Starting phenix.real_space_refine on Sat May 17 18:07:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vcr_43139/05_2025/8vcr_43139.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vcr_43139/05_2025/8vcr_43139.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vcr_43139/05_2025/8vcr_43139.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vcr_43139/05_2025/8vcr_43139.map" model { file = "/net/cci-nas-00/data/ceres_data/8vcr_43139/05_2025/8vcr_43139.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vcr_43139/05_2025/8vcr_43139.cif" } resolution = 3.0 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= 0.012 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 78 5.16 5 C 10110 2.51 5 N 2667 2.21 5 O 3132 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 69 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 15987 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 3411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3411 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 24, 'TRANS': 420} Chain: "D" Number of atoms: 1009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1009 Classifications: {'peptide': 128} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 122} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 1009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1009 Classifications: {'peptide': 128} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 122} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 811 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "G" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 811 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "H" Number of atoms: 1009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1009 Classifications: {'peptide': 128} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 122} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 811 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "B" Number of atoms: 3411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3411 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 24, 'TRANS': 420} Chain: "C" Number of atoms: 3411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3411 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 24, 'TRANS': 420} Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 11.37, per 1000 atoms: 0.71 Number of scatterers: 15987 At special positions: 0 Unit cell: (111.86, 111.86, 172.96, 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 78 16.00 O 3132 8.00 N 2667 7.00 C 10110 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=27, symmetry=0 Simple disulfide: pdb=" SG CYS A 704 " - pdb=" SG CYS B 790 " distance=2.07 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 790 " - pdb=" SG CYS C 704 " distance=2.02 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " 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=2.02 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 100 " - pdb=" SG CYS D 100E" distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.03 Simple disulfide: pdb=" SG CYS E 100 " - pdb=" SG CYS E 100E" distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 100 " - pdb=" SG CYS H 100E" distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS B 704 " - pdb=" SG CYS C 790 " distance=2.01 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " 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=2.02 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.03 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 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 Links applied BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " NAG-ASN " NAG A1301 " - " ASN A 709 " " NAG A1302 " - " ASN A 717 " " NAG A1303 " - " ASN A1098 " " NAG A1304 " - " ASN A1134 " " NAG B1301 " - " ASN B 709 " " NAG B1302 " - " ASN B 717 " " NAG B1303 " - " ASN B1098 " " NAG B1304 " - " ASN B1134 " " NAG C1301 " - " ASN C 709 " " NAG C1302 " - " ASN C 717 " " NAG C1303 " - " ASN C1098 " " NAG C1304 " - " ASN C1134 " " NAG D 301 " - " ASN D 31 " " NAG E 301 " - " ASN E 31 " " NAG H 301 " - " ASN H 31 " " NAG I 1 " - " ASN A 801 " " NAG J 1 " - " ASN B 801 " " NAG K 1 " - " ASN C 801 " Time building additional restraints: 4.16 Conformation dependent library (CDL) restraints added in 2.1 seconds 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3774 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 30 sheets defined 37.1% alpha, 33.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.23 Creating SS restraints... Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.868A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.944A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.851A pdb=" N LEU A 821 " --> pdb=" O PRO A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 842 removed outlier: 3.861A pdb=" N GLY A 838 " --> pdb=" O ILE A 834 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASP A 839 " --> pdb=" O LYS A 835 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N CYS A 840 " --> pdb=" O GLN A 836 " (cutoff:3.500A) Processing helix chain 'A' and resid 844 through 846 No H-bonds generated for 'chain 'A' and resid 844 through 846' Processing helix chain 'A' and resid 847 through 855 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.703A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.281A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.847A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.420A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 4.223A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 65 removed outlier: 3.555A pdb=" N ASN D 64 " --> pdb=" O PRO D 61 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N SER D 65 " --> pdb=" O SER D 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 61 through 65' Processing helix chain 'D' and resid 83 through 87 removed outlier: 3.524A pdb=" N THR D 87 " --> pdb=" O ALA D 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 65 removed outlier: 3.554A pdb=" N ASN E 64 " --> pdb=" O PRO E 61 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N SER E 65 " --> pdb=" O SER E 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 61 through 65' Processing helix chain 'E' and resid 83 through 87 removed outlier: 3.524A pdb=" N THR E 87 " --> pdb=" O ALA E 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 83 removed outlier: 3.503A pdb=" N ASP F 82 " --> pdb=" O GLN F 79 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N PHE F 83 " --> pdb=" O SER F 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 79 through 83' Processing helix chain 'G' and resid 79 through 83 removed outlier: 3.502A pdb=" N ASP G 82 " --> pdb=" O GLN G 79 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N PHE G 83 " --> pdb=" O SER G 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 79 through 83' Processing helix chain 'H' and resid 61 through 65 removed outlier: 3.554A pdb=" N ASN H 64 " --> pdb=" O PRO H 61 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N SER H 65 " --> pdb=" O SER H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 61 through 65' Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.523A pdb=" N THR H 87 " --> pdb=" O ALA H 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.503A pdb=" N ASP L 82 " --> pdb=" O GLN L 79 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N PHE L 83 " --> pdb=" O SER L 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 79 through 83' Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.868A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.946A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.851A pdb=" N LEU B 821 " --> pdb=" O PRO B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 832 through 842 removed outlier: 3.862A pdb=" N GLY B 838 " --> pdb=" O ILE B 834 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASP B 839 " --> pdb=" O LYS B 835 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N CYS B 840 " --> pdb=" O GLN B 836 " (cutoff:3.500A) Processing helix chain 'B' and resid 844 through 846 No H-bonds generated for 'chain 'B' and resid 844 through 846' Processing helix chain 'B' and resid 847 through 855 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.703A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.280A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.848A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.421A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 4.222A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.868A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.946A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.852A pdb=" N LEU C 821 " --> pdb=" O PRO C 817 " (cutoff:3.500A) Processing helix chain 'C' and resid 832 through 842 removed outlier: 3.862A pdb=" N GLY C 838 " --> pdb=" O ILE C 834 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASP C 839 " --> pdb=" O LYS C 835 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N CYS C 840 " --> pdb=" O GLN C 836 " (cutoff:3.500A) Processing helix chain 'C' and resid 844 through 846 No H-bonds generated for 'chain 'C' and resid 844 through 846' Processing helix chain 'C' and resid 847 through 855 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.703A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.280A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.847A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.419A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 4.222A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.408A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.408A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AA4, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.265A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AA6, first strand: chain 'D' and resid 11 through 12 removed outlier: 6.366A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 11 through 12 removed outlier: 6.967A pdb=" N CYS D 92 " --> pdb=" O PRO D 102 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ARG D 94 " --> pdb=" O LEU D 100J" (cutoff:3.500A) removed outlier: 4.591A pdb=" N LEU D 100J" --> pdb=" O ARG D 94 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N PHE D 96 " --> pdb=" O ASN D 100H" (cutoff:3.500A) removed outlier: 5.027A pdb=" N PHE D 100F" --> pdb=" O GLY D 98 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N CYS D 100 " --> pdb=" O SER D 100D" (cutoff:3.500A) removed outlier: 6.545A pdb=" N SER D 100D" --> pdb=" O CYS D 100 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AA9, first strand: chain 'E' and resid 11 through 12 removed outlier: 6.366A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 11 through 12 removed outlier: 6.966A pdb=" N CYS E 92 " --> pdb=" O PRO E 102 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ARG E 94 " --> pdb=" O LEU E 100J" (cutoff:3.500A) removed outlier: 4.591A pdb=" N LEU E 100J" --> pdb=" O ARG E 94 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N PHE E 96 " --> pdb=" O ASN E 100H" (cutoff:3.500A) removed outlier: 5.027A pdb=" N PHE E 100F" --> pdb=" O GLY E 98 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N CYS E 100 " --> pdb=" O SER E 100D" (cutoff:3.500A) removed outlier: 6.545A pdb=" N SER E 100D" --> pdb=" O CYS E 100 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 4 through 6 removed outlier: 3.874A pdb=" N GLU F 70 " --> pdb=" O SER F 67 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.582A pdb=" N LEU F 33 " --> pdb=" O HIS F 49 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N HIS F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 10 through 13 removed outlier: 3.621A pdb=" N THR F 97 " --> pdb=" O GLN F 90 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 4 through 6 removed outlier: 3.875A pdb=" N GLU G 70 " --> pdb=" O SER G 67 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 10 through 13 removed outlier: 6.583A pdb=" N LEU G 33 " --> pdb=" O HIS G 49 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N HIS G 49 " --> pdb=" O LEU G 33 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N TRP G 35 " --> pdb=" O LEU G 47 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 10 through 13 removed outlier: 3.621A pdb=" N THR G 97 " --> pdb=" O GLN G 90 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB9, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.365A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.967A pdb=" N CYS H 92 " --> pdb=" O PRO H 102 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ARG H 94 " --> pdb=" O LEU H 100J" (cutoff:3.500A) removed outlier: 4.592A pdb=" N LEU H 100J" --> pdb=" O ARG H 94 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N PHE H 96 " --> pdb=" O ASN H 100H" (cutoff:3.500A) removed outlier: 5.028A pdb=" N PHE H 100F" --> pdb=" O GLY H 98 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N CYS H 100 " --> pdb=" O SER H 100D" (cutoff:3.500A) removed outlier: 6.545A pdb=" N SER H 100D" --> pdb=" O CYS H 100 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 4 through 6 removed outlier: 3.874A pdb=" N GLU L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.582A pdb=" N LEU L 33 " --> pdb=" O HIS L 49 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N HIS L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.621A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.408A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.408A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AC8, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.265A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.408A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.408A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AD3, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.265A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 852 hydrogen bonds defined for protein. 2394 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: 5.99 Time building geometry restraints manager: 4.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4881 1.33 - 1.46: 3105 1.46 - 1.58: 8250 1.58 - 1.70: 0 1.70 - 1.82: 102 Bond restraints: 16338 Sorted by residual: bond pdb=" CA ASN H 31 " pdb=" C ASN H 31 " ideal model delta sigma weight residual 1.524 1.472 0.051 1.33e-02 5.65e+03 1.49e+01 bond pdb=" CA ASN E 31 " pdb=" C ASN E 31 " ideal model delta sigma weight residual 1.524 1.475 0.049 1.33e-02 5.65e+03 1.36e+01 bond pdb=" C ASN E 31 " pdb=" N SER E 32 " ideal model delta sigma weight residual 1.334 1.302 0.033 1.38e-02 5.25e+03 5.57e+00 bond pdb=" C ASN H 31 " pdb=" N SER H 32 " ideal model delta sigma weight residual 1.334 1.303 0.031 1.38e-02 5.25e+03 5.12e+00 bond pdb=" CA ASN D 31 " pdb=" C ASN D 31 " ideal model delta sigma weight residual 1.524 1.496 0.028 1.33e-02 5.65e+03 4.39e+00 ... (remaining 16333 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 21560 1.92 - 3.84: 598 3.84 - 5.77: 66 5.77 - 7.69: 15 7.69 - 9.61: 6 Bond angle restraints: 22245 Sorted by residual: angle pdb=" CA CYS C 840 " pdb=" CB CYS C 840 " pdb=" SG CYS C 840 " ideal model delta sigma weight residual 114.40 123.02 -8.62 2.30e+00 1.89e-01 1.41e+01 angle pdb=" CA CYS A 840 " pdb=" CB CYS A 840 " pdb=" SG CYS A 840 " ideal model delta sigma weight residual 114.40 123.02 -8.62 2.30e+00 1.89e-01 1.40e+01 angle pdb=" CA CYS B 840 " pdb=" CB CYS B 840 " pdb=" SG CYS B 840 " ideal model delta sigma weight residual 114.40 123.00 -8.60 2.30e+00 1.89e-01 1.40e+01 angle pdb=" CA CYS A 851 " pdb=" CB CYS A 851 " pdb=" SG CYS A 851 " ideal model delta sigma weight residual 114.40 121.64 -7.24 2.30e+00 1.89e-01 9.91e+00 angle pdb=" CA CYS C 851 " pdb=" CB CYS C 851 " pdb=" SG CYS C 851 " ideal model delta sigma weight residual 114.40 121.63 -7.23 2.30e+00 1.89e-01 9.89e+00 ... (remaining 22240 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 9271 17.91 - 35.83: 590 35.83 - 53.74: 108 53.74 - 71.65: 39 71.65 - 89.57: 30 Dihedral angle restraints: 10038 sinusoidal: 4149 harmonic: 5889 Sorted by residual: dihedral pdb=" CA ARG A1039 " pdb=" C ARG A1039 " pdb=" N VAL A1040 " pdb=" CA VAL A1040 " ideal model delta harmonic sigma weight residual 180.00 -154.59 -25.41 0 5.00e+00 4.00e-02 2.58e+01 dihedral pdb=" CA ARG C1039 " pdb=" C ARG C1039 " pdb=" N VAL C1040 " pdb=" CA VAL C1040 " ideal model delta harmonic sigma weight residual -180.00 -154.62 -25.38 0 5.00e+00 4.00e-02 2.58e+01 dihedral pdb=" CA ARG B1039 " pdb=" C ARG B1039 " pdb=" N VAL B1040 " pdb=" CA VAL B1040 " ideal model delta harmonic sigma weight residual -180.00 -154.63 -25.37 0 5.00e+00 4.00e-02 2.58e+01 ... (remaining 10035 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 2093 0.066 - 0.133: 479 0.133 - 0.199: 23 0.199 - 0.265: 1 0.265 - 0.332: 2 Chirality restraints: 2598 Sorted by residual: chirality pdb=" C1 NAG H 301 " pdb=" ND2 ASN H 31 " pdb=" C2 NAG H 301 " pdb=" O5 NAG H 301 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.75e+00 chirality pdb=" C1 NAG E 301 " pdb=" ND2 ASN E 31 " pdb=" C2 NAG E 301 " pdb=" O5 NAG E 301 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" C1 NAG D 301 " pdb=" ND2 ASN D 31 " pdb=" C2 NAG D 301 " pdb=" O5 NAG D 301 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.50e+00 ... (remaining 2595 not shown) Planarity restraints: 2859 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG H 301 " 0.143 2.00e-02 2.50e+03 1.18e-01 1.73e+02 pdb=" C7 NAG H 301 " -0.040 2.00e-02 2.50e+03 pdb=" C8 NAG H 301 " 0.106 2.00e-02 2.50e+03 pdb=" N2 NAG H 301 " -0.189 2.00e-02 2.50e+03 pdb=" O7 NAG H 301 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 301 " 0.122 2.00e-02 2.50e+03 1.01e-01 1.28e+02 pdb=" C7 NAG D 301 " -0.034 2.00e-02 2.50e+03 pdb=" C8 NAG D 301 " 0.092 2.00e-02 2.50e+03 pdb=" N2 NAG D 301 " -0.162 2.00e-02 2.50e+03 pdb=" O7 NAG D 301 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 301 " -0.115 2.00e-02 2.50e+03 9.53e-02 1.13e+02 pdb=" C7 NAG E 301 " 0.032 2.00e-02 2.50e+03 pdb=" C8 NAG E 301 " -0.087 2.00e-02 2.50e+03 pdb=" N2 NAG E 301 " 0.152 2.00e-02 2.50e+03 pdb=" O7 NAG E 301 " 0.018 2.00e-02 2.50e+03 ... (remaining 2856 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 308 2.69 - 3.24: 15452 3.24 - 3.80: 24591 3.80 - 4.35: 33733 4.35 - 4.90: 57526 Nonbonded interactions: 131610 Sorted by model distance: nonbonded pdb=" NZ LYS G 39 " pdb=" O GLU G 81 " model vdw 2.139 3.120 nonbonded pdb=" NZ LYS F 39 " pdb=" O GLU F 81 " model vdw 2.140 3.120 nonbonded pdb=" NZ LYS L 39 " pdb=" O GLU L 81 " model vdw 2.140 3.120 nonbonded pdb=" NZ LYS A 811 " pdb=" OD2 ASP A 820 " model vdw 2.215 3.120 nonbonded pdb=" NZ LYS C 811 " pdb=" OD2 ASP C 820 " model vdw 2.215 3.120 ... (remaining 131605 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: 0.11 Found NCS groups: ncs_group { reference = chain 'G' selection = chain 'F' selection = chain 'L' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } ncs_group { reference = chain 'I' selection = chain 'K' selection = chain 'J' } ncs_group { reference = chain 'E' selection = chain 'D' selection = chain 'H' } 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: 13.290 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: 0.020 Extract box with map and model: 0.620 Check model and map are aligned: 0.130 Set scattering table: 0.150 Process input model: 40.200 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.080 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:11.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.053 16386 Z= 0.350 Angle : 0.779 9.611 22362 Z= 0.405 Chirality : 0.052 0.332 2598 Planarity : 0.006 0.118 2841 Dihedral : 13.519 89.567 6183 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.18), residues: 2022 helix: 0.58 (0.20), residues: 588 sheet: 0.54 (0.23), residues: 483 loop : -0.48 (0.20), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP H 103 HIS 0.010 0.003 HIS E 77 PHE 0.019 0.002 PHE C1121 TYR 0.027 0.003 TYR E 52 ARG 0.012 0.001 ARG C1019 Details of bonding type rmsd link_NAG-ASN : bond 0.00638 ( 18) link_NAG-ASN : angle 2.40791 ( 54) link_BETA1-4 : bond 0.00073 ( 3) link_BETA1-4 : angle 1.99350 ( 9) hydrogen bonds : bond 0.21754 ( 786) hydrogen bonds : angle 8.24553 ( 2394) SS BOND : bond 0.00945 ( 27) SS BOND : angle 1.83618 ( 54) covalent geometry : bond 0.00839 (16338) covalent geometry : angle 0.76569 (22245) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 390 time to evaluate : 1.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 723 THR cc_start: 0.8219 (p) cc_final: 0.8014 (m) REVERT: A 772 VAL cc_start: 0.8513 (t) cc_final: 0.8217 (p) REVERT: A 780 GLU cc_start: 0.7197 (mm-30) cc_final: 0.6930 (mm-30) REVERT: A 833 PHE cc_start: 0.7173 (m-10) cc_final: 0.6148 (t80) REVERT: A 837 TYR cc_start: 0.7946 (t80) cc_final: 0.7557 (t80) REVERT: A 854 LYS cc_start: 0.8148 (tttt) cc_final: 0.7762 (tttt) REVERT: A 855 PHE cc_start: 0.8145 (m-80) cc_final: 0.7830 (m-80) REVERT: A 858 LEU cc_start: 0.8169 (mt) cc_final: 0.7901 (mm) REVERT: A 952 VAL cc_start: 0.8354 (t) cc_final: 0.7938 (p) REVERT: A 994 ASP cc_start: 0.7305 (m-30) cc_final: 0.7002 (m-30) REVERT: A 1010 GLN cc_start: 0.7710 (tp40) cc_final: 0.7462 (tp40) REVERT: A 1122 VAL cc_start: 0.8075 (t) cc_final: 0.7803 (p) REVERT: L 5 THR cc_start: 0.8181 (m) cc_final: 0.7948 (p) REVERT: L 28 SER cc_start: 0.8211 (t) cc_final: 0.7958 (p) REVERT: B 723 THR cc_start: 0.8165 (p) cc_final: 0.7951 (p) REVERT: B 752 LEU cc_start: 0.8376 (mt) cc_final: 0.8141 (mt) REVERT: B 772 VAL cc_start: 0.8544 (t) cc_final: 0.8317 (t) REVERT: B 833 PHE cc_start: 0.7321 (m-10) cc_final: 0.6367 (t80) REVERT: B 866 THR cc_start: 0.8488 (p) cc_final: 0.8077 (t) REVERT: B 905 ARG cc_start: 0.8381 (mmt90) cc_final: 0.8163 (mmm-85) REVERT: B 927 PHE cc_start: 0.8057 (t80) cc_final: 0.7854 (t80) REVERT: B 1098 ASN cc_start: 0.7525 (p0) cc_final: 0.7322 (p0) REVERT: C 735 SER cc_start: 0.7922 (t) cc_final: 0.7719 (p) REVERT: C 780 GLU cc_start: 0.7189 (mm-30) cc_final: 0.6974 (mm-30) REVERT: C 837 TYR cc_start: 0.8026 (t80) cc_final: 0.7660 (t80) REVERT: C 854 LYS cc_start: 0.8105 (tttt) cc_final: 0.7897 (tttt) REVERT: C 957 GLU cc_start: 0.7260 (tp30) cc_final: 0.6833 (tp30) REVERT: C 964 LYS cc_start: 0.7976 (mtpp) cc_final: 0.7728 (ttmm) REVERT: C 994 ASP cc_start: 0.7385 (m-30) cc_final: 0.7146 (m-30) REVERT: C 995 ARG cc_start: 0.7913 (mtp85) cc_final: 0.7413 (mmm-85) REVERT: C 1122 VAL cc_start: 0.8329 (t) cc_final: 0.8117 (p) outliers start: 0 outliers final: 1 residues processed: 390 average time/residue: 1.0744 time to fit residues: 470.1861 Evaluate side-chains 353 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 352 time to evaluate : 1.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 95 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 167 optimal weight: 0.6980 chunk 150 optimal weight: 0.4980 chunk 83 optimal weight: 0.4980 chunk 51 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 80 optimal weight: 0.5980 chunk 155 optimal weight: 0.9990 chunk 60 optimal weight: 0.0870 chunk 94 optimal weight: 0.5980 chunk 115 optimal weight: 0.1980 chunk 179 optimal weight: 0.9990 overall best weight: 0.3758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 GLN A 804 GLN A 824 ASN A1108 ASN B 751 ASN B 804 GLN B 824 ASN B1010 GLN C 804 GLN C 824 ASN C 872 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.117664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.100225 restraints weight = 22836.959| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 2.12 r_work: 0.3064 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16386 Z= 0.179 Angle : 0.637 10.574 22362 Z= 0.324 Chirality : 0.044 0.169 2598 Planarity : 0.005 0.047 2841 Dihedral : 6.111 58.263 2627 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.83 % Allowed : 8.29 % Favored : 89.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.18), residues: 2022 helix: 1.63 (0.21), residues: 594 sheet: 0.77 (0.24), residues: 453 loop : -0.30 (0.19), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 103 HIS 0.004 0.001 HIS G 49 PHE 0.026 0.002 PHE C 927 TYR 0.022 0.002 TYR B1067 ARG 0.006 0.000 ARG A 815 Details of bonding type rmsd link_NAG-ASN : bond 0.00208 ( 18) link_NAG-ASN : angle 1.74837 ( 54) link_BETA1-4 : bond 0.00235 ( 3) link_BETA1-4 : angle 1.12612 ( 9) hydrogen bonds : bond 0.06366 ( 786) hydrogen bonds : angle 5.78387 ( 2394) SS BOND : bond 0.00494 ( 27) SS BOND : angle 2.07377 ( 54) covalent geometry : bond 0.00409 (16338) covalent geometry : angle 0.62382 (22245) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 371 time to evaluate : 1.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 780 GLU cc_start: 0.7782 (mm-30) cc_final: 0.7551 (mm-30) REVERT: A 833 PHE cc_start: 0.7090 (m-10) cc_final: 0.6158 (t80) REVERT: A 837 TYR cc_start: 0.7879 (t80) cc_final: 0.7582 (t80) REVERT: A 854 LYS cc_start: 0.8249 (tttt) cc_final: 0.8045 (tttt) REVERT: A 855 PHE cc_start: 0.7908 (m-80) cc_final: 0.7531 (m-80) REVERT: A 873 TYR cc_start: 0.8133 (m-10) cc_final: 0.7878 (m-10) REVERT: A 952 VAL cc_start: 0.8379 (t) cc_final: 0.8000 (p) REVERT: A 994 ASP cc_start: 0.7928 (m-30) cc_final: 0.7533 (m-30) REVERT: A 1010 GLN cc_start: 0.8415 (tp40) cc_final: 0.8180 (tp40) REVERT: A 1028 LYS cc_start: 0.8578 (mttp) cc_final: 0.8327 (mttt) REVERT: A 1138 TYR cc_start: 0.7281 (t80) cc_final: 0.7010 (t80) REVERT: D 80 LEU cc_start: 0.8552 (tt) cc_final: 0.8310 (tp) REVERT: F 5 THR cc_start: 0.8582 (OUTLIER) cc_final: 0.8254 (p) REVERT: G 5 THR cc_start: 0.8492 (m) cc_final: 0.8208 (p) REVERT: B 833 PHE cc_start: 0.7248 (m-10) cc_final: 0.6373 (t80) REVERT: B 866 THR cc_start: 0.8569 (p) cc_final: 0.8211 (t) REVERT: B 1092 GLU cc_start: 0.7782 (mt-10) cc_final: 0.7555 (mt-10) REVERT: C 752 LEU cc_start: 0.8538 (mt) cc_final: 0.8323 (mm) REVERT: C 780 GLU cc_start: 0.7779 (mm-30) cc_final: 0.7562 (mm-30) REVERT: C 855 PHE cc_start: 0.7898 (m-80) cc_final: 0.7576 (m-80) REVERT: C 860 VAL cc_start: 0.8947 (m) cc_final: 0.8612 (t) REVERT: C 957 GLU cc_start: 0.8144 (tp30) cc_final: 0.7549 (tp30) REVERT: C 994 ASP cc_start: 0.8077 (m-30) cc_final: 0.7817 (m-30) REVERT: C 1018 ILE cc_start: 0.8431 (OUTLIER) cc_final: 0.8208 (mp) REVERT: C 1031 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.8052 (mt-10) outliers start: 32 outliers final: 8 residues processed: 378 average time/residue: 1.0546 time to fit residues: 450.8605 Evaluate side-chains 359 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 348 time to evaluate : 1.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1031 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 93 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 133 optimal weight: 1.9990 chunk 186 optimal weight: 0.8980 chunk 163 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 127 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 87 optimal weight: 0.0770 chunk 20 optimal weight: 0.2980 chunk 193 optimal weight: 0.9990 overall best weight: 0.6540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 824 ASN A1108 ASN L 38 GLN B 824 ASN B1010 GLN C 804 GLN C 824 ASN C 872 GLN C 901 GLN C 969 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.115994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.098576 restraints weight = 22641.227| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 2.13 r_work: 0.3059 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 16386 Z= 0.259 Angle : 0.655 9.725 22362 Z= 0.333 Chirality : 0.046 0.193 2598 Planarity : 0.005 0.062 2841 Dihedral : 5.819 54.555 2627 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.12 % Allowed : 10.52 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.18), residues: 2022 helix: 1.56 (0.20), residues: 612 sheet: 0.65 (0.23), residues: 477 loop : -0.53 (0.20), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 103 HIS 0.007 0.002 HIS H 77 PHE 0.025 0.002 PHE B1121 TYR 0.019 0.002 TYR B1067 ARG 0.003 0.000 ARG A 815 Details of bonding type rmsd link_NAG-ASN : bond 0.00414 ( 18) link_NAG-ASN : angle 1.86860 ( 54) link_BETA1-4 : bond 0.00257 ( 3) link_BETA1-4 : angle 1.41403 ( 9) hydrogen bonds : bond 0.06291 ( 786) hydrogen bonds : angle 5.62141 ( 2394) SS BOND : bond 0.00424 ( 27) SS BOND : angle 1.93176 ( 54) covalent geometry : bond 0.00619 (16338) covalent geometry : angle 0.64215 (22245) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 362 time to evaluate : 1.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 780 GLU cc_start: 0.7758 (mm-30) cc_final: 0.7487 (mm-30) REVERT: A 833 PHE cc_start: 0.7140 (m-10) cc_final: 0.6201 (t80) REVERT: A 837 TYR cc_start: 0.7933 (t80) cc_final: 0.7482 (t80) REVERT: A 854 LYS cc_start: 0.8250 (tttt) cc_final: 0.8023 (tttt) REVERT: A 855 PHE cc_start: 0.7956 (m-80) cc_final: 0.7421 (m-80) REVERT: A 873 TYR cc_start: 0.8236 (m-10) cc_final: 0.7812 (m-10) REVERT: A 952 VAL cc_start: 0.8410 (t) cc_final: 0.8035 (p) REVERT: A 957 GLU cc_start: 0.8133 (tp30) cc_final: 0.7707 (tp30) REVERT: A 994 ASP cc_start: 0.7883 (m-30) cc_final: 0.7457 (m-30) REVERT: A 1116 THR cc_start: 0.8336 (t) cc_final: 0.8025 (p) REVERT: A 1138 TYR cc_start: 0.7389 (t80) cc_final: 0.7127 (t80) REVERT: A 1139 ASP cc_start: 0.7628 (t0) cc_final: 0.7354 (m-30) REVERT: G 4 MET cc_start: 0.8815 (OUTLIER) cc_final: 0.8488 (mmm) REVERT: B 727 LEU cc_start: 0.8334 (mt) cc_final: 0.8102 (mp) REVERT: B 739 THR cc_start: 0.8619 (m) cc_final: 0.8397 (t) REVERT: B 773 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7375 (tm-30) REVERT: B 866 THR cc_start: 0.8507 (p) cc_final: 0.8175 (t) REVERT: B 873 TYR cc_start: 0.8016 (m-10) cc_final: 0.7741 (m-10) REVERT: B 1010 GLN cc_start: 0.8366 (OUTLIER) cc_final: 0.8068 (mm-40) REVERT: B 1031 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.7977 (mt-10) REVERT: B 1092 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7461 (mt-10) REVERT: C 731 MET cc_start: 0.8472 (OUTLIER) cc_final: 0.8237 (ptm) REVERT: C 780 GLU cc_start: 0.7799 (mm-30) cc_final: 0.7487 (mm-30) REVERT: C 855 PHE cc_start: 0.7934 (m-80) cc_final: 0.7667 (m-80) REVERT: C 860 VAL cc_start: 0.8825 (m) cc_final: 0.8592 (t) REVERT: C 957 GLU cc_start: 0.8121 (tp30) cc_final: 0.7500 (tp30) REVERT: C 967 SER cc_start: 0.8586 (m) cc_final: 0.8362 (p) REVERT: C 994 ASP cc_start: 0.7928 (m-30) cc_final: 0.7662 (m-30) REVERT: C 1031 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7961 (mt-10) outliers start: 37 outliers final: 18 residues processed: 368 average time/residue: 1.0907 time to fit residues: 451.1446 Evaluate side-chains 377 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 354 time to evaluate : 1.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain G residue 4 MET Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 1031 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 128 optimal weight: 0.9980 chunk 122 optimal weight: 0.0770 chunk 159 optimal weight: 0.8980 chunk 120 optimal weight: 0.0980 chunk 144 optimal weight: 0.2980 chunk 121 optimal weight: 0.5980 chunk 136 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 132 optimal weight: 0.2980 chunk 88 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 overall best weight: 0.2738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 824 ASN A1108 ASN C 824 ASN C 872 GLN C 901 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.118776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.101495 restraints weight = 22562.649| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.13 r_work: 0.3090 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16386 Z= 0.136 Angle : 0.572 10.638 22362 Z= 0.287 Chirality : 0.042 0.167 2598 Planarity : 0.004 0.055 2841 Dihedral : 5.335 50.266 2625 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.34 % Allowed : 12.06 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.18), residues: 2022 helix: 1.95 (0.21), residues: 615 sheet: 0.74 (0.23), residues: 483 loop : -0.44 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 103 HIS 0.003 0.001 HIS D 77 PHE 0.018 0.002 PHE C 927 TYR 0.019 0.001 TYR B1067 ARG 0.004 0.000 ARG C 815 Details of bonding type rmsd link_NAG-ASN : bond 0.00130 ( 18) link_NAG-ASN : angle 1.66826 ( 54) link_BETA1-4 : bond 0.00187 ( 3) link_BETA1-4 : angle 1.30124 ( 9) hydrogen bonds : bond 0.05046 ( 786) hydrogen bonds : angle 5.22700 ( 2394) SS BOND : bond 0.00333 ( 27) SS BOND : angle 1.81163 ( 54) covalent geometry : bond 0.00307 (16338) covalent geometry : angle 0.55943 (22245) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 349 time to evaluate : 1.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 773 GLU cc_start: 0.7770 (mm-30) cc_final: 0.7375 (tm-30) REVERT: A 780 GLU cc_start: 0.7736 (mm-30) cc_final: 0.7504 (mm-30) REVERT: A 833 PHE cc_start: 0.7096 (m-10) cc_final: 0.6158 (t80) REVERT: A 837 TYR cc_start: 0.7771 (t80) cc_final: 0.7288 (t80) REVERT: A 866 THR cc_start: 0.8518 (p) cc_final: 0.8197 (t) REVERT: A 873 TYR cc_start: 0.8190 (m-10) cc_final: 0.7867 (m-10) REVERT: A 952 VAL cc_start: 0.8387 (t) cc_final: 0.8001 (p) REVERT: A 957 GLU cc_start: 0.8129 (tp30) cc_final: 0.7661 (tp30) REVERT: A 994 ASP cc_start: 0.7808 (m-30) cc_final: 0.7435 (m-30) REVERT: A 1010 GLN cc_start: 0.8330 (OUTLIER) cc_final: 0.7860 (mp10) REVERT: A 1138 TYR cc_start: 0.7289 (t80) cc_final: 0.6985 (t80) REVERT: A 1139 ASP cc_start: 0.7564 (OUTLIER) cc_final: 0.7312 (m-30) REVERT: F 5 THR cc_start: 0.8585 (OUTLIER) cc_final: 0.8197 (p) REVERT: G 5 THR cc_start: 0.8497 (m) cc_final: 0.8185 (p) REVERT: H 89 LEU cc_start: 0.8777 (tp) cc_final: 0.8531 (tt) REVERT: B 773 GLU cc_start: 0.7802 (mm-30) cc_final: 0.7163 (tm-30) REVERT: B 866 THR cc_start: 0.8408 (p) cc_final: 0.8071 (t) REVERT: B 873 TYR cc_start: 0.7995 (m-10) cc_final: 0.7794 (m-10) REVERT: B 1010 GLN cc_start: 0.8264 (OUTLIER) cc_final: 0.8061 (mm-40) REVERT: B 1031 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7961 (mt-10) REVERT: B 1092 GLU cc_start: 0.7654 (mt-10) cc_final: 0.7427 (mt-10) REVERT: C 780 GLU cc_start: 0.7733 (mm-30) cc_final: 0.7466 (mm-30) REVERT: C 860 VAL cc_start: 0.8780 (m) cc_final: 0.8519 (t) REVERT: C 957 GLU cc_start: 0.8127 (tp30) cc_final: 0.7511 (tp30) REVERT: C 967 SER cc_start: 0.8609 (m) cc_final: 0.8389 (p) REVERT: C 994 ASP cc_start: 0.7918 (m-30) cc_final: 0.7626 (m-30) REVERT: C 1031 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7919 (mt-10) outliers start: 41 outliers final: 18 residues processed: 364 average time/residue: 1.0301 time to fit residues: 421.2158 Evaluate side-chains 369 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 345 time to evaluate : 1.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1139 ASP Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1038 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 166 optimal weight: 1.9990 chunk 195 optimal weight: 0.9990 chunk 148 optimal weight: 0.8980 chunk 84 optimal weight: 0.9980 chunk 153 optimal weight: 0.9990 chunk 117 optimal weight: 0.8980 chunk 123 optimal weight: 0.0970 chunk 143 optimal weight: 1.9990 chunk 120 optimal weight: 0.4980 chunk 173 optimal weight: 0.2980 chunk 57 optimal weight: 0.9980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 824 ASN B 824 ASN B 935 GLN B 954 GLN C 804 GLN C 824 ASN C 872 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.117858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.100520 restraints weight = 22672.303| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 2.07 r_work: 0.3098 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 16386 Z= 0.217 Angle : 0.611 10.474 22362 Z= 0.308 Chirality : 0.044 0.177 2598 Planarity : 0.005 0.060 2841 Dihedral : 5.180 42.013 2625 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.20 % Allowed : 11.72 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.18), residues: 2022 helix: 1.85 (0.20), residues: 618 sheet: 0.78 (0.23), residues: 483 loop : -0.51 (0.20), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 103 HIS 0.006 0.002 HIS H 77 PHE 0.021 0.002 PHE B1121 TYR 0.019 0.002 TYR B1067 ARG 0.007 0.000 ARG A1014 Details of bonding type rmsd link_NAG-ASN : bond 0.00306 ( 18) link_NAG-ASN : angle 1.74904 ( 54) link_BETA1-4 : bond 0.00232 ( 3) link_BETA1-4 : angle 1.45971 ( 9) hydrogen bonds : bond 0.05625 ( 786) hydrogen bonds : angle 5.34192 ( 2394) SS BOND : bond 0.00327 ( 27) SS BOND : angle 1.85452 ( 54) covalent geometry : bond 0.00515 (16338) covalent geometry : angle 0.59876 (22245) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 358 time to evaluate : 2.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 780 GLU cc_start: 0.7778 (mm-30) cc_final: 0.7548 (mm-30) REVERT: A 833 PHE cc_start: 0.7078 (m-10) cc_final: 0.6344 (t80) REVERT: A 837 TYR cc_start: 0.8017 (t80) cc_final: 0.7626 (t80) REVERT: A 855 PHE cc_start: 0.8071 (m-80) cc_final: 0.7580 (m-80) REVERT: A 952 VAL cc_start: 0.8552 (t) cc_final: 0.8192 (p) REVERT: A 957 GLU cc_start: 0.8105 (tp30) cc_final: 0.7741 (tp30) REVERT: A 994 ASP cc_start: 0.7834 (m-30) cc_final: 0.7486 (m-30) REVERT: A 1010 GLN cc_start: 0.8326 (OUTLIER) cc_final: 0.7917 (mp10) REVERT: A 1031 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.7917 (mt-10) REVERT: A 1138 TYR cc_start: 0.7393 (t80) cc_final: 0.7077 (t80) REVERT: A 1139 ASP cc_start: 0.7649 (OUTLIER) cc_final: 0.7358 (m-30) REVERT: F 5 THR cc_start: 0.8633 (OUTLIER) cc_final: 0.8252 (p) REVERT: B 773 GLU cc_start: 0.7891 (mm-30) cc_final: 0.7319 (tm-30) REVERT: B 866 THR cc_start: 0.8680 (p) cc_final: 0.8308 (t) REVERT: B 873 TYR cc_start: 0.8150 (m-10) cc_final: 0.7907 (m-10) REVERT: B 1010 GLN cc_start: 0.8355 (OUTLIER) cc_final: 0.8081 (mm-40) REVERT: B 1031 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.8024 (mt-10) REVERT: C 731 MET cc_start: 0.8471 (OUTLIER) cc_final: 0.8268 (ptm) REVERT: C 780 GLU cc_start: 0.7732 (mm-30) cc_final: 0.7467 (mm-30) REVERT: C 855 PHE cc_start: 0.8015 (m-80) cc_final: 0.7765 (m-80) REVERT: C 860 VAL cc_start: 0.8862 (m) cc_final: 0.8594 (t) REVERT: C 957 GLU cc_start: 0.8124 (tp30) cc_final: 0.7599 (tp30) REVERT: C 994 ASP cc_start: 0.7935 (m-30) cc_final: 0.7671 (m-30) REVERT: C 1031 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7951 (mt-10) REVERT: C 1139 ASP cc_start: 0.7522 (t0) cc_final: 0.7301 (t0) outliers start: 56 outliers final: 32 residues processed: 376 average time/residue: 1.0752 time to fit residues: 455.7213 Evaluate side-chains 393 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 353 time to evaluate : 1.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1139 ASP Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 96 LEU Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1038 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 52 optimal weight: 0.9990 chunk 167 optimal weight: 0.4980 chunk 107 optimal weight: 0.9980 chunk 41 optimal weight: 0.7980 chunk 57 optimal weight: 0.0170 chunk 122 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 38 optimal weight: 0.0870 chunk 108 optimal weight: 0.9990 chunk 36 optimal weight: 0.4980 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 824 ASN B 935 GLN B 954 GLN B1002 GLN C 804 GLN C 824 ASN C 872 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.118838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.101579 restraints weight = 22453.987| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.06 r_work: 0.3114 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16386 Z= 0.166 Angle : 0.575 11.353 22362 Z= 0.289 Chirality : 0.043 0.162 2598 Planarity : 0.005 0.057 2841 Dihedral : 4.830 37.691 2625 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.26 % Allowed : 12.46 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.18), residues: 2022 helix: 1.96 (0.21), residues: 618 sheet: 0.81 (0.23), residues: 483 loop : -0.49 (0.20), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 103 HIS 0.005 0.001 HIS H 77 PHE 0.015 0.002 PHE B1121 TYR 0.019 0.002 TYR B1067 ARG 0.005 0.000 ARG A1014 Details of bonding type rmsd link_NAG-ASN : bond 0.00187 ( 18) link_NAG-ASN : angle 1.63610 ( 54) link_BETA1-4 : bond 0.00271 ( 3) link_BETA1-4 : angle 1.48038 ( 9) hydrogen bonds : bond 0.05091 ( 786) hydrogen bonds : angle 5.15605 ( 2394) SS BOND : bond 0.00270 ( 27) SS BOND : angle 1.65904 ( 54) covalent geometry : bond 0.00388 (16338) covalent geometry : angle 0.56400 (22245) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 347 time to evaluate : 1.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 773 GLU cc_start: 0.7794 (mm-30) cc_final: 0.7493 (tm-30) REVERT: A 780 GLU cc_start: 0.7731 (mm-30) cc_final: 0.7530 (mm-30) REVERT: A 833 PHE cc_start: 0.7046 (m-10) cc_final: 0.6305 (t80) REVERT: A 837 TYR cc_start: 0.8007 (t80) cc_final: 0.7474 (t80) REVERT: A 855 PHE cc_start: 0.8034 (m-80) cc_final: 0.7493 (m-80) REVERT: A 866 THR cc_start: 0.8614 (p) cc_final: 0.8300 (t) REVERT: A 952 VAL cc_start: 0.8542 (t) cc_final: 0.8178 (p) REVERT: A 957 GLU cc_start: 0.8069 (tp30) cc_final: 0.7733 (tp30) REVERT: A 994 ASP cc_start: 0.7874 (m-30) cc_final: 0.7525 (m-30) REVERT: A 1010 GLN cc_start: 0.8303 (OUTLIER) cc_final: 0.8065 (mm110) REVERT: A 1031 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.7877 (mt-10) REVERT: A 1138 TYR cc_start: 0.7381 (t80) cc_final: 0.7067 (t80) REVERT: A 1139 ASP cc_start: 0.7588 (OUTLIER) cc_final: 0.7285 (m-30) REVERT: F 5 THR cc_start: 0.8619 (OUTLIER) cc_final: 0.8270 (p) REVERT: G 5 THR cc_start: 0.8540 (m) cc_final: 0.8245 (p) REVERT: B 773 GLU cc_start: 0.7851 (mm-30) cc_final: 0.7274 (tm-30) REVERT: B 833 PHE cc_start: 0.7162 (m-10) cc_final: 0.6549 (t80) REVERT: B 866 THR cc_start: 0.8656 (p) cc_final: 0.8298 (t) REVERT: B 873 TYR cc_start: 0.8159 (m-10) cc_final: 0.7927 (m-10) REVERT: B 1010 GLN cc_start: 0.8383 (OUTLIER) cc_final: 0.8117 (mm-40) REVERT: B 1031 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7971 (mt-10) REVERT: C 731 MET cc_start: 0.8468 (OUTLIER) cc_final: 0.8260 (ptm) REVERT: C 780 GLU cc_start: 0.7654 (mm-30) cc_final: 0.7398 (mm-30) REVERT: C 855 PHE cc_start: 0.7995 (m-80) cc_final: 0.7691 (m-80) REVERT: C 860 VAL cc_start: 0.8834 (m) cc_final: 0.8568 (t) REVERT: C 945 LEU cc_start: 0.8087 (mm) cc_final: 0.7846 (mt) REVERT: C 957 GLU cc_start: 0.8111 (tp30) cc_final: 0.7610 (tp30) REVERT: C 994 ASP cc_start: 0.7923 (m-30) cc_final: 0.7664 (m-30) REVERT: C 1031 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7940 (mt-10) REVERT: C 1073 LYS cc_start: 0.8423 (OUTLIER) cc_final: 0.8085 (mtmm) REVERT: C 1139 ASP cc_start: 0.7496 (t0) cc_final: 0.7290 (t0) outliers start: 57 outliers final: 36 residues processed: 368 average time/residue: 1.0812 time to fit residues: 449.6616 Evaluate side-chains 390 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 345 time to evaluate : 1.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1139 ASP Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 96 LEU Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1073 LYS Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 35 optimal weight: 0.9990 chunk 196 optimal weight: 0.7980 chunk 41 optimal weight: 0.2980 chunk 33 optimal weight: 0.5980 chunk 32 optimal weight: 0.0980 chunk 89 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 chunk 152 optimal weight: 0.5980 chunk 98 optimal weight: 0.8980 chunk 78 optimal weight: 0.9980 chunk 129 optimal weight: 0.4980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 764 ASN A 824 ASN B 935 GLN B 954 GLN C 804 GLN C 824 ASN C 872 GLN C 969 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.118662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.101275 restraints weight = 22546.635| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.07 r_work: 0.3110 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16386 Z= 0.179 Angle : 0.584 11.332 22362 Z= 0.293 Chirality : 0.043 0.186 2598 Planarity : 0.005 0.057 2841 Dihedral : 4.661 37.818 2625 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.43 % Allowed : 12.81 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.18), residues: 2022 helix: 1.94 (0.20), residues: 621 sheet: 0.85 (0.24), residues: 468 loop : -0.50 (0.19), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 103 HIS 0.005 0.001 HIS H 77 PHE 0.017 0.002 PHE B1121 TYR 0.019 0.002 TYR B1067 ARG 0.005 0.000 ARG A1014 Details of bonding type rmsd link_NAG-ASN : bond 0.00226 ( 18) link_NAG-ASN : angle 1.65816 ( 54) link_BETA1-4 : bond 0.00296 ( 3) link_BETA1-4 : angle 1.53602 ( 9) hydrogen bonds : bond 0.05153 ( 786) hydrogen bonds : angle 5.14697 ( 2394) SS BOND : bond 0.00265 ( 27) SS BOND : angle 1.74344 ( 54) covalent geometry : bond 0.00420 (16338) covalent geometry : angle 0.57256 (22245) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 352 time to evaluate : 1.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 773 GLU cc_start: 0.7801 (mm-30) cc_final: 0.7471 (tm-30) REVERT: A 837 TYR cc_start: 0.8004 (t80) cc_final: 0.7524 (t80) REVERT: A 866 THR cc_start: 0.8640 (p) cc_final: 0.8321 (t) REVERT: A 952 VAL cc_start: 0.8526 (t) cc_final: 0.8168 (p) REVERT: A 957 GLU cc_start: 0.8045 (tp30) cc_final: 0.7706 (tp30) REVERT: A 994 ASP cc_start: 0.7868 (m-30) cc_final: 0.7521 (m-30) REVERT: A 1010 GLN cc_start: 0.8299 (OUTLIER) cc_final: 0.8069 (mm110) REVERT: A 1031 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.7909 (mt-10) REVERT: A 1138 TYR cc_start: 0.7411 (t80) cc_final: 0.7069 (t80) REVERT: A 1139 ASP cc_start: 0.7599 (OUTLIER) cc_final: 0.7304 (m-30) REVERT: D 78 PHE cc_start: 0.8822 (p90) cc_final: 0.8570 (p90) REVERT: F 5 THR cc_start: 0.8633 (OUTLIER) cc_final: 0.8298 (p) REVERT: B 773 GLU cc_start: 0.7853 (mm-30) cc_final: 0.7222 (tm-30) REVERT: B 866 THR cc_start: 0.8596 (p) cc_final: 0.8320 (t) REVERT: B 1031 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7983 (mt-10) REVERT: B 1098 ASN cc_start: 0.8049 (p0) cc_final: 0.7771 (p0) REVERT: C 731 MET cc_start: 0.8474 (OUTLIER) cc_final: 0.8266 (ptm) REVERT: C 773 GLU cc_start: 0.7826 (mm-30) cc_final: 0.7478 (tm-30) REVERT: C 780 GLU cc_start: 0.7653 (mm-30) cc_final: 0.7397 (mm-30) REVERT: C 855 PHE cc_start: 0.7973 (m-80) cc_final: 0.7687 (m-80) REVERT: C 860 VAL cc_start: 0.8826 (m) cc_final: 0.8555 (t) REVERT: C 945 LEU cc_start: 0.8061 (mm) cc_final: 0.7826 (mt) REVERT: C 957 GLU cc_start: 0.8094 (tp30) cc_final: 0.7601 (tp30) REVERT: C 994 ASP cc_start: 0.7921 (m-30) cc_final: 0.7662 (m-30) REVERT: C 1031 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.7952 (mt-10) REVERT: C 1073 LYS cc_start: 0.8457 (OUTLIER) cc_final: 0.8117 (mtmm) REVERT: C 1139 ASP cc_start: 0.7494 (t0) cc_final: 0.7293 (t0) outliers start: 60 outliers final: 35 residues processed: 377 average time/residue: 1.0674 time to fit residues: 452.3593 Evaluate side-chains 392 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 349 time to evaluate : 1.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1139 ASP Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 96 LEU Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1073 LYS Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 144 optimal weight: 0.0970 chunk 186 optimal weight: 0.8980 chunk 125 optimal weight: 0.9990 chunk 170 optimal weight: 0.6980 chunk 163 optimal weight: 0.0040 chunk 113 optimal weight: 0.9990 chunk 168 optimal weight: 5.9990 chunk 173 optimal weight: 0.0870 chunk 160 optimal weight: 0.9980 chunk 76 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 overall best weight: 0.3568 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 824 ASN A 935 GLN F 32 ASN B 935 GLN B 954 GLN C 804 GLN C 824 ASN C 872 GLN C 954 GLN C 969 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.119151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.101771 restraints weight = 22419.166| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.06 r_work: 0.3119 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16386 Z= 0.159 Angle : 0.572 11.691 22362 Z= 0.287 Chirality : 0.043 0.158 2598 Planarity : 0.004 0.055 2841 Dihedral : 4.509 37.120 2625 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.14 % Allowed : 13.49 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.18), residues: 2022 helix: 1.99 (0.20), residues: 621 sheet: 0.95 (0.24), residues: 453 loop : -0.42 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 103 HIS 0.004 0.001 HIS H 77 PHE 0.015 0.002 PHE B1121 TYR 0.019 0.002 TYR B1067 ARG 0.004 0.000 ARG A1014 Details of bonding type rmsd link_NAG-ASN : bond 0.00185 ( 18) link_NAG-ASN : angle 1.61897 ( 54) link_BETA1-4 : bond 0.00287 ( 3) link_BETA1-4 : angle 1.49994 ( 9) hydrogen bonds : bond 0.04958 ( 786) hydrogen bonds : angle 5.04844 ( 2394) SS BOND : bond 0.00270 ( 27) SS BOND : angle 1.84901 ( 54) covalent geometry : bond 0.00369 (16338) covalent geometry : angle 0.55966 (22245) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 352 time to evaluate : 1.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 773 GLU cc_start: 0.7788 (mm-30) cc_final: 0.7477 (tm-30) REVERT: A 833 PHE cc_start: 0.7190 (m-10) cc_final: 0.6233 (t80) REVERT: A 837 TYR cc_start: 0.7905 (t80) cc_final: 0.7472 (t80) REVERT: A 855 PHE cc_start: 0.7981 (m-80) cc_final: 0.7514 (m-80) REVERT: A 866 THR cc_start: 0.8667 (p) cc_final: 0.8349 (t) REVERT: A 952 VAL cc_start: 0.8507 (t) cc_final: 0.8141 (p) REVERT: A 957 GLU cc_start: 0.8024 (tp30) cc_final: 0.7730 (tp30) REVERT: A 994 ASP cc_start: 0.7846 (m-30) cc_final: 0.7503 (m-30) REVERT: A 1010 GLN cc_start: 0.8290 (OUTLIER) cc_final: 0.8059 (mm110) REVERT: A 1031 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.7910 (mt-10) REVERT: A 1138 TYR cc_start: 0.7374 (t80) cc_final: 0.7018 (t80) REVERT: A 1139 ASP cc_start: 0.7618 (OUTLIER) cc_final: 0.7311 (m-30) REVERT: D 78 PHE cc_start: 0.8796 (p90) cc_final: 0.8536 (p90) REVERT: D 111 VAL cc_start: 0.8457 (t) cc_final: 0.8199 (m) REVERT: F 5 THR cc_start: 0.8647 (m) cc_final: 0.8309 (p) REVERT: B 773 GLU cc_start: 0.7813 (mm-30) cc_final: 0.7165 (tm-30) REVERT: B 873 TYR cc_start: 0.8154 (m-10) cc_final: 0.7905 (m-10) REVERT: B 953 ASN cc_start: 0.8310 (m-40) cc_final: 0.8104 (m-40) REVERT: B 1031 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7952 (mt-10) REVERT: B 1098 ASN cc_start: 0.8055 (p0) cc_final: 0.7772 (p0) REVERT: C 731 MET cc_start: 0.8481 (OUTLIER) cc_final: 0.8268 (ptm) REVERT: C 780 GLU cc_start: 0.7651 (mm-30) cc_final: 0.7406 (mm-30) REVERT: C 855 PHE cc_start: 0.7930 (m-80) cc_final: 0.7665 (m-80) REVERT: C 860 VAL cc_start: 0.8808 (m) cc_final: 0.8530 (t) REVERT: C 957 GLU cc_start: 0.8125 (tp30) cc_final: 0.7663 (tp30) REVERT: C 994 ASP cc_start: 0.7916 (m-30) cc_final: 0.7655 (m-30) REVERT: C 1031 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7951 (mt-10) REVERT: C 1073 LYS cc_start: 0.8470 (OUTLIER) cc_final: 0.8142 (mtmm) outliers start: 55 outliers final: 39 residues processed: 373 average time/residue: 1.0570 time to fit residues: 443.4678 Evaluate side-chains 394 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 348 time to evaluate : 1.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1139 ASP Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 96 LEU Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1073 LYS Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 71 optimal weight: 0.9990 chunk 155 optimal weight: 0.5980 chunk 35 optimal weight: 0.6980 chunk 132 optimal weight: 0.9980 chunk 146 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 171 optimal weight: 0.9990 chunk 195 optimal weight: 0.9990 chunk 9 optimal weight: 0.3980 chunk 173 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 764 ASN A 824 ASN A 935 GLN A1108 ASN B 872 GLN B 935 GLN B 954 GLN C 804 GLN C 824 ASN C 872 GLN C 969 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.117543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.100094 restraints weight = 22580.438| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 2.07 r_work: 0.3082 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 16386 Z= 0.239 Angle : 0.628 11.396 22362 Z= 0.316 Chirality : 0.045 0.171 2598 Planarity : 0.005 0.060 2841 Dihedral : 4.654 38.164 2625 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.26 % Allowed : 13.55 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.18), residues: 2022 helix: 1.86 (0.20), residues: 621 sheet: 0.92 (0.24), residues: 453 loop : -0.52 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 103 HIS 0.006 0.002 HIS H 77 PHE 0.022 0.002 PHE B1121 TYR 0.024 0.002 TYR D 50 ARG 0.004 0.000 ARG A1014 Details of bonding type rmsd link_NAG-ASN : bond 0.00322 ( 18) link_NAG-ASN : angle 1.74083 ( 54) link_BETA1-4 : bond 0.00175 ( 3) link_BETA1-4 : angle 1.60680 ( 9) hydrogen bonds : bond 0.05566 ( 786) hydrogen bonds : angle 5.23209 ( 2394) SS BOND : bond 0.00431 ( 27) SS BOND : angle 2.25714 ( 54) covalent geometry : bond 0.00570 (16338) covalent geometry : angle 0.61257 (22245) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 355 time to evaluate : 1.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 773 GLU cc_start: 0.7789 (mm-30) cc_final: 0.7468 (tm-30) REVERT: A 833 PHE cc_start: 0.7269 (m-10) cc_final: 0.6261 (t80) REVERT: A 837 TYR cc_start: 0.8031 (t80) cc_final: 0.7523 (t80) REVERT: A 855 PHE cc_start: 0.8097 (m-80) cc_final: 0.7559 (m-80) REVERT: A 866 THR cc_start: 0.8687 (p) cc_final: 0.8372 (t) REVERT: A 952 VAL cc_start: 0.8521 (t) cc_final: 0.8163 (p) REVERT: A 957 GLU cc_start: 0.8052 (tp30) cc_final: 0.7733 (tp30) REVERT: A 994 ASP cc_start: 0.7867 (m-30) cc_final: 0.7527 (m-30) REVERT: A 1010 GLN cc_start: 0.8308 (OUTLIER) cc_final: 0.7899 (mp10) REVERT: A 1031 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.7920 (mt-10) REVERT: A 1138 TYR cc_start: 0.7445 (t80) cc_final: 0.7059 (t80) REVERT: A 1139 ASP cc_start: 0.7643 (OUTLIER) cc_final: 0.7332 (m-30) REVERT: F 5 THR cc_start: 0.8656 (m) cc_final: 0.8271 (p) REVERT: G 5 THR cc_start: 0.8590 (m) cc_final: 0.8276 (p) REVERT: B 773 GLU cc_start: 0.7845 (mm-30) cc_final: 0.7184 (tm-30) REVERT: B 873 TYR cc_start: 0.8154 (m-10) cc_final: 0.7913 (m-10) REVERT: B 1031 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.8003 (mt-10) REVERT: B 1098 ASN cc_start: 0.8056 (p0) cc_final: 0.7774 (p0) REVERT: C 731 MET cc_start: 0.8477 (OUTLIER) cc_final: 0.8276 (ptm) REVERT: C 773 GLU cc_start: 0.7800 (mm-30) cc_final: 0.7468 (tm-30) REVERT: C 780 GLU cc_start: 0.7667 (mm-30) cc_final: 0.7399 (mm-30) REVERT: C 804 GLN cc_start: 0.8448 (mm110) cc_final: 0.8021 (mp-120) REVERT: C 855 PHE cc_start: 0.7975 (m-80) cc_final: 0.7641 (m-80) REVERT: C 860 VAL cc_start: 0.8806 (m) cc_final: 0.8560 (t) REVERT: C 957 GLU cc_start: 0.8087 (tp30) cc_final: 0.7630 (tp30) REVERT: C 994 ASP cc_start: 0.7923 (m-30) cc_final: 0.7675 (m-30) REVERT: C 1031 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7953 (mt-10) REVERT: C 1073 LYS cc_start: 0.8479 (OUTLIER) cc_final: 0.8131 (mtmm) outliers start: 57 outliers final: 38 residues processed: 377 average time/residue: 0.9858 time to fit residues: 420.0943 Evaluate side-chains 395 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 350 time to evaluate : 1.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1139 ASP Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 96 LEU Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 95 LEU Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1073 LYS Chi-restraints excluded: chain C residue 1086 LYS Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 119 optimal weight: 0.0370 chunk 79 optimal weight: 0.0770 chunk 16 optimal weight: 0.0000 chunk 143 optimal weight: 0.9990 chunk 159 optimal weight: 0.9980 chunk 71 optimal weight: 0.6980 chunk 115 optimal weight: 0.0470 chunk 170 optimal weight: 0.0970 chunk 129 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 chunk 186 optimal weight: 0.5980 overall best weight: 0.0516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 824 ASN A 935 GLN A1108 ASN B 935 GLN B 949 GLN C 751 ASN C 824 ASN C 872 GLN C 954 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.121214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.103910 restraints weight = 22657.783| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.13 r_work: 0.3134 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 16386 Z= 0.101 Angle : 0.550 12.060 22362 Z= 0.276 Chirality : 0.041 0.192 2598 Planarity : 0.004 0.048 2841 Dihedral : 4.252 34.483 2625 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.54 % Allowed : 15.49 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.19), residues: 2022 helix: 2.14 (0.21), residues: 624 sheet: 0.99 (0.25), residues: 453 loop : -0.41 (0.19), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 47 HIS 0.004 0.001 HIS C1048 PHE 0.018 0.001 PHE C 927 TYR 0.019 0.001 TYR A1067 ARG 0.004 0.000 ARG A1014 Details of bonding type rmsd link_NAG-ASN : bond 0.00157 ( 18) link_NAG-ASN : angle 1.48153 ( 54) link_BETA1-4 : bond 0.00330 ( 3) link_BETA1-4 : angle 1.29970 ( 9) hydrogen bonds : bond 0.04129 ( 786) hydrogen bonds : angle 4.77415 ( 2394) SS BOND : bond 0.00297 ( 27) SS BOND : angle 1.73807 ( 54) covalent geometry : bond 0.00209 (16338) covalent geometry : angle 0.53955 (22245) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 356 time to evaluate : 1.827 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 773 GLU cc_start: 0.7678 (mm-30) cc_final: 0.7308 (tm-30) REVERT: A 815 ARG cc_start: 0.8235 (ttp80) cc_final: 0.7900 (ttp-170) REVERT: A 833 PHE cc_start: 0.7248 (m-10) cc_final: 0.6275 (t80) REVERT: A 837 TYR cc_start: 0.7722 (t80) cc_final: 0.7276 (t80) REVERT: A 952 VAL cc_start: 0.8333 (t) cc_final: 0.7945 (p) REVERT: A 957 GLU cc_start: 0.8115 (tp30) cc_final: 0.7838 (tp30) REVERT: A 994 ASP cc_start: 0.7762 (m-30) cc_final: 0.7412 (m-30) REVERT: A 1010 GLN cc_start: 0.8298 (OUTLIER) cc_final: 0.8040 (mm110) REVERT: A 1031 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7802 (mt-10) REVERT: A 1138 TYR cc_start: 0.7245 (t80) cc_final: 0.6905 (t80) REVERT: A 1139 ASP cc_start: 0.7598 (OUTLIER) cc_final: 0.7297 (m-30) REVERT: D 78 PHE cc_start: 0.8671 (p90) cc_final: 0.7587 (p90) REVERT: D 111 VAL cc_start: 0.8523 (t) cc_final: 0.8261 (m) REVERT: F 5 THR cc_start: 0.8579 (m) cc_final: 0.8273 (p) REVERT: B 773 GLU cc_start: 0.7695 (mm-30) cc_final: 0.6916 (tm-30) REVERT: B 797 PHE cc_start: 0.7864 (m-80) cc_final: 0.7124 (m-80) REVERT: B 858 LEU cc_start: 0.8044 (mt) cc_final: 0.7782 (mm) REVERT: B 873 TYR cc_start: 0.8028 (m-10) cc_final: 0.7723 (m-10) REVERT: B 905 ARG cc_start: 0.8530 (mmt180) cc_final: 0.8212 (mmt180) REVERT: B 994 ASP cc_start: 0.7873 (m-30) cc_final: 0.7586 (m-30) REVERT: B 1031 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7808 (mt-10) REVERT: B 1098 ASN cc_start: 0.8040 (p0) cc_final: 0.7745 (p0) REVERT: C 773 GLU cc_start: 0.7739 (mm-30) cc_final: 0.7346 (tm-30) REVERT: C 780 GLU cc_start: 0.7588 (mm-30) cc_final: 0.7352 (mm-30) REVERT: C 804 GLN cc_start: 0.8414 (mm110) cc_final: 0.7977 (mp-120) REVERT: C 855 PHE cc_start: 0.7700 (m-80) cc_final: 0.7388 (m-80) REVERT: C 860 VAL cc_start: 0.8751 (m) cc_final: 0.8445 (t) REVERT: C 945 LEU cc_start: 0.7808 (mm) cc_final: 0.7603 (mt) REVERT: C 957 GLU cc_start: 0.8101 (tp30) cc_final: 0.7559 (tp30) REVERT: C 994 ASP cc_start: 0.7802 (m-30) cc_final: 0.7525 (m-30) REVERT: C 1071 GLN cc_start: 0.8576 (mt0) cc_final: 0.8100 (mt0) REVERT: C 1073 LYS cc_start: 0.8474 (OUTLIER) cc_final: 0.8078 (mtmm) outliers start: 27 outliers final: 16 residues processed: 366 average time/residue: 1.0818 time to fit residues: 450.2593 Evaluate side-chains 369 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 348 time to evaluate : 1.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1139 ASP Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 96 LEU Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1073 LYS Chi-restraints excluded: chain C residue 1086 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 164 optimal weight: 0.8980 chunk 165 optimal weight: 0.2980 chunk 169 optimal weight: 0.9990 chunk 101 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 764 ASN A 824 ASN A 935 GLN A1113 GLN B 954 GLN B1010 GLN B1135 ASN C 751 ASN C 824 ASN C 872 GLN C 969 ASN C1135 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.117503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.099991 restraints weight = 22429.569| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.06 r_work: 0.3081 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 16386 Z= 0.287 Angle : 0.663 11.122 22362 Z= 0.334 Chirality : 0.047 0.173 2598 Planarity : 0.005 0.059 2841 Dihedral : 4.626 37.524 2625 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.12 % Allowed : 15.67 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.18), residues: 2022 helix: 1.83 (0.20), residues: 621 sheet: 0.96 (0.24), residues: 453 loop : -0.55 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 103 HIS 0.007 0.002 HIS D 77 PHE 0.027 0.002 PHE B 823 TYR 0.027 0.002 TYR D 50 ARG 0.005 0.000 ARG A1014 Details of bonding type rmsd link_NAG-ASN : bond 0.00399 ( 18) link_NAG-ASN : angle 1.79331 ( 54) link_BETA1-4 : bond 0.00280 ( 3) link_BETA1-4 : angle 1.58355 ( 9) hydrogen bonds : bond 0.05792 ( 786) hydrogen bonds : angle 5.26741 ( 2394) SS BOND : bond 0.00384 ( 27) SS BOND : angle 2.30196 ( 54) covalent geometry : bond 0.00687 (16338) covalent geometry : angle 0.64811 (22245) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11872.90 seconds wall clock time: 206 minutes 6.25 seconds (12366.25 seconds total)