc_final: 0.7907 (mp) REVERT: B 497 PHE cc_start: 0.5941 (m-10) cc_final: 0.5607 (m-80) REVERT: B 858 LEU cc_start: 0.9324 (OUTLIER) cc_final: 0.8924 (pp) REVERT: D 2 MET cc_start: 0.3838 (mmp) cc_final: 0.3023 (mtm) REVERT: D 36 TRP cc_start: 0.3220 (m100) cc_final: 0.2822 (m100) REVERT: E 4 LEU cc_start: 0.2725 (OUTLIER) cc_final: 0.2427 (tp) REVERT: G 274 THR cc_start: 0.9061 (OUTLIER) cc_final: 0.8851 (p) REVERT: G 347 PHE cc_start: 0.7452 (OUTLIER) cc_final: 0.6803 (t80) REVERT: G 855 PHE cc_start: 0.6925 (OUTLIER) cc_final: 0.6419 (t80) REVERT: H 2 MET cc_start: 0.7785 (ptm) cc_final: 0.6047 (mmp) REVERT: H 3 GLN cc_start: 0.6949 (mp10) cc_final: 0.6511 (pp30) REVERT: H 23 LYS cc_start: 0.7695 (tptp) cc_final: 0.7353 (mppt) REVERT: H 35 GLN cc_start: 0.5360 (OUTLIER) cc_final: 0.5124 (pm20) REVERT: H 38 ARG cc_start: 0.5011 (OUTLIER) cc_final: 0.4684 (ttt180) REVERT: H 118 MET cc_start: 0.8006 (tpp) cc_final: 0.6903 (pmm) REVERT: M 118 MET cc_start: 0.5824 (mmt) cc_final: 0.5193 (mmt) outliers start: 80 outliers final: 52 residues processed: 306 average time/residue: 0.4978 time to fit residues: 255.9912 Evaluate side-chains 281 residues out of total 3198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 220 time to evaluate : 3.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 659 SER Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1082 CYS Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1142 GLN Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 97 PRO Chi-restraints excluded: chain G residue 240 THR Chi-restraints excluded: chain G residue 274 THR Chi-restraints excluded: chain G residue 347 PHE Chi-restraints excluded: chain G residue 393 THR Chi-restraints excluded: chain G residue 432 CYS Chi-restraints excluded: chain G residue 534 VAL Chi-restraints excluded: chain G residue 615 VAL Chi-restraints excluded: chain G residue 855 PHE Chi-restraints excluded: chain G residue 859 THR Chi-restraints excluded: chain G residue 977 LEU Chi-restraints excluded: chain G residue 997 ILE Chi-restraints excluded: chain G residue 1136 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 12 LYS Chi-restraints excluded: chain H residue 35 GLN Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 100 HIS Chi-restraints excluded: chain H residue 110 PHE Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 97 PRO Chi-restraints excluded: chain M residue 52 VAL Chi-restraints excluded: chain M residue 74 MET Chi-restraints excluded: chain M residue 75 SER Chi-restraints excluded: chain M residue 105 THR Chi-restraints excluded: chain N residue 97 PRO Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 167 optimal weight: 0.0970 chunk 56 optimal weight: 0.9980 chunk 328 optimal weight: 0.8980 chunk 187 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 170 optimal weight: 0.0770 chunk 34 optimal weight: 3.9990 chunk 297 optimal weight: 2.9990 chunk 109 optimal weight: 9.9990 chunk 41 optimal weight: 10.0000 chunk 310 optimal weight: 0.9980 overall best weight: 0.6136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 354 ASN ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 31 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 = 0.4154 r_free = 0.4154 target = 0.147401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.097718 restraints weight = 56668.239| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.73 r_work: 0.3214 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.3917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 28996 Z= 0.119 Angle : 0.595 10.039 39496 Z= 0.309 Chirality : 0.045 0.270 4497 Planarity : 0.006 0.135 5109 Dihedral : 5.041 58.163 3925 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.83 % Favored : 93.92 % Rotamer: Outliers : 2.52 % Allowed : 14.75 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.07 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.14), residues: 3602 helix: 0.74 (0.21), residues: 647 sheet: -0.37 (0.17), residues: 921 loop : -1.82 (0.13), residues: 2034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 36 HIS 0.004 0.001 HIS L 92 PHE 0.019 0.001 PHE B 168 TYR 0.018 0.001 TYR B 170 ARG 0.004 0.000 ARG H 67 Details of bonding type rmsd hydrogen bonds : bond 0.03041 ( 961) hydrogen bonds : angle 5.22351 ( 2664) SS BOND : bond 0.00493 ( 46) SS BOND : angle 1.64589 ( 92) covalent geometry : bond 0.00274 (28949) covalent geometry : angle 0.59079 (39404) Misc. bond : bond 0.00111 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 3198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 246 time to evaluate : 3.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 ASN cc_start: 0.6093 (m-40) cc_final: 0.5794 (p0) REVERT: A 440 ASN cc_start: 0.8615 (t160) cc_final: 0.8325 (m110) REVERT: B 239 GLN cc_start: 0.6340 (mm110) cc_final: 0.5805 (tp40) REVERT: B 246 ARG cc_start: 0.5762 (pmt170) cc_final: 0.4953 (mmt180) REVERT: B 335 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8470 (mm) REVERT: B 353 TRP cc_start: 0.7760 (p-90) cc_final: 0.7499 (p-90) REVERT: B 434 ILE cc_start: 0.8289 (OUTLIER) cc_final: 0.7935 (mp) REVERT: B 858 LEU cc_start: 0.9278 (OUTLIER) cc_final: 0.8911 (pp) REVERT: D 2 MET cc_start: 0.3642 (mmp) cc_final: 0.2934 (mtm) REVERT: E 4 LEU cc_start: 0.2421 (OUTLIER) cc_final: 0.2151 (tp) REVERT: G 274 THR cc_start: 0.9088 (OUTLIER) cc_final: 0.8860 (p) REVERT: G 347 PHE cc_start: 0.7407 (OUTLIER) cc_final: 0.6841 (t80) REVERT: G 855 PHE cc_start: 0.6839 (OUTLIER) cc_final: 0.6386 (t80) REVERT: H 2 MET cc_start: 0.7813 (ptm) cc_final: 0.6052 (mmp) REVERT: H 3 GLN cc_start: 0.7002 (mp10) cc_final: 0.6676 (pp30) REVERT: H 18 VAL cc_start: 0.8013 (p) cc_final: 0.7802 (m) REVERT: H 34 MET cc_start: 0.6963 (tpt) cc_final: 0.6713 (tpt) REVERT: H 46 GLU cc_start: 0.6160 (pt0) cc_final: 0.5906 (pt0) REVERT: H 118 MET cc_start: 0.7996 (tpp) cc_final: 0.6867 (pmm) REVERT: M 118 MET cc_start: 0.5867 (mmt) cc_final: 0.5243 (mmt) outliers start: 79 outliers final: 48 residues processed: 308 average time/residue: 0.3653 time to fit residues: 187.8498 Evaluate side-chains 273 residues out of total 3198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 218 time to evaluate : 3.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 659 SER Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1082 CYS Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1142 GLN Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 97 PRO Chi-restraints excluded: chain G residue 240 THR Chi-restraints excluded: chain G residue 274 THR Chi-restraints excluded: chain G residue 347 PHE Chi-restraints excluded: chain G residue 432 CYS Chi-restraints excluded: chain G residue 534 VAL Chi-restraints excluded: chain G residue 551 VAL Chi-restraints excluded: chain G residue 615 VAL Chi-restraints excluded: chain G residue 855 PHE Chi-restraints excluded: chain G residue 977 LEU Chi-restraints excluded: chain G residue 1136 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 12 LYS Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 110 PHE Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 97 PRO Chi-restraints excluded: chain M residue 74 MET Chi-restraints excluded: chain M residue 75 SER Chi-restraints excluded: chain M residue 105 THR Chi-restraints excluded: chain N residue 97 PRO Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 14 optimal weight: 0.0570 chunk 281 optimal weight: 0.9980 chunk 323 optimal weight: 9.9990 chunk 137 optimal weight: 0.4980 chunk 47 optimal weight: 0.0970 chunk 342 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 chunk 223 optimal weight: 4.9990 chunk 93 optimal weight: 0.9990 chunk 262 optimal weight: 9.9990 chunk 27 optimal weight: 9.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 GLN A1011 GLN ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 388 ASN ** G 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.147504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.097874 restraints weight = 56773.388| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.77 r_work: 0.3203 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.4104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 28996 Z= 0.115 Angle : 0.584 8.898 39496 Z= 0.304 Chirality : 0.045 0.259 4497 Planarity : 0.006 0.126 5109 Dihedral : 4.833 57.015 3923 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.86 % Favored : 93.89 % Rotamer: Outliers : 2.43 % Allowed : 15.23 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.07 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.14), residues: 3602 helix: 0.86 (0.21), residues: 645 sheet: -0.35 (0.17), residues: 920 loop : -1.73 (0.13), residues: 2037 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 353 HIS 0.003 0.000 HIS G1088 PHE 0.017 0.001 PHE B 377 TYR 0.016 0.001 TYR B 170 ARG 0.009 0.000 ARG B 355 Details of bonding type rmsd hydrogen bonds : bond 0.02944 ( 961) hydrogen bonds : angle 5.11084 ( 2664) SS BOND : bond 0.00601 ( 46) SS BOND : angle 1.53585 ( 92) covalent geometry : bond 0.00264 (28949) covalent geometry : angle 0.57973 (39404) Misc. bond : bond 0.00102 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 3198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 231 time to evaluate : 3.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7589 (mp) REVERT: A 211 ASN cc_start: 0.5908 (m-40) cc_final: 0.5645 (p0) REVERT: A 378 LYS cc_start: 0.7809 (ptpp) cc_final: 0.7497 (ptpt) REVERT: A 440 ASN cc_start: 0.8674 (t160) cc_final: 0.8384 (m110) REVERT: A 580 GLN cc_start: 0.4977 (OUTLIER) cc_final: 0.4379 (tm-30) REVERT: B 239 GLN cc_start: 0.6403 (mm110) cc_final: 0.5779 (tp40) REVERT: B 246 ARG cc_start: 0.5770 (pmt170) cc_final: 0.4948 (mmt180) REVERT: B 353 TRP cc_start: 0.7765 (p-90) cc_final: 0.7292 (p-90) REVERT: B 434 ILE cc_start: 0.8272 (OUTLIER) cc_final: 0.7973 (mp) REVERT: D 2 MET cc_start: 0.4118 (mmp) cc_final: 0.3449 (mtm) REVERT: D 36 TRP cc_start: 0.3148 (m100) cc_final: 0.2673 (m100) REVERT: E 4 LEU cc_start: 0.3094 (OUTLIER) cc_final: 0.2820 (tp) REVERT: G 274 THR cc_start: 0.9089 (OUTLIER) cc_final: 0.8858 (p) REVERT: G 347 PHE cc_start: 0.7384 (OUTLIER) cc_final: 0.6773 (t80) REVERT: G 453 TYR cc_start: 0.7010 (p90) cc_final: 0.6705 (p90) REVERT: G 617 CYS cc_start: 0.7050 (m) cc_final: 0.6795 (p) REVERT: G 855 PHE cc_start: 0.6870 (OUTLIER) cc_final: 0.6404 (t80) REVERT: G 1136 THR cc_start: 0.9195 (OUTLIER) cc_final: 0.8993 (p) REVERT: H 2 MET cc_start: 0.7818 (ptm) cc_final: 0.6038 (mmp) REVERT: H 18 VAL cc_start: 0.8064 (p) cc_final: 0.7843 (m) REVERT: H 23 LYS cc_start: 0.7782 (tptp) cc_final: 0.7439 (mptt) REVERT: H 70 ILE cc_start: 0.6675 (pt) cc_final: 0.6247 (mt) REVERT: H 81 LEU cc_start: 0.4015 (OUTLIER) cc_final: 0.3781 (tp) REVERT: H 118 MET cc_start: 0.8100 (tpp) cc_final: 0.6927 (pmm) REVERT: M 118 MET cc_start: 0.5953 (mmt) cc_final: 0.5321 (mmt) outliers start: 76 outliers final: 50 residues processed: 288 average time/residue: 0.4047 time to fit residues: 196.3369 Evaluate side-chains 275 residues out of total 3198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 216 time to evaluate : 3.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 659 SER Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1082 CYS Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 274 THR Chi-restraints excluded: chain G residue 347 PHE Chi-restraints excluded: chain G residue 391 CYS Chi-restraints excluded: chain G residue 393 THR Chi-restraints excluded: chain G residue 432 CYS Chi-restraints excluded: chain G residue 534 VAL Chi-restraints excluded: chain G residue 551 VAL Chi-restraints excluded: chain G residue 615 VAL Chi-restraints excluded: chain G residue 855 PHE Chi-restraints excluded: chain G residue 859 THR Chi-restraints excluded: chain G residue 977 LEU Chi-restraints excluded: chain G residue 1136 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 12 LYS Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 100 HIS Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 97 PRO Chi-restraints excluded: chain M residue 2 MET Chi-restraints excluded: chain M residue 52 VAL Chi-restraints excluded: chain M residue 74 MET Chi-restraints excluded: chain M residue 75 SER Chi-restraints excluded: chain M residue 105 THR Chi-restraints excluded: chain N residue 97 PRO Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 266 optimal weight: 1.9990 chunk 209 optimal weight: 8.9990 chunk 210 optimal weight: 30.0000 chunk 101 optimal weight: 0.0170 chunk 120 optimal weight: 3.9990 chunk 336 optimal weight: 8.9990 chunk 295 optimal weight: 0.5980 chunk 70 optimal weight: 0.0020 chunk 264 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 355 optimal weight: 0.8980 overall best weight: 0.7028 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 907 ASN ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 388 ASN ** G 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 955 ASN H 3 GLN H 6 GLN ** H 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.146996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.097052 restraints weight = 56815.132| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.74 r_work: 0.3217 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.4307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 28996 Z= 0.121 Angle : 0.583 9.771 39496 Z= 0.305 Chirality : 0.045 0.252 4497 Planarity : 0.005 0.116 5109 Dihedral : 4.760 56.895 3921 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.66 % Favored : 94.11 % Rotamer: Outliers : 2.62 % Allowed : 15.36 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.07 % Twisted General : 0.03 % 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: -1.21 (0.14), residues: 3602 helix: 0.96 (0.21), residues: 642 sheet: -0.21 (0.17), residues: 893 loop : -1.73 (0.13), residues: 2067 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 36 HIS 0.003 0.001 HIS G1088 PHE 0.031 0.001 PHE B 497 TYR 0.017 0.001 TYR B1067 ARG 0.005 0.000 ARG H 62 Details of bonding type rmsd hydrogen bonds : bond 0.02966 ( 961) hydrogen bonds : angle 5.08868 ( 2664) SS BOND : bond 0.00431 ( 46) SS BOND : angle 1.55116 ( 92) covalent geometry : bond 0.00283 (28949) covalent geometry : angle 0.57921 (39404) Misc. bond : bond 0.00085 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 3198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 229 time to evaluate : 4.291 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 117 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7639 (mp) REVERT: A 211 ASN cc_start: 0.6079 (m-40) cc_final: 0.5638 (p0) REVERT: A 378 LYS cc_start: 0.7826 (ptpp) cc_final: 0.7532 (ptpt) REVERT: A 440 ASN cc_start: 0.8679 (t160) cc_final: 0.8383 (m110) REVERT: B 239 GLN cc_start: 0.6750 (mm110) cc_final: 0.6096 (tp40) REVERT: B 353 TRP cc_start: 0.7856 (p-90) cc_final: 0.7552 (p-90) REVERT: B 434 ILE cc_start: 0.8215 (OUTLIER) cc_final: 0.7940 (mp) REVERT: B 858 LEU cc_start: 0.9283 (OUTLIER) cc_final: 0.8879 (pp) REVERT: D 2 MET cc_start: 0.4213 (mmp) cc_final: 0.3594 (mtm) REVERT: G 274 THR cc_start: 0.9151 (OUTLIER) cc_final: 0.8935 (p) REVERT: G 347 PHE cc_start: 0.7546 (OUTLIER) cc_final: 0.6922 (t80) REVERT: G 617 CYS cc_start: 0.7397 (m) cc_final: 0.7014 (p) REVERT: G 855 PHE cc_start: 0.7152 (OUTLIER) cc_final: 0.6579 (t80) REVERT: H 2 MET cc_start: 0.6861 (ptm) cc_final: 0.5748 (mmp) REVERT: H 18 VAL cc_start: 0.8115 (p) cc_final: 0.7785 (m) REVERT: H 34 MET cc_start: 0.7516 (tpt) cc_final: 0.7175 (tpp) REVERT: H 70 ILE cc_start: 0.6688 (pt) cc_final: 0.6239 (mt) REVERT: H 87 ARG cc_start: 0.6431 (mpp-170) cc_final: 0.6195 (mtm180) REVERT: H 118 MET cc_start: 0.8121 (tpp) cc_final: 0.6939 (pmm) REVERT: L 36 TRP cc_start: 0.5180 (m100) cc_final: 0.4273 (m100) REVERT: M 118 MET cc_start: 0.5916 (mmt) cc_final: 0.5292 (mmt) outliers start: 82 outliers final: 53 residues processed: 290 average time/residue: 0.4468 time to fit residues: 218.6898 Evaluate side-chains 277 residues out of total 3198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 218 time to evaluate : 5.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 659 SER Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1082 CYS Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1142 GLN Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 274 THR Chi-restraints excluded: chain G residue 347 PHE Chi-restraints excluded: chain G residue 391 CYS Chi-restraints excluded: chain G residue 393 THR Chi-restraints excluded: chain G residue 432 CYS Chi-restraints excluded: chain G residue 534 VAL Chi-restraints excluded: chain G residue 551 VAL Chi-restraints excluded: chain G residue 615 VAL Chi-restraints excluded: chain G residue 855 PHE Chi-restraints excluded: chain G residue 859 THR Chi-restraints excluded: chain G residue 977 LEU Chi-restraints excluded: chain G residue 1050 MET Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 100 HIS Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 97 PRO Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain M residue 2 MET Chi-restraints excluded: chain M residue 52 VAL Chi-restraints excluded: chain M residue 74 MET Chi-restraints excluded: chain M residue 105 THR Chi-restraints excluded: chain N residue 97 PRO Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 354 optimal weight: 9.9990 chunk 122 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 227 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 chunk 26 optimal weight: 9.9990 chunk 37 optimal weight: 6.9990 chunk 232 optimal weight: 4.9990 chunk 208 optimal weight: 30.0000 chunk 101 optimal weight: 1.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN A1011 GLN ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 388 ASN ** G 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 955 ASN ** H 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.141941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.090742 restraints weight = 56687.618| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 2.65 r_work: 0.3116 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.4569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 28996 Z= 0.289 Angle : 0.702 9.612 39496 Z= 0.367 Chirality : 0.049 0.200 4497 Planarity : 0.005 0.100 5109 Dihedral : 5.306 57.703 3921 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.00 % Favored : 92.84 % Rotamer: Outliers : 2.08 % Allowed : 16.32 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.07 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.14), residues: 3602 helix: 0.50 (0.21), residues: 653 sheet: -0.44 (0.17), residues: 944 loop : -1.85 (0.13), residues: 2005 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP N 98 HIS 0.007 0.001 HIS A1048 PHE 0.018 0.002 PHE M 29 TYR 0.020 0.002 TYR A1067 ARG 0.007 0.001 ARG G1039 Details of bonding type rmsd hydrogen bonds : bond 0.03744 ( 961) hydrogen bonds : angle 5.42999 ( 2664) SS BOND : bond 0.00634 ( 46) SS BOND : angle 2.16193 ( 92) covalent geometry : bond 0.00678 (28949) covalent geometry : angle 0.69528 (39404) Misc. bond : bond 0.00083 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 3198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 219 time to evaluate : 3.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 ASN cc_start: 0.5979 (m-40) cc_final: 0.5573 (p0) REVERT: A 226 LEU cc_start: 0.7590 (mt) cc_final: 0.7352 (mt) REVERT: A 378 LYS cc_start: 0.8013 (ptpp) cc_final: 0.7728 (ptpt) REVERT: B 239 GLN cc_start: 0.7258 (mm110) cc_final: 0.6443 (tt0) REVERT: B 353 TRP cc_start: 0.8055 (p-90) cc_final: 0.7715 (p-90) REVERT: B 434 ILE cc_start: 0.8345 (OUTLIER) cc_final: 0.8028 (mp) REVERT: B 497 PHE cc_start: 0.5206 (m-80) cc_final: 0.4372 (t80) REVERT: B 858 LEU cc_start: 0.9283 (OUTLIER) cc_final: 0.8867 (pp) REVERT: B 918 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.7947 (mp0) REVERT: B 981 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.7833 (pp) REVERT: B 1138 TYR cc_start: 0.8681 (t80) cc_final: 0.8476 (t80) REVERT: D 2 MET cc_start: 0.4441 (mmp) cc_final: 0.3843 (mtm) REVERT: G 347 PHE cc_start: 0.7606 (OUTLIER) cc_final: 0.6956 (t80) REVERT: G 617 CYS cc_start: 0.7565 (m) cc_final: 0.7262 (p) REVERT: G 855 PHE cc_start: 0.7387 (OUTLIER) cc_final: 0.6839 (t80) REVERT: H 34 MET cc_start: 0.7752 (tpt) cc_final: 0.7315 (tpp) REVERT: L 36 TRP cc_start: 0.5071 (m100) cc_final: 0.4291 (m100) outliers start: 65 outliers final: 47 residues processed: 270 average time/residue: 0.4014 time to fit residues: 180.9252 Evaluate side-chains 261 residues out of total 3198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 208 time to evaluate : 3.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 659 SER Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1082 CYS Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 274 THR Chi-restraints excluded: chain G residue 347 PHE Chi-restraints excluded: chain G residue 391 CYS Chi-restraints excluded: chain G residue 393 THR Chi-restraints excluded: chain G residue 432 CYS Chi-restraints excluded: chain G residue 551 VAL Chi-restraints excluded: chain G residue 615 VAL Chi-restraints excluded: chain G residue 855 PHE Chi-restraints excluded: chain G residue 859 THR Chi-restraints excluded: chain G residue 1050 MET Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain M residue 52 VAL Chi-restraints excluded: chain M residue 71 THR Chi-restraints excluded: chain M residue 74 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 164 optimal weight: 1.9990 chunk 328 optimal weight: 5.9990 chunk 262 optimal weight: 10.0000 chunk 304 optimal weight: 0.7980 chunk 142 optimal weight: 0.2980 chunk 29 optimal weight: 5.9990 chunk 94 optimal weight: 0.9990 chunk 266 optimal weight: 1.9990 chunk 20 optimal weight: 0.2980 chunk 149 optimal weight: 0.2980 chunk 91 optimal weight: 0.9990 overall best weight: 0.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 ASN A 907 ASN B 498 GLN B 856 ASN G 388 ASN G 450 ASN ** G 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN ** H 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.145486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.095286 restraints weight = 56623.731| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 2.77 r_work: 0.3189 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.4737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 28996 Z= 0.118 Angle : 0.610 14.750 39496 Z= 0.317 Chirality : 0.045 0.227 4497 Planarity : 0.005 0.097 5109 Dihedral : 4.952 58.334 3921 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.64 % Favored : 94.20 % Rotamer: Outliers : 1.47 % Allowed : 16.99 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.07 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.14), residues: 3602 helix: 0.74 (0.21), residues: 655 sheet: -0.25 (0.17), residues: 897 loop : -1.73 (0.13), residues: 2050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP M 36 HIS 0.003 0.001 HIS L 92 PHE 0.013 0.001 PHE B 238 TYR 0.015 0.001 TYR A1067 ARG 0.005 0.000 ARG A 408 Details of bonding type rmsd hydrogen bonds : bond 0.03072 ( 961) hydrogen bonds : angle 5.16006 ( 2664) SS BOND : bond 0.00410 ( 46) SS BOND : angle 1.51518 ( 92) covalent geometry : bond 0.00273 (28949) covalent geometry : angle 0.60669 (39404) Misc. bond : bond 0.00072 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7204 Ramachandran restraints generated. 3602 Oldfield, 0 Emsley, 3602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 3198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 217 time to evaluate : 3.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 ASN cc_start: 0.5972 (m-40) cc_final: 0.5590 (m-40) REVERT: A 378 LYS cc_start: 0.7774 (ptpp) cc_final: 0.7475 (ptpt) REVERT: A 418 ILE cc_start: 0.7857 (mm) cc_final: 0.7556 (pt) REVERT: A 440 ASN cc_start: 0.8616 (t0) cc_final: 0.8372 (m110) REVERT: B 239 GLN cc_start: 0.6809 (mm110) cc_final: 0.6109 (tp40) REVERT: B 353 TRP cc_start: 0.7929 (p-90) cc_final: 0.7515 (p-90) REVERT: B 434 ILE cc_start: 0.8246 (OUTLIER) cc_final: 0.7928 (mp) REVERT: B 497 PHE cc_start: 0.4857 (m-80) cc_final: 0.4138 (t80) REVERT: B 858 LEU cc_start: 0.9293 (OUTLIER) cc_final: 0.8902 (pp) REVERT: B 918 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.7960 (mp0) REVERT: D 2 MET cc_start: 0.4395 (mmp) cc_final: 0.3929 (mtm) REVERT: G 347 PHE cc_start: 0.7533 (OUTLIER) cc_final: 0.6878 (t80) REVERT: G 617 CYS cc_start: 0.7495 (m) cc_final: 0.7039 (p) REVERT: G 855 PHE cc_start: 0.7171 (OUTLIER) cc_final: 0.6594 (t80) REVERT: H 18 VAL cc_start: 0.7747 (p) cc_final: 0.7384 (m) REVERT: H 34 MET cc_start: 0.7691 (tpt) cc_final: 0.7355 (tpp) REVERT: H 38 ARG cc_start: 0.5106 (ttt-90) cc_final: 0.4829 (ttt180) REVERT: H 73 ASP cc_start: 0.6017 (p0) cc_final: 0.5688 (p0) REVERT: H 80 TYR cc_start: 0.6015 (m-80) cc_final: 0.5793 (m-80) REVERT: H 94 TYR cc_start: 0.6791 (m-10) cc_final: 0.5806 (m-80) REVERT: H 118 MET cc_start: 0.8098 (tpp) cc_final: 0.6810 (pmm) outliers start: 46 outliers final: 35 residues processed: 255 average time/residue: 0.3900 time to fit residues: 165.4569 Evaluate side-chains 248 residues out of total 3198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 208 time to evaluate : 4.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 659 SER Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1082 CYS Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 274 THR Chi-restraints excluded: chain G residue 347 PHE Chi-restraints excluded: chain G residue 432 CYS Chi-restraints excluded: chain G residue 551 VAL Chi-restraints excluded: chain G residue 615 VAL Chi-restraints excluded: chain G residue 855 PHE Chi-restraints excluded: chain G residue 859 THR Chi-restraints excluded: chain G residue 977 LEU Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain M residue 52 VAL Chi-restraints excluded: chain M residue 74 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 258 optimal weight: 9.9990 chunk 54 optimal weight: 0.9980 chunk 253 optimal weight: 3.9990 chunk 315 optimal weight: 0.5980 chunk 246 optimal weight: 6.9990 chunk 333 optimal weight: 7.9990 chunk 355 optimal weight: 0.2980 chunk 29 optimal weight: 20.0000 chunk 36 optimal weight: 9.9990 chunk 260 optimal weight: 8.9990 chunk 308 optimal weight: 0.7980 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN ** H 103 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 = 0.4107 r_free = 0.4107 target = 0.143789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.092796 restraints weight = 56686.094| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 2.68 r_work: 0.3171 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.4824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 28996 Z= 0.168 Angle : 0.625 12.138 39496 Z= 0.323 Chirality : 0.046 0.194 4497 Planarity : 0.005 0.098 5109 Dihedral : 4.949 58.087 3921 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.00 % Favored : 93.84 % Rotamer: Outliers : 1.79 % Allowed : 16.76 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.07 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.14), residues: 3602 helix: 0.69 (0.21), residues: 668 sheet: -0.28 (0.17), residues: 897 loop : -1.73 (0.13), residues: 2037 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 98 HIS 0.004 0.001 HIS A1048 PHE 0.021 0.001 PHE B 168 TYR 0.017 0.001 TYR A1067 ARG 0.007 0.000 ARG D 87 Details of bonding type rmsd hydrogen bonds : bond 0.03232 ( 961) hydrogen bonds : angle 5.15783 ( 2664) SS BOND : bond 0.00496 ( 46) SS BOND : angle 1.66409 ( 92) covalent geometry : bond 0.00399 (28949) covalent geometry : angle 0.62027 (39404) Misc. bond : bond 0.00081 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 25406.35 seconds wall clock time: 445 minutes 27.40 seconds (26727.40 seconds total)