Starting phenix.real_space_refine on Tue Jun 24 09:43:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wcp_32427/06_2025/7wcp_32427_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wcp_32427/06_2025/7wcp_32427.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wcp_32427/06_2025/7wcp_32427.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wcp_32427/06_2025/7wcp_32427.map" model { file = "/net/cci-nas-00/data/ceres_data/7wcp_32427/06_2025/7wcp_32427_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wcp_32427/06_2025/7wcp_32427_neut.cif" } resolution = 3.01 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= 0.072 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 126 5.16 5 C 18007 2.51 5 N 4745 2.21 5 O 5450 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 61 residue(s): 1.37s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 28328 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" 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: "B" 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: "C" 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: "D" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 926 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "E" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 826 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 103} Chain: "H" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 926 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "L" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 826 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 103} Chain: "M" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 926 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "N" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 826 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 103} Time building chain proxies: 16.16, per 1000 atoms: 0.57 Number of scatterers: 28328 At special positions: 0 Unit cell: (204.12, 153.36, 189, 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 126 16.00 O 5450 8.00 N 4745 7.00 C 18007 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=43, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.06 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=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.87 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.05 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.05 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.04 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 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=2.02 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 C 131 " - pdb=" SG CYS C 166 " distance=2.02 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.05 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.02 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=1.91 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 95 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 95 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " 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=0, symmetry=0 Time building additional restraints: 6.14 Conformation dependent library (CDL) restraints added in 3.3 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: 6824 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 60 sheets defined 19.4% alpha, 28.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.03 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 removed outlier: 3.546A pdb=" N LEU A 303 " --> pdb=" O THR A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.133A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 390 removed outlier: 3.721A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) removed outlier: 3.727A 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 409 removed outlier: 3.922A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.533A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.553A pdb=" N TYR A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 754 removed outlier: 4.080A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.846A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (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 886 through 890 removed outlier: 3.558A pdb=" N ALA A 890 " --> pdb=" O THR A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 removed outlier: 3.675A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 917 removed outlier: 4.243A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 912 through 917' Processing helix chain 'A' and resid 919 through 939 removed outlier: 3.772A pdb=" N SER A 939 " --> pdb=" O GLN A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 964 removed outlier: 4.133A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR A 961 " --> pdb=" O GLN A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 983 removed outlier: 3.645A pdb=" N ARG A 983 " --> pdb=" O ASP A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 991 through 1032 removed outlier: 3.512A pdb=" N LEU A1024 " --> pdb=" O ALA A1020 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 removed outlier: 3.521A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.395A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.785A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 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: 3.836A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 811 through 815 removed outlier: 4.191A pdb=" N LYS B 814 " --> pdb=" O LYS B 811 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ARG B 815 " --> pdb=" O PRO B 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 811 through 815' Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.525A pdb=" N GLN B 872 " --> pdb=" O GLU B 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.563A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 940 removed outlier: 3.520A pdb=" N LYS B 933 " --> pdb=" O SER B 929 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.091A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 977 through 982 removed outlier: 3.707A pdb=" N LEU B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 988 through 1032 removed outlier: 3.789A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N ASP B 994 " --> pdb=" O GLU B 990 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA B1016 " --> pdb=" O LEU B1012 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1145 removed outlier: 3.721A pdb=" N LEU B1145 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.911A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.651A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 752 through 757 Processing helix chain 'C' and resid 761 through 783 removed outlier: 3.553A pdb=" N ARG C 765 " --> pdb=" O THR C 761 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.715A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 936 removed outlier: 3.547A pdb=" N LYS C 933 " --> pdb=" O SER C 929 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 955 removed outlier: 3.697A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 958 through 964 Processing helix chain 'C' and resid 976 through 983 removed outlier: 3.803A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 990 through 1032 removed outlier: 3.599A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLN C1002 " --> pdb=" O THR C 998 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.630A pdb=" N SER E 83 " --> pdb=" O SER E 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.630A pdb=" N SER L 83 " --> pdb=" O SER L 80 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 83 removed outlier: 3.629A pdb=" N SER N 83 " --> pdb=" O SER N 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.550A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 9.469A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.229A 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 Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 7.305A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.806A 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: 3.639A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 317 removed outlier: 6.576A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 4.090A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.859A pdb=" N GLY A 431 " --> pdb=" O TYR A 380 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N TYR A 380 " --> pdb=" O GLY A 431 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL A 433 " --> pdb=" O LYS A 378 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.839A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 665 through 667 removed outlier: 6.687A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.454A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 713 through 728 removed outlier: 6.625A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.309A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 787 through 790 removed outlier: 5.788A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1076 through 1078 removed outlier: 3.780A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.572A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.104A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLU B 96 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 9.234A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.503A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.931A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.690A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 324 through 325 removed outlier: 6.548A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 8.643A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.074A pdb=" N VAL B 433 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 573 through 576 removed outlier: 6.502A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.562A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 702 through 703 Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 7.023A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 728 removed outlier: 7.023A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.224A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD5, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.550A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.357A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 9.436A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 47 through 55 removed outlier: 7.347A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.417A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ASN C 122 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 317 removed outlier: 6.976A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.018A pdb=" N GLY C 431 " --> pdb=" O TYR C 380 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N TYR C 380 " --> pdb=" O GLY C 431 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL C 433 " --> pdb=" O LYS C 378 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE2, first strand: chain 'C' and resid 542 through 543 Processing sheet with id=AE3, first strand: chain 'C' and resid 551 through 554 Processing sheet with id=AE4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.148A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 712 through 714 Processing sheet with id=AE6, first strand: chain 'C' and resid 719 through 728 removed outlier: 7.000A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.211A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.321A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AF1, first strand: chain 'D' and resid 4 through 7 removed outlier: 3.681A pdb=" N LEU D 80 " --> pdb=" O LEU D 20 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 57 through 59 removed outlier: 6.688A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N VAL D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N MET D 34 " --> pdb=" O VAL D 50 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 57 through 59 removed outlier: 6.688A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N VAL D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N MET D 34 " --> pdb=" O VAL D 50 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 4 through 5 removed outlier: 3.967A pdb=" N THR E 5 " --> pdb=" O ARG E 24 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 10 through 13 removed outlier: 3.548A pdb=" N GLU E 105 " --> pdb=" O LEU E 11 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N LEU E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N TYR E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'H' and resid 4 through 7 removed outlier: 3.681A pdb=" N LEU H 80 " --> pdb=" O LEU H 20 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.688A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.688A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'L' and resid 4 through 5 removed outlier: 3.966A pdb=" N THR L 5 " --> pdb=" O ARG L 24 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.549A pdb=" N GLU L 105 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'M' and resid 4 through 7 removed outlier: 3.680A pdb=" N LEU M 80 " --> pdb=" O LEU M 20 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'M' and resid 57 through 59 removed outlier: 6.688A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N VAL M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N MET M 34 " --> pdb=" O VAL M 50 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'M' and resid 57 through 59 removed outlier: 6.688A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N VAL M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N MET M 34 " --> pdb=" O VAL M 50 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'N' and resid 4 through 5 removed outlier: 3.967A pdb=" N THR N 5 " --> pdb=" O ARG N 24 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'N' and resid 10 through 13 removed outlier: 3.548A pdb=" N GLU N 105 " --> pdb=" O LEU N 11 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LEU N 33 " --> pdb=" O TYR N 49 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N TYR N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) 1048 hydrogen bonds defined for protein. 2838 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: 12.72 Time building geometry restraints manager: 7.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.11 - 1.27: 4681 1.27 - 1.42: 7771 1.42 - 1.58: 16337 1.58 - 1.73: 6 1.73 - 1.88: 154 Bond restraints: 28949 Sorted by residual: bond pdb=" C ASN C 616 " pdb=" O ASN C 616 " ideal model delta sigma weight residual 1.234 1.123 0.111 1.20e-02 6.94e+03 8.62e+01 bond pdb=" C GLU C1072 " pdb=" O GLU C1072 " ideal model delta sigma weight residual 1.233 1.115 0.118 1.32e-02 5.74e+03 8.00e+01 bond pdb=" C THR C1076 " pdb=" O THR C1076 " ideal model delta sigma weight residual 1.235 1.122 0.113 1.28e-02 6.10e+03 7.84e+01 bond pdb=" C VAL A 615 " pdb=" O VAL A 615 " ideal model delta sigma weight residual 1.237 1.133 0.104 1.29e-02 6.01e+03 6.54e+01 bond pdb=" CA GLU C1072 " pdb=" C GLU C1072 " ideal model delta sigma weight residual 1.527 1.419 0.108 1.41e-02 5.03e+03 5.89e+01 ... (remaining 28944 not shown) Histogram of bond angle deviations from ideal: 0.00 - 12.04: 39375 12.04 - 24.09: 16 24.09 - 36.13: 0 36.13 - 48.17: 0 48.17 - 60.22: 1 Bond angle restraints: 39392 Sorted by residual: angle pdb=" C PHE C 329 " pdb=" N PRO C 330 " pdb=" CD PRO C 330 " ideal model delta sigma weight residual 125.00 64.78 60.22 4.10e+00 5.95e-02 2.16e+02 angle pdb=" C ASN C 657 " pdb=" CA ASN C 657 " pdb=" CB ASN C 657 " ideal model delta sigma weight residual 109.56 89.04 20.52 1.65e+00 3.67e-01 1.55e+02 angle pdb=" C PHE C 329 " pdb=" N PRO C 330 " pdb=" CA PRO C 330 " ideal model delta sigma weight residual 119.84 133.54 -13.70 1.25e+00 6.40e-01 1.20e+02 angle pdb=" N VAL A 915 " pdb=" CA VAL A 915 " pdb=" C VAL A 915 " ideal model delta sigma weight residual 112.96 104.40 8.56 1.00e+00 1.00e+00 7.32e+01 angle pdb=" C ASN C 334 " pdb=" N LEU C 335 " pdb=" CA LEU C 335 " ideal model delta sigma weight residual 120.87 109.57 11.30 1.42e+00 4.96e-01 6.33e+01 ... (remaining 39387 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 15503 17.98 - 35.96: 1367 35.96 - 53.93: 283 53.93 - 71.91: 47 71.91 - 89.89: 35 Dihedral angle restraints: 17235 sinusoidal: 6604 harmonic: 10631 Sorted by residual: dihedral pdb=" C ASN C 657 " pdb=" N ASN C 657 " pdb=" CA ASN C 657 " pdb=" CB ASN C 657 " ideal model delta harmonic sigma weight residual -122.60 -95.76 -26.84 0 2.50e+00 1.60e-01 1.15e+02 dihedral pdb=" CA PRO B 986 " pdb=" C PRO B 986 " pdb=" N PRO B 987 " pdb=" CA PRO B 987 " ideal model delta harmonic sigma weight residual 180.00 130.89 49.11 0 5.00e+00 4.00e-02 9.65e+01 dihedral pdb=" C CYS C 617 " pdb=" N CYS C 617 " pdb=" CA CYS C 617 " pdb=" CB CYS C 617 " ideal model delta harmonic sigma weight residual -122.60 -145.44 22.84 0 2.50e+00 1.60e-01 8.34e+01 ... (remaining 17232 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.176: 4342 0.176 - 0.353: 120 0.353 - 0.529: 8 0.529 - 0.706: 4 0.706 - 0.882: 2 Chirality restraints: 4476 Sorted by residual: chirality pdb=" CA CYS C 617 " pdb=" N CYS C 617 " pdb=" C CYS C 617 " pdb=" CB CYS C 617 " both_signs ideal model delta sigma weight residual False 2.51 1.63 0.88 2.00e-01 2.50e+01 1.95e+01 chirality pdb=" CA ASN C 331 " pdb=" N ASN C 331 " pdb=" C ASN C 331 " pdb=" CB ASN C 331 " both_signs ideal model delta sigma weight residual False 2.51 1.75 0.76 2.00e-01 2.50e+01 1.44e+01 chirality pdb=" CG LEU B 821 " pdb=" CB LEU B 821 " pdb=" CD1 LEU B 821 " pdb=" CD2 LEU B 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 4473 not shown) Planarity restraints: 5118 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE C 329 " 0.183 5.00e-02 4.00e+02 2.24e-01 8.05e+01 pdb=" N PRO C 330 " -0.372 5.00e-02 4.00e+02 pdb=" CA PRO C 330 " 0.171 5.00e-02 4.00e+02 pdb=" CD PRO C 330 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 906 " 0.050 2.00e-02 2.50e+03 4.71e-02 3.89e+01 pdb=" CG PHE C 906 " -0.108 2.00e-02 2.50e+03 pdb=" CD1 PHE C 906 " 0.031 2.00e-02 2.50e+03 pdb=" CD2 PHE C 906 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE C 906 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE C 906 " 0.019 2.00e-02 2.50e+03 pdb=" CZ PHE C 906 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 906 " -0.036 2.00e-02 2.50e+03 3.56e-02 2.22e+01 pdb=" CG PHE A 906 " 0.081 2.00e-02 2.50e+03 pdb=" CD1 PHE A 906 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 PHE A 906 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE A 906 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE A 906 " -0.013 2.00e-02 2.50e+03 pdb=" CZ PHE A 906 " -0.007 2.00e-02 2.50e+03 ... (remaining 5115 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.31: 34 2.31 - 2.96: 13448 2.96 - 3.61: 39553 3.61 - 4.25: 64655 4.25 - 4.90: 110979 Nonbonded interactions: 228669 Sorted by model distance: nonbonded pdb=" CG PRO C 330 " pdb=" CA GLN C 580 " model vdw 1.667 3.870 nonbonded pdb=" CG PRO C 330 " pdb=" CB GLN C 580 " model vdw 1.831 3.840 nonbonded pdb=" CG PRO C 330 " pdb=" CG GLN C 580 " model vdw 1.946 3.840 nonbonded pdb=" CD1 ILE C 332 " pdb=" CA PRO C 527 " model vdw 1.996 3.890 nonbonded pdb=" CB PRO C 330 " pdb=" CB GLN C 580 " model vdw 2.022 3.840 ... (remaining 228664 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 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 'B' 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)) selection = (chain 'C' 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)) } 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: 3.790 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: 1.020 Check model and map are aligned: 0.190 Set scattering table: 0.270 Process input model: 62.870 Find NCS groups from input model: 1.350 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 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 : 0.015 0.842 28992 Z= 0.685 Angle : 1.292 60.217 39478 Z= 0.699 Chirality : 0.080 0.882 4476 Planarity : 0.009 0.224 5118 Dihedral : 14.693 89.891 10282 Min Nonbonded Distance : 1.667 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.61 % Favored : 92.17 % Rotamer: Outliers : 1.57 % Allowed : 0.93 % Favored : 97.50 % Cbeta Deviations : 0.32 % Peptide Plane: Cis-proline : 1.66 % Cis-general : 0.00 % Twisted Proline : 1.10 % 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: -2.72 (0.12), residues: 3602 helix: -2.31 (0.16), residues: 683 sheet: -0.50 (0.16), residues: 892 loop : -2.30 (0.12), residues: 2027 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.004 TRP B 353 HIS 0.012 0.002 HIS A 207 PHE 0.108 0.004 PHE C 906 TYR 0.059 0.004 TYR C 904 ARG 0.040 0.002 ARG H 31 Details of bonding type rmsd hydrogen bonds : bond 0.15078 ( 1010) hydrogen bonds : angle 8.43944 ( 2838) SS BOND : bond 0.13005 ( 43) SS BOND : angle 4.78062 ( 86) covalent geometry : bond 0.01426 (28949) covalent geometry : angle 1.27355 (39392) *********************** 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 265 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 216 time to evaluate : 2.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 365 TYR cc_start: 0.7731 (m-10) cc_final: 0.7421 (m-10) REVERT: C 65 PHE cc_start: 0.8134 (m-80) cc_final: 0.7449 (m-10) REVERT: C 904 TYR cc_start: 0.8354 (m-10) cc_final: 0.7937 (m-10) REVERT: C 1142 GLN cc_start: 0.8510 (tt0) cc_final: 0.8159 (tp-100) REVERT: D 34 MET cc_start: 0.4228 (OUTLIER) cc_final: 0.3728 (ptt) REVERT: E 45 ARG cc_start: 0.5712 (OUTLIER) cc_final: 0.4624 (mmp80) REVERT: N 46 LEU cc_start: 0.2166 (OUTLIER) cc_final: 0.1627 (mp) outliers start: 49 outliers final: 15 residues processed: 248 average time/residue: 0.4102 time to fit residues: 162.9399 Evaluate side-chains 187 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 169 time to evaluate : 2.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 330 PRO Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 1073 LYS Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain D residue 34 MET Chi-restraints excluded: chain D residue 103 TYR Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain M residue 34 MET Chi-restraints excluded: chain M residue 113 VAL Chi-restraints excluded: chain N residue 24 ARG Chi-restraints excluded: chain N residue 46 LEU Chi-restraints excluded: chain N residue 74 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 304 optimal weight: 9.9990 chunk 273 optimal weight: 0.7980 chunk 151 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 chunk 184 optimal weight: 0.8980 chunk 146 optimal weight: 0.9990 chunk 282 optimal weight: 7.9990 chunk 109 optimal weight: 7.9990 chunk 172 optimal weight: 0.6980 chunk 210 optimal weight: 1.9990 chunk 327 optimal weight: 9.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 282 ASN A 474 GLN A 801 ASN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN A 960 ASN A1135 ASN B 474 GLN B 762 GLN B 957 GLN B1054 GLN B1071 GLN C 606 ASN C 613 GLN C 901 GLN ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.175227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.110196 restraints weight = 48107.450| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.92 r_work: 0.3105 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 28992 Z= 0.146 Angle : 0.658 17.442 39478 Z= 0.346 Chirality : 0.046 0.275 4476 Planarity : 0.006 0.084 5118 Dihedral : 6.634 58.513 3984 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.89 % Favored : 94.09 % Rotamer: Outliers : 1.09 % Allowed : 6.29 % Favored : 92.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % Cis-general : 0.00 % Twisted Proline : 1.10 % 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: -1.99 (0.13), residues: 3602 helix: -0.77 (0.19), residues: 662 sheet: -0.44 (0.16), residues: 919 loop : -2.00 (0.12), residues: 2021 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 353 HIS 0.005 0.001 HIS B1048 PHE 0.023 0.001 PHE C 906 TYR 0.028 0.002 TYR B 369 ARG 0.008 0.000 ARG E 24 Details of bonding type rmsd hydrogen bonds : bond 0.03836 ( 1010) hydrogen bonds : angle 6.27435 ( 2838) SS BOND : bond 0.00614 ( 43) SS BOND : angle 1.87422 ( 86) covalent geometry : bond 0.00338 (28949) covalent geometry : angle 0.65312 (39392) *********************** 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 235 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 201 time to evaluate : 2.891 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 856 ASN cc_start: 0.8469 (p0) cc_final: 0.8264 (p0) REVERT: B 365 TYR cc_start: 0.7732 (m-10) cc_final: 0.7526 (m-10) REVERT: B 368 LEU cc_start: 0.8038 (mt) cc_final: 0.7555 (tt) REVERT: B 574 ASP cc_start: 0.8521 (t70) cc_final: 0.8205 (t0) REVERT: B 821 LEU cc_start: 0.8816 (tp) cc_final: 0.8609 (tt) REVERT: B 823 PHE cc_start: 0.8401 (m-80) cc_final: 0.8165 (m-80) REVERT: B 855 PHE cc_start: 0.7152 (OUTLIER) cc_final: 0.6815 (t80) REVERT: B 869 MET cc_start: 0.9003 (mtm) cc_final: 0.8626 (mtm) REVERT: C 65 PHE cc_start: 0.8178 (m-80) cc_final: 0.7401 (m-10) REVERT: C 329 PHE cc_start: 0.4543 (OUTLIER) cc_final: 0.3942 (m-80) REVERT: C 1073 LYS cc_start: 0.8583 (OUTLIER) cc_final: 0.8145 (mtpp) REVERT: C 1142 GLN cc_start: 0.8589 (tt0) cc_final: 0.8370 (tp40) REVERT: E 4 MET cc_start: 0.4082 (mmm) cc_final: 0.3516 (mmt) REVERT: E 45 ARG cc_start: 0.5813 (OUTLIER) cc_final: 0.4733 (mmp80) REVERT: H 31 ARG cc_start: 0.5041 (ttp80) cc_final: 0.4817 (tmm-80) outliers start: 34 outliers final: 17 residues processed: 225 average time/residue: 0.4587 time to fit residues: 172.2793 Evaluate side-chains 196 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 175 time to evaluate : 3.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 1073 LYS Chi-restraints excluded: chain D residue 103 TYR Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain M residue 34 MET Chi-restraints excluded: chain N residue 74 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 68 optimal weight: 0.9980 chunk 119 optimal weight: 1.9990 chunk 181 optimal weight: 4.9990 chunk 350 optimal weight: 9.9990 chunk 242 optimal weight: 9.9990 chunk 199 optimal weight: 10.0000 chunk 158 optimal weight: 0.6980 chunk 138 optimal weight: 3.9990 chunk 259 optimal weight: 1.9990 chunk 311 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN B 563 GLN B 762 GLN B1054 GLN ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.173045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.102901 restraints weight = 47438.410| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.60 r_work: 0.3096 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 28992 Z= 0.206 Angle : 0.636 13.636 39478 Z= 0.334 Chirality : 0.047 0.208 4476 Planarity : 0.005 0.083 5118 Dihedral : 5.802 45.200 3965 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.66 % Favored : 93.31 % Rotamer: Outliers : 1.41 % Allowed : 9.34 % Favored : 89.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % Cis-general : 0.00 % Twisted Proline : 1.10 % 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: -1.75 (0.13), residues: 3602 helix: -0.26 (0.20), residues: 665 sheet: -0.44 (0.16), residues: 929 loop : -1.89 (0.13), residues: 2008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 36 HIS 0.005 0.001 HIS B1048 PHE 0.027 0.002 PHE C 906 TYR 0.022 0.002 TYR C1067 ARG 0.006 0.000 ARG A 190 Details of bonding type rmsd hydrogen bonds : bond 0.03835 ( 1010) hydrogen bonds : angle 5.84958 ( 2838) SS BOND : bond 0.00548 ( 43) SS BOND : angle 1.45118 ( 86) covalent geometry : bond 0.00494 (28949) covalent geometry : angle 0.63315 (39392) *********************** 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 237 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 193 time to evaluate : 3.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 GLN cc_start: 0.6835 (mm110) cc_final: 0.6599 (tp40) REVERT: A 568 ASP cc_start: 0.8733 (t0) cc_final: 0.8344 (p0) REVERT: A 666 ILE cc_start: 0.9417 (OUTLIER) cc_final: 0.9088 (mp) REVERT: A 697 MET cc_start: 0.9089 (ptm) cc_final: 0.8774 (ptp) REVERT: A 856 ASN cc_start: 0.8609 (p0) cc_final: 0.8314 (p0) REVERT: A 960 ASN cc_start: 0.8381 (m-40) cc_final: 0.8074 (t0) REVERT: B 133 PHE cc_start: 0.7914 (m-80) cc_final: 0.7503 (m-80) REVERT: B 368 LEU cc_start: 0.7883 (OUTLIER) cc_final: 0.7305 (tt) REVERT: B 574 ASP cc_start: 0.8230 (t70) cc_final: 0.7841 (t0) REVERT: B 855 PHE cc_start: 0.6769 (OUTLIER) cc_final: 0.6448 (t80) REVERT: C 65 PHE cc_start: 0.7966 (m-80) cc_final: 0.7096 (m-10) REVERT: C 329 PHE cc_start: 0.4064 (OUTLIER) cc_final: 0.3628 (m-80) REVERT: C 950 ASN cc_start: 0.8784 (t0) cc_final: 0.8144 (t0) REVERT: C 1142 GLN cc_start: 0.8634 (tt0) cc_final: 0.8257 (tp-100) REVERT: D 34 MET cc_start: 0.5068 (pmm) cc_final: 0.4022 (mtt) REVERT: E 4 MET cc_start: 0.4006 (mmm) cc_final: 0.3556 (mmt) REVERT: E 45 ARG cc_start: 0.5810 (OUTLIER) cc_final: 0.4740 (mmp80) outliers start: 44 outliers final: 24 residues processed: 223 average time/residue: 0.3800 time to fit residues: 139.8180 Evaluate side-chains 208 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 179 time to evaluate : 3.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain D residue 103 TYR Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain M residue 34 MET Chi-restraints excluded: chain N residue 74 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 143 optimal weight: 4.9990 chunk 293 optimal weight: 0.5980 chunk 171 optimal weight: 0.3980 chunk 212 optimal weight: 2.9990 chunk 7 optimal weight: 10.0000 chunk 199 optimal weight: 8.9990 chunk 350 optimal weight: 6.9990 chunk 94 optimal weight: 0.7980 chunk 274 optimal weight: 0.4980 chunk 99 optimal weight: 0.9980 chunk 72 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 762 GLN ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 ASN L 32 ASN ** N 90 GLN ** 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 = 0.4300 r_free = 0.4300 target = 0.175401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.104680 restraints weight = 47991.962| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.19 r_work: 0.3174 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 28992 Z= 0.112 Angle : 0.557 12.125 39478 Z= 0.294 Chirality : 0.044 0.229 4476 Planarity : 0.005 0.082 5118 Dihedral : 5.301 45.944 3960 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.72 % Favored : 94.25 % Rotamer: Outliers : 1.45 % Allowed : 10.82 % Favored : 87.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % Cis-general : 0.00 % Twisted Proline : 1.10 % 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: -1.47 (0.13), residues: 3602 helix: 0.31 (0.20), residues: 656 sheet: -0.41 (0.16), residues: 930 loop : -1.74 (0.13), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 886 HIS 0.003 0.000 HIS B1088 PHE 0.021 0.001 PHE C 168 TYR 0.020 0.001 TYR A 904 ARG 0.006 0.000 ARG A 190 Details of bonding type rmsd hydrogen bonds : bond 0.03247 ( 1010) hydrogen bonds : angle 5.46018 ( 2838) SS BOND : bond 0.00535 ( 43) SS BOND : angle 1.23195 ( 86) covalent geometry : bond 0.00256 (28949) covalent geometry : angle 0.55435 (39392) *********************** 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 233 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 188 time to evaluate : 3.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 856 ASN cc_start: 0.8487 (p0) cc_final: 0.8180 (p0) REVERT: A 858 LEU cc_start: 0.9299 (OUTLIER) cc_final: 0.9094 (pp) REVERT: B 368 LEU cc_start: 0.7893 (OUTLIER) cc_final: 0.7403 (tt) REVERT: B 574 ASP cc_start: 0.8090 (t70) cc_final: 0.7747 (t0) REVERT: B 855 PHE cc_start: 0.6806 (OUTLIER) cc_final: 0.6423 (t80) REVERT: C 65 PHE cc_start: 0.7919 (m-80) cc_final: 0.7005 (m-10) REVERT: C 329 PHE cc_start: 0.4295 (OUTLIER) cc_final: 0.3967 (m-80) REVERT: C 950 ASN cc_start: 0.8665 (t0) cc_final: 0.8457 (m-40) REVERT: E 4 MET cc_start: 0.4257 (mmm) cc_final: 0.3781 (mmt) REVERT: E 45 ARG cc_start: 0.5903 (ptm-80) cc_final: 0.4839 (mmp80) REVERT: L 4 MET cc_start: 0.3164 (OUTLIER) cc_final: 0.2648 (mmp) REVERT: L 58 ILE cc_start: 0.1719 (OUTLIER) cc_final: 0.1320 (tp) outliers start: 45 outliers final: 23 residues processed: 222 average time/residue: 0.4912 time to fit residues: 183.8212 Evaluate side-chains 205 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 176 time to evaluate : 3.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 1013 ILE Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain D residue 103 TYR Chi-restraints excluded: chain H residue 59 TYR Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain M residue 34 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 354 optimal weight: 20.0000 chunk 355 optimal weight: 5.9990 chunk 340 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 chunk 192 optimal weight: 0.9990 chunk 233 optimal weight: 10.0000 chunk 250 optimal weight: 0.2980 chunk 132 optimal weight: 10.0000 chunk 188 optimal weight: 0.8980 chunk 191 optimal weight: 0.8980 chunk 223 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1054 GLN B 762 GLN ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN N 90 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.174971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.104270 restraints weight = 47709.377| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.18 r_work: 0.3162 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 28992 Z= 0.126 Angle : 0.556 10.932 39478 Z= 0.291 Chirality : 0.044 0.213 4476 Planarity : 0.005 0.082 5118 Dihedral : 5.019 44.768 3954 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.25 % Favored : 93.73 % Rotamer: Outliers : 1.45 % Allowed : 12.33 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % Cis-general : 0.00 % Twisted Proline : 1.10 % 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: -1.33 (0.14), residues: 3602 helix: 0.47 (0.21), residues: 662 sheet: -0.24 (0.17), residues: 914 loop : -1.71 (0.13), residues: 2026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 36 HIS 0.003 0.001 HIS B1088 PHE 0.023 0.001 PHE B 168 TYR 0.017 0.001 TYR C1067 ARG 0.006 0.000 ARG A 190 Details of bonding type rmsd hydrogen bonds : bond 0.03238 ( 1010) hydrogen bonds : angle 5.28792 ( 2838) SS BOND : bond 0.00453 ( 43) SS BOND : angle 1.49668 ( 86) covalent geometry : bond 0.00292 (28949) covalent geometry : angle 0.55187 (39392) *********************** 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 230 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 185 time to evaluate : 3.925 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 390 LEU cc_start: 0.8520 (tp) cc_final: 0.8206 (tp) REVERT: A 666 ILE cc_start: 0.9401 (OUTLIER) cc_final: 0.9077 (mp) REVERT: B 368 LEU cc_start: 0.7746 (OUTLIER) cc_final: 0.7231 (tt) REVERT: B 574 ASP cc_start: 0.8119 (t70) cc_final: 0.7783 (t0) REVERT: B 855 PHE cc_start: 0.6790 (OUTLIER) cc_final: 0.6539 (t80) REVERT: C 65 PHE cc_start: 0.7888 (m-80) cc_final: 0.7101 (m-10) REVERT: C 950 ASN cc_start: 0.8759 (t0) cc_final: 0.8522 (m-40) REVERT: D 34 MET cc_start: 0.5518 (pmm) cc_final: 0.4388 (ppp) REVERT: E 4 MET cc_start: 0.4018 (mmm) cc_final: 0.3418 (mmt) REVERT: E 45 ARG cc_start: 0.5988 (ptm-80) cc_final: 0.4804 (mmp80) REVERT: L 4 MET cc_start: 0.3143 (OUTLIER) cc_final: 0.2655 (mmp) REVERT: L 24 ARG cc_start: 0.7304 (tmm160) cc_final: 0.7051 (tmm160) outliers start: 45 outliers final: 30 residues processed: 217 average time/residue: 0.3967 time to fit residues: 145.1312 Evaluate side-chains 205 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 171 time to evaluate : 2.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain D residue 103 TYR Chi-restraints excluded: chain H residue 59 TYR Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain M residue 34 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 163 optimal weight: 0.9980 chunk 255 optimal weight: 4.9990 chunk 263 optimal weight: 1.9990 chunk 214 optimal weight: 0.8980 chunk 16 optimal weight: 8.9990 chunk 203 optimal weight: 0.0970 chunk 308 optimal weight: 1.9990 chunk 304 optimal weight: 3.9990 chunk 276 optimal weight: 1.9990 chunk 307 optimal weight: 5.9990 chunk 175 optimal weight: 1.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 ASN A 856 ASN ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.174138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.102784 restraints weight = 47420.641| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.30 r_work: 0.3146 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 28992 Z= 0.153 Angle : 0.560 10.259 39478 Z= 0.294 Chirality : 0.045 0.211 4476 Planarity : 0.005 0.079 5118 Dihedral : 4.988 50.912 3952 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.16 % Favored : 93.81 % Rotamer: Outliers : 1.83 % Allowed : 13.17 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % Cis-general : 0.00 % Twisted Proline : 1.10 % 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: -1.27 (0.14), residues: 3602 helix: 0.56 (0.21), residues: 658 sheet: -0.23 (0.17), residues: 923 loop : -1.68 (0.13), residues: 2021 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 886 HIS 0.002 0.001 HIS B1048 PHE 0.016 0.001 PHE B 168 TYR 0.027 0.001 TYR A 904 ARG 0.006 0.000 ARG C 328 Details of bonding type rmsd hydrogen bonds : bond 0.03314 ( 1010) hydrogen bonds : angle 5.24141 ( 2838) SS BOND : bond 0.00431 ( 43) SS BOND : angle 1.30963 ( 86) covalent geometry : bond 0.00365 (28949) covalent geometry : angle 0.55714 (39392) *********************** 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 240 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 183 time to evaluate : 2.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 GLN cc_start: 0.7029 (mm110) cc_final: 0.6776 (tp40) REVERT: A 390 LEU cc_start: 0.8510 (tp) cc_final: 0.8203 (tp) REVERT: A 918 GLU cc_start: 0.9099 (OUTLIER) cc_final: 0.7899 (mp0) REVERT: B 133 PHE cc_start: 0.7928 (m-80) cc_final: 0.7520 (m-80) REVERT: B 368 LEU cc_start: 0.7610 (OUTLIER) cc_final: 0.7159 (tt) REVERT: B 574 ASP cc_start: 0.8115 (t70) cc_final: 0.7783 (t0) REVERT: B 1045 LYS cc_start: 0.8753 (mmmt) cc_final: 0.8316 (mmtm) REVERT: C 65 PHE cc_start: 0.7861 (m-80) cc_final: 0.7065 (m-10) REVERT: C 950 ASN cc_start: 0.8778 (t0) cc_final: 0.8551 (m-40) REVERT: D 34 MET cc_start: 0.5444 (pmm) cc_final: 0.5122 (pmm) REVERT: E 4 MET cc_start: 0.4075 (mmm) cc_final: 0.3096 (mmt) REVERT: E 45 ARG cc_start: 0.5846 (OUTLIER) cc_final: 0.4791 (mmp80) REVERT: L 4 MET cc_start: 0.3271 (OUTLIER) cc_final: 0.2826 (mmp) REVERT: L 24 ARG cc_start: 0.7272 (tmm160) cc_final: 0.6963 (tmm160) outliers start: 57 outliers final: 44 residues processed: 227 average time/residue: 0.3822 time to fit residues: 144.3358 Evaluate side-chains 222 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 174 time to evaluate : 3.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain D residue 103 TYR Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain H residue 59 TYR Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain M residue 34 MET Chi-restraints excluded: chain M residue 112 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 134 optimal weight: 10.0000 chunk 282 optimal weight: 0.8980 chunk 32 optimal weight: 9.9990 chunk 186 optimal weight: 1.9990 chunk 183 optimal weight: 0.9980 chunk 142 optimal weight: 9.9990 chunk 303 optimal weight: 0.0870 chunk 234 optimal weight: 7.9990 chunk 305 optimal weight: 20.0000 chunk 278 optimal weight: 3.9990 chunk 167 optimal weight: 0.5980 overall best weight: 0.9160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 856 ASN B1106 GLN ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 ASN ** N 90 GLN ** 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 = 0.4289 r_free = 0.4289 target = 0.174605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.105446 restraints weight = 47481.908| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.60 r_work: 0.3129 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 28992 Z= 0.128 Angle : 0.544 9.955 39478 Z= 0.285 Chirality : 0.045 0.339 4476 Planarity : 0.005 0.081 5118 Dihedral : 4.875 51.484 3952 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 1.77 % Allowed : 13.90 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % Cis-general : 0.00 % Twisted Proline : 1.10 % 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: -1.20 (0.14), residues: 3602 helix: 0.68 (0.21), residues: 656 sheet: -0.19 (0.17), residues: 919 loop : -1.65 (0.13), residues: 2027 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 886 HIS 0.003 0.001 HIS B1088 PHE 0.013 0.001 PHE C 168 TYR 0.019 0.001 TYR D 103 ARG 0.006 0.000 ARG A 190 Details of bonding type rmsd hydrogen bonds : bond 0.03174 ( 1010) hydrogen bonds : angle 5.16184 ( 2838) SS BOND : bond 0.00446 ( 43) SS BOND : angle 1.23349 ( 86) covalent geometry : bond 0.00303 (28949) covalent geometry : angle 0.54138 (39392) *********************** 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 243 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 188 time to evaluate : 3.474 Fit side-chains revert: symmetry clash REVERT: A 239 GLN cc_start: 0.6814 (mm110) cc_final: 0.6574 (tp40) REVERT: A 390 LEU cc_start: 0.8467 (tp) cc_final: 0.8154 (tp) REVERT: A 918 GLU cc_start: 0.9109 (OUTLIER) cc_final: 0.7914 (mp0) REVERT: B 380 TYR cc_start: 0.7498 (t80) cc_final: 0.7254 (t80) REVERT: B 536 ASN cc_start: 0.8129 (m-40) cc_final: 0.7884 (m-40) REVERT: B 574 ASP cc_start: 0.8106 (t70) cc_final: 0.7774 (t0) REVERT: B 1045 LYS cc_start: 0.8772 (mmmt) cc_final: 0.8311 (mmtm) REVERT: C 65 PHE cc_start: 0.7820 (m-80) cc_final: 0.6953 (m-10) REVERT: C 125 ASN cc_start: 0.7450 (m-40) cc_final: 0.6598 (p0) REVERT: C 935 GLN cc_start: 0.8658 (OUTLIER) cc_final: 0.8383 (tt0) REVERT: C 950 ASN cc_start: 0.8750 (t0) cc_final: 0.8532 (m-40) REVERT: D 34 MET cc_start: 0.5394 (pmm) cc_final: 0.5173 (pmm) REVERT: E 4 MET cc_start: 0.3873 (mmm) cc_final: 0.2931 (mmt) REVERT: E 45 ARG cc_start: 0.5869 (OUTLIER) cc_final: 0.4862 (mmp80) REVERT: L 4 MET cc_start: 0.3365 (mmt) cc_final: 0.2978 (mmp) REVERT: M 34 MET cc_start: 0.1310 (OUTLIER) cc_final: 0.1096 (mmm) outliers start: 55 outliers final: 40 residues processed: 231 average time/residue: 0.4895 time to fit residues: 191.1876 Evaluate side-chains 221 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 177 time to evaluate : 3.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 935 GLN Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain D residue 103 TYR Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain H residue 59 TYR Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain M residue 34 MET Chi-restraints excluded: chain M residue 112 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 121 optimal weight: 0.9980 chunk 261 optimal weight: 0.0670 chunk 139 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 203 optimal weight: 1.9990 chunk 167 optimal weight: 0.7980 chunk 212 optimal weight: 3.9990 chunk 134 optimal weight: 20.0000 chunk 36 optimal weight: 10.0000 chunk 221 optimal weight: 0.9990 chunk 91 optimal weight: 0.2980 overall best weight: 0.6320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 556 ASN B 751 ASN B1106 GLN C 955 ASN ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 GLN ** 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 = 0.4297 r_free = 0.4297 target = 0.175173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.106577 restraints weight = 47525.933| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.59 r_work: 0.3150 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 28992 Z= 0.109 Angle : 0.532 9.533 39478 Z= 0.278 Chirality : 0.044 0.228 4476 Planarity : 0.004 0.080 5118 Dihedral : 4.688 35.542 3952 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 1.73 % Allowed : 14.29 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % Cis-general : 0.00 % Twisted Proline : 1.10 % 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: -1.13 (0.14), residues: 3602 helix: 0.78 (0.21), residues: 662 sheet: -0.16 (0.17), residues: 928 loop : -1.62 (0.13), residues: 2012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 35 HIS 0.003 0.000 HIS B1088 PHE 0.013 0.001 PHE C 168 TYR 0.016 0.001 TYR A1067 ARG 0.007 0.000 ARG A 190 Details of bonding type rmsd hydrogen bonds : bond 0.03030 ( 1010) hydrogen bonds : angle 5.02199 ( 2838) SS BOND : bond 0.00381 ( 43) SS BOND : angle 1.15321 ( 86) covalent geometry : bond 0.00255 (28949) covalent geometry : angle 0.52939 (39392) *********************** 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 247 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 193 time to evaluate : 3.116 Fit side-chains REVERT: A 239 GLN cc_start: 0.6723 (mm110) cc_final: 0.6511 (tp40) REVERT: A 390 LEU cc_start: 0.8461 (tp) cc_final: 0.8138 (tp) REVERT: A 918 GLU cc_start: 0.9077 (OUTLIER) cc_final: 0.7907 (mp0) REVERT: B 380 TYR cc_start: 0.7443 (t80) cc_final: 0.7219 (t80) REVERT: B 536 ASN cc_start: 0.8064 (m-40) cc_final: 0.7804 (m-40) REVERT: B 574 ASP cc_start: 0.8061 (t70) cc_final: 0.7730 (t0) REVERT: B 900 MET cc_start: 0.9070 (mtp) cc_final: 0.8818 (ttm) REVERT: B 1045 LYS cc_start: 0.8776 (mmmt) cc_final: 0.8329 (mmtm) REVERT: C 65 PHE cc_start: 0.7830 (m-80) cc_final: 0.7148 (m-10) REVERT: C 125 ASN cc_start: 0.7436 (m-40) cc_final: 0.6596 (p0) REVERT: C 329 PHE cc_start: 0.4128 (OUTLIER) cc_final: 0.3613 (m-80) REVERT: C 935 GLN cc_start: 0.8639 (OUTLIER) cc_final: 0.8395 (tt0) REVERT: C 950 ASN cc_start: 0.8713 (t0) cc_final: 0.8505 (m-40) REVERT: E 4 MET cc_start: 0.3850 (mmm) cc_final: 0.2873 (mmt) REVERT: E 45 ARG cc_start: 0.5960 (OUTLIER) cc_final: 0.4882 (mmp80) REVERT: L 4 MET cc_start: 0.3253 (mmt) cc_final: 0.2883 (mmp) REVERT: M 34 MET cc_start: 0.1380 (OUTLIER) cc_final: 0.0869 (mmm) outliers start: 54 outliers final: 40 residues processed: 237 average time/residue: 0.3988 time to fit residues: 156.7156 Evaluate side-chains 220 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 175 time to evaluate : 3.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 935 GLN Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain H residue 59 TYR Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain M residue 34 MET Chi-restraints excluded: chain M residue 111 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 210 optimal weight: 1.9990 chunk 351 optimal weight: 0.9990 chunk 223 optimal weight: 0.9990 chunk 187 optimal weight: 0.5980 chunk 310 optimal weight: 5.9990 chunk 128 optimal weight: 0.9980 chunk 311 optimal weight: 10.0000 chunk 280 optimal weight: 0.5980 chunk 259 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 319 optimal weight: 6.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1113 GLN B 957 GLN ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.175007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.104464 restraints weight = 47456.629| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.30 r_work: 0.3170 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 28992 Z= 0.120 Angle : 0.543 10.287 39478 Z= 0.282 Chirality : 0.044 0.216 4476 Planarity : 0.004 0.081 5118 Dihedral : 4.663 35.140 3950 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 1.61 % Allowed : 14.64 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % Cis-general : 0.00 % Twisted Proline : 1.10 % 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: -1.08 (0.14), residues: 3602 helix: 0.82 (0.21), residues: 661 sheet: -0.10 (0.17), residues: 928 loop : -1.60 (0.13), residues: 2013 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 36 HIS 0.003 0.001 HIS B1088 PHE 0.013 0.001 PHE B 168 TYR 0.021 0.001 TYR A 170 ARG 0.007 0.000 ARG A 190 Details of bonding type rmsd hydrogen bonds : bond 0.03081 ( 1010) hydrogen bonds : angle 5.01249 ( 2838) SS BOND : bond 0.00400 ( 43) SS BOND : angle 1.24809 ( 86) covalent geometry : bond 0.00285 (28949) covalent geometry : angle 0.54012 (39392) *********************** 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 233 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 183 time to evaluate : 2.953 Fit side-chains REVERT: A 239 GLN cc_start: 0.6948 (mm110) cc_final: 0.6697 (tp40) REVERT: A 390 LEU cc_start: 0.8480 (tp) cc_final: 0.8151 (tp) REVERT: A 455 LEU cc_start: 0.6391 (mt) cc_final: 0.6172 (mp) REVERT: B 536 ASN cc_start: 0.8032 (m-40) cc_final: 0.7787 (m-40) REVERT: B 574 ASP cc_start: 0.8062 (t70) cc_final: 0.7737 (t0) REVERT: B 740 MET cc_start: 0.8484 (OUTLIER) cc_final: 0.8148 (mtp) REVERT: B 1045 LYS cc_start: 0.8769 (mmmt) cc_final: 0.8350 (mmtm) REVERT: C 65 PHE cc_start: 0.7805 (m-80) cc_final: 0.7059 (m-10) REVERT: C 125 ASN cc_start: 0.7390 (m-40) cc_final: 0.6547 (p0) REVERT: C 329 PHE cc_start: 0.4406 (OUTLIER) cc_final: 0.3833 (m-80) REVERT: C 935 GLN cc_start: 0.8627 (OUTLIER) cc_final: 0.8370 (tt0) REVERT: C 950 ASN cc_start: 0.8733 (t0) cc_final: 0.8530 (m-40) REVERT: E 4 MET cc_start: 0.4069 (mmm) cc_final: 0.3650 (mmt) REVERT: E 45 ARG cc_start: 0.5797 (OUTLIER) cc_final: 0.5005 (mmp80) REVERT: L 4 MET cc_start: 0.3376 (mmt) cc_final: 0.3003 (mmp) REVERT: M 34 MET cc_start: 0.1600 (mpp) cc_final: 0.0990 (mmm) outliers start: 50 outliers final: 42 residues processed: 223 average time/residue: 0.3639 time to fit residues: 134.9123 Evaluate side-chains 225 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 179 time to evaluate : 3.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 935 GLN Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 69 optimal weight: 0.9980 chunk 338 optimal weight: 10.0000 chunk 104 optimal weight: 5.9990 chunk 68 optimal weight: 0.7980 chunk 46 optimal weight: 9.9990 chunk 2 optimal weight: 5.9990 chunk 29 optimal weight: 7.9990 chunk 292 optimal weight: 0.5980 chunk 26 optimal weight: 0.4980 chunk 301 optimal weight: 10.0000 chunk 70 optimal weight: 2.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1113 GLN B1071 GLN ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.173964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.103446 restraints weight = 47359.149| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.26 r_work: 0.3152 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 28992 Z= 0.151 Angle : 0.560 9.170 39478 Z= 0.291 Chirality : 0.045 0.207 4476 Planarity : 0.005 0.081 5118 Dihedral : 4.698 34.841 3947 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 1.64 % Allowed : 14.74 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % Cis-general : 0.00 % Twisted Proline : 1.10 % 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: -1.10 (0.14), residues: 3602 helix: 0.75 (0.21), residues: 660 sheet: -0.10 (0.17), residues: 927 loop : -1.60 (0.13), residues: 2015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 35 HIS 0.003 0.001 HIS B1048 PHE 0.024 0.001 PHE C 168 TYR 0.018 0.001 TYR C1067 ARG 0.007 0.000 ARG A 190 Details of bonding type rmsd hydrogen bonds : bond 0.03230 ( 1010) hydrogen bonds : angle 5.05021 ( 2838) SS BOND : bond 0.00419 ( 43) SS BOND : angle 1.31806 ( 86) covalent geometry : bond 0.00361 (28949) covalent geometry : angle 0.55730 (39392) ********************** 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 236 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 185 time to evaluate : 3.431 Fit side-chains REVERT: A 239 GLN cc_start: 0.7001 (mm110) cc_final: 0.6720 (tp40) REVERT: A 390 LEU cc_start: 0.8561 (tp) cc_final: 0.8248 (tp) REVERT: A 455 LEU cc_start: 0.6406 (mt) cc_final: 0.6206 (mp) REVERT: A 804 GLN cc_start: 0.8451 (pm20) cc_final: 0.7750 (mm-40) REVERT: A 918 GLU cc_start: 0.9093 (OUTLIER) cc_final: 0.8010 (mp0) REVERT: B 133 PHE cc_start: 0.7916 (m-80) cc_final: 0.7469 (m-80) REVERT: B 536 ASN cc_start: 0.8005 (m-40) cc_final: 0.7775 (m-40) REVERT: B 574 ASP cc_start: 0.7983 (t70) cc_final: 0.7676 (t0) REVERT: B 740 MET cc_start: 0.8468 (OUTLIER) cc_final: 0.8114 (mtp) REVERT: B 1045 LYS cc_start: 0.8764 (mmmt) cc_final: 0.8335 (mmtm) REVERT: C 65 PHE cc_start: 0.7869 (m-80) cc_final: 0.7177 (m-10) REVERT: C 125 ASN cc_start: 0.7387 (m-40) cc_final: 0.6575 (p0) REVERT: C 329 PHE cc_start: 0.4571 (OUTLIER) cc_final: 0.3921 (m-80) REVERT: C 935 GLN cc_start: 0.8640 (OUTLIER) cc_final: 0.8343 (tt0) REVERT: C 957 GLN cc_start: 0.8740 (pp30) cc_final: 0.8434 (pp30) REVERT: D 34 MET cc_start: 0.5357 (pmm) cc_final: 0.3914 (ppp) REVERT: E 4 MET cc_start: 0.4114 (mmm) cc_final: 0.3732 (mmt) REVERT: E 45 ARG cc_start: 0.5526 (ptm-80) cc_final: 0.4777 (mmp80) REVERT: L 4 MET cc_start: 0.3401 (mmt) cc_final: 0.2457 (mmp) REVERT: M 34 MET cc_start: 0.1696 (OUTLIER) cc_final: 0.1022 (mmm) REVERT: N 4 MET cc_start: -0.0748 (mmm) cc_final: -0.1431 (mmt) outliers start: 51 outliers final: 43 residues processed: 226 average time/residue: 0.3908 time to fit residues: 146.9612 Evaluate side-chains 226 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 178 time to evaluate : 3.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 935 GLN Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain M residue 34 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 291 optimal weight: 2.9990 chunk 194 optimal weight: 0.7980 chunk 248 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 43 optimal weight: 9.9990 chunk 120 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 272 optimal weight: 0.6980 chunk 157 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1113 GLN B 234 ASN ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.174975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.106173 restraints weight = 47407.787| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.60 r_work: 0.3145 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 28992 Z= 0.118 Angle : 0.540 8.938 39478 Z= 0.281 Chirality : 0.044 0.235 4476 Planarity : 0.004 0.082 5118 Dihedral : 4.606 35.346 3947 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 1.48 % Allowed : 15.03 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % Cis-general : 0.00 % Twisted Proline : 1.10 % 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: -1.00 (0.14), residues: 3602 helix: 0.90 (0.21), residues: 654 sheet: -0.04 (0.17), residues: 921 loop : -1.55 (0.13), residues: 2027 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP H 36 HIS 0.003 0.001 HIS B1088 PHE 0.025 0.001 PHE C 168 TYR 0.023 0.001 TYR A 170 ARG 0.007 0.000 ARG A 190 Details of bonding type rmsd hydrogen bonds : bond 0.03069 ( 1010) hydrogen bonds : angle 4.98643 ( 2838) SS BOND : bond 0.00383 ( 43) SS BOND : angle 1.19381 ( 86) covalent geometry : bond 0.00280 (28949) covalent geometry : angle 0.53720 (39392) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 32903.63 seconds wall clock time: 573 minutes 40.72 seconds (34420.72 seconds total)