Starting phenix.real_space_refine on Thu Sep 18 10:15:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vcr_43139/09_2025/8vcr_43139.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vcr_43139/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8vcr_43139/09_2025/8vcr_43139.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vcr_43139/09_2025/8vcr_43139.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8vcr_43139/09_2025/8vcr_43139.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vcr_43139/09_2025/8vcr_43139.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 4.08, per 1000 atoms: 0.26 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: 1.37 Conformation dependent library (CDL) restraints added in 792.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.70 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: 3.26 Time building geometry restraints manager: 1.79 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' } 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: 16.480 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: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.960 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.040 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:6.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.830 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.012 0.001 ARG C1019 TYR 0.027 0.003 TYR E 52 PHE 0.019 0.002 PHE C1121 TRP 0.019 0.003 TRP H 103 HIS 0.010 0.003 HIS E 77 Details of bonding type rmsd covalent geometry : bond 0.00839 (16338) covalent geometry : angle 0.76569 (22245) SS BOND : bond 0.00945 ( 27) SS BOND : angle 1.83618 ( 54) hydrogen bonds : bond 0.21754 ( 786) hydrogen bonds : angle 8.24553 ( 2394) link_BETA1-4 : bond 0.00073 ( 3) link_BETA1-4 : angle 1.99350 ( 9) link_NAG-ASN : bond 0.00638 ( 18) link_NAG-ASN : angle 2.40791 ( 54) *********************** 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 : 0.559 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: 0.5307 time to fit residues: 231.5463 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 : 0.616 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.7980 chunk 194 optimal weight: 0.5980 chunk 107 optimal weight: 0.0870 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.0870 chunk 130 optimal weight: 0.0970 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 0.0670 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 overall best weight: 0.1872 ------------------------------------------------------------------------------- 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 L 38 GLN 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.118418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.100839 restraints weight = 22902.291| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.14 r_work: 0.3093 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16386 Z= 0.133 Angle : 0.613 11.361 22362 Z= 0.309 Chirality : 0.042 0.163 2598 Planarity : 0.004 0.044 2841 Dihedral : 6.005 58.743 2627 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.83 % Allowed : 8.35 % Favored : 89.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.77 (0.18), residues: 2022 helix: 1.61 (0.21), residues: 609 sheet: 0.80 (0.24), residues: 453 loop : -0.30 (0.20), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 815 TYR 0.021 0.001 TYR B1067 PHE 0.026 0.002 PHE C 927 TRP 0.010 0.001 TRP D 103 HIS 0.003 0.001 HIS G 49 Details of bonding type rmsd covalent geometry : bond 0.00282 (16338) covalent geometry : angle 0.60061 (22245) SS BOND : bond 0.00618 ( 27) SS BOND : angle 2.05032 ( 54) hydrogen bonds : bond 0.05650 ( 786) hydrogen bonds : angle 5.60995 ( 2394) link_BETA1-4 : bond 0.00324 ( 3) link_BETA1-4 : angle 0.97750 ( 9) link_NAG-ASN : bond 0.00173 ( 18) link_NAG-ASN : angle 1.68599 ( 54) *********************** 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 : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 780 GLU cc_start: 0.7741 (mm-30) cc_final: 0.7532 (mm-30) REVERT: A 833 PHE cc_start: 0.7096 (m-10) cc_final: 0.6221 (t80) REVERT: A 855 PHE cc_start: 0.7823 (m-80) cc_final: 0.7540 (m-80) REVERT: A 952 VAL cc_start: 0.8359 (t) cc_final: 0.7973 (p) REVERT: A 957 GLU cc_start: 0.8053 (tp30) cc_final: 0.7837 (tp30) REVERT: A 994 ASP cc_start: 0.7945 (m-30) cc_final: 0.7539 (m-30) REVERT: A 1010 GLN cc_start: 0.8411 (tp40) cc_final: 0.8157 (tp40) REVERT: A 1028 LYS cc_start: 0.8524 (mttp) cc_final: 0.8292 (mttt) REVERT: A 1138 TYR cc_start: 0.7255 (t80) cc_final: 0.6991 (t80) REVERT: F 5 THR cc_start: 0.8529 (OUTLIER) cc_final: 0.8271 (p) REVERT: G 5 THR cc_start: 0.8456 (m) cc_final: 0.8226 (p) REVERT: B 833 PHE cc_start: 0.7235 (m-10) cc_final: 0.6431 (t80) REVERT: B 866 THR cc_start: 0.8558 (p) cc_final: 0.8202 (t) REVERT: B 905 ARG cc_start: 0.8493 (mmt90) cc_final: 0.8281 (mmt-90) REVERT: B 1092 GLU cc_start: 0.7791 (mt-10) cc_final: 0.7562 (mt-10) REVERT: C 860 VAL cc_start: 0.8947 (m) cc_final: 0.8609 (t) REVERT: C 957 GLU cc_start: 0.8133 (tp30) cc_final: 0.7529 (tp30) REVERT: C 994 ASP cc_start: 0.8117 (m-30) cc_final: 0.7861 (m-30) REVERT: C 1031 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.8001 (mt-10) outliers start: 32 outliers final: 7 residues processed: 378 average time/residue: 0.5148 time to fit residues: 218.6921 Evaluate side-chains 357 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 348 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain F residue 5 THR 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 C residue 747 THR 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 165 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 141 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 97 optimal weight: 0.9990 chunk 49 optimal weight: 0.2980 chunk 133 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 188 optimal weight: 0.0770 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 824 ASN A1108 ASN B 762 GLN B 804 GLN B 824 ASN B 872 GLN B1010 GLN C 804 GLN C 824 ASN C 872 GLN C 901 GLN C 969 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.117229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.099715 restraints weight = 23094.898| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 2.15 r_work: 0.3062 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 16386 Z= 0.228 Angle : 0.624 10.235 22362 Z= 0.317 Chirality : 0.044 0.188 2598 Planarity : 0.005 0.056 2841 Dihedral : 5.754 56.912 2625 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.77 % Allowed : 10.58 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.74 (0.18), residues: 2022 helix: 1.74 (0.20), residues: 615 sheet: 0.67 (0.23), residues: 483 loop : -0.43 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1014 TYR 0.020 0.002 TYR C1067 PHE 0.021 0.002 PHE C 927 TRP 0.016 0.002 TRP D 103 HIS 0.005 0.002 HIS H 77 Details of bonding type rmsd covalent geometry : bond 0.00541 (16338) covalent geometry : angle 0.61262 (22245) SS BOND : bond 0.00410 ( 27) SS BOND : angle 1.85948 ( 54) hydrogen bonds : bond 0.05973 ( 786) hydrogen bonds : angle 5.50407 ( 2394) link_BETA1-4 : bond 0.00195 ( 3) link_BETA1-4 : angle 1.25463 ( 9) link_NAG-ASN : bond 0.00345 ( 18) link_NAG-ASN : angle 1.77950 ( 54) *********************** 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 378 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 347 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 773 GLU cc_start: 0.7800 (mm-30) cc_final: 0.7385 (tm-30) REVERT: A 780 GLU cc_start: 0.7791 (mm-30) cc_final: 0.7549 (mm-30) REVERT: A 833 PHE cc_start: 0.7104 (m-10) cc_final: 0.6167 (t80) REVERT: A 837 TYR cc_start: 0.7931 (t80) cc_final: 0.7514 (t80) REVERT: A 855 PHE cc_start: 0.7903 (m-80) cc_final: 0.7347 (m-80) REVERT: A 952 VAL cc_start: 0.8404 (t) cc_final: 0.8028 (p) REVERT: A 957 GLU cc_start: 0.8116 (tp30) cc_final: 0.7692 (tp30) REVERT: A 994 ASP cc_start: 0.7885 (m-30) cc_final: 0.7460 (m-30) REVERT: A 1031 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.7994 (mt-10) REVERT: A 1138 TYR cc_start: 0.7335 (t80) cc_final: 0.7020 (t80) REVERT: F 5 THR cc_start: 0.8615 (OUTLIER) cc_final: 0.8219 (p) REVERT: B 727 LEU cc_start: 0.8350 (mt) cc_final: 0.8118 (mp) REVERT: B 773 GLU cc_start: 0.7846 (mm-30) cc_final: 0.7385 (tm-30) REVERT: B 860 VAL cc_start: 0.8830 (m) cc_final: 0.8596 (t) REVERT: B 866 THR cc_start: 0.8566 (p) cc_final: 0.8212 (t) REVERT: B 873 TYR cc_start: 0.8002 (m-10) cc_final: 0.7706 (m-10) REVERT: B 905 ARG cc_start: 0.8528 (mmt90) cc_final: 0.8219 (mmt180) REVERT: B 1031 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.8013 (mt-10) REVERT: B 1092 GLU cc_start: 0.7743 (mt-10) cc_final: 0.7530 (mt-10) REVERT: C 855 PHE cc_start: 0.7939 (m-80) cc_final: 0.7594 (m-80) REVERT: C 860 VAL cc_start: 0.8857 (m) cc_final: 0.8606 (t) REVERT: C 957 GLU cc_start: 0.8128 (tp30) cc_final: 0.7506 (tp30) REVERT: C 994 ASP cc_start: 0.7980 (m-30) cc_final: 0.7696 (m-30) REVERT: C 1031 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.7994 (mt-10) outliers start: 31 outliers final: 12 residues processed: 351 average time/residue: 0.5542 time to fit residues: 217.3718 Evaluate side-chains 356 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 340 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1031 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 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 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 C residue 947 LYS Chi-restraints excluded: chain C residue 1018 ILE 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 173 optimal weight: 0.3980 chunk 0 optimal weight: 1.9990 chunk 182 optimal weight: 0.6980 chunk 162 optimal weight: 0.5980 chunk 48 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 chunk 113 optimal weight: 0.9980 chunk 99 optimal weight: 0.0870 chunk 101 optimal weight: 0.9990 chunk 82 optimal weight: 0.8980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 824 ASN ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN B 824 ASN C 804 GLN C 824 ASN C 872 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.117780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.100359 restraints weight = 22732.976| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 2.13 r_work: 0.3073 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 16386 Z= 0.196 Angle : 0.603 10.749 22362 Z= 0.303 Chirality : 0.044 0.174 2598 Planarity : 0.005 0.058 2841 Dihedral : 5.489 53.421 2625 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.57 % Allowed : 11.55 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.80 (0.18), residues: 2022 helix: 1.85 (0.21), residues: 612 sheet: 0.74 (0.23), residues: 483 loop : -0.45 (0.20), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1014 TYR 0.019 0.002 TYR B1067 PHE 0.019 0.002 PHE B1121 TRP 0.013 0.002 TRP D 103 HIS 0.005 0.001 HIS H 77 Details of bonding type rmsd covalent geometry : bond 0.00460 (16338) covalent geometry : angle 0.59115 (22245) SS BOND : bond 0.00357 ( 27) SS BOND : angle 1.80003 ( 54) hydrogen bonds : bond 0.05513 ( 786) hydrogen bonds : angle 5.33840 ( 2394) link_BETA1-4 : bond 0.00229 ( 3) link_BETA1-4 : angle 1.33575 ( 9) link_NAG-ASN : bond 0.00235 ( 18) link_NAG-ASN : angle 1.71307 ( 54) *********************** 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 397 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 352 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 773 GLU cc_start: 0.7778 (mm-30) cc_final: 0.7396 (tm-30) REVERT: A 780 GLU cc_start: 0.7763 (mm-30) cc_final: 0.7533 (mm-30) REVERT: A 833 PHE cc_start: 0.7124 (m-10) cc_final: 0.6190 (t80) REVERT: A 837 TYR cc_start: 0.7906 (t80) cc_final: 0.7475 (t80) REVERT: A 855 PHE cc_start: 0.7830 (m-80) cc_final: 0.7344 (m-80) REVERT: A 866 THR cc_start: 0.8537 (p) cc_final: 0.8216 (t) REVERT: A 952 VAL cc_start: 0.8403 (t) cc_final: 0.8023 (p) REVERT: A 957 GLU cc_start: 0.8147 (tp30) cc_final: 0.7716 (tp30) REVERT: A 994 ASP cc_start: 0.7861 (m-30) cc_final: 0.7468 (m-30) REVERT: A 1010 GLN cc_start: 0.8340 (OUTLIER) cc_final: 0.8085 (mm110) REVERT: A 1138 TYR cc_start: 0.7335 (t80) cc_final: 0.7002 (t80) REVERT: E 79 SER cc_start: 0.8661 (OUTLIER) cc_final: 0.8445 (p) REVERT: F 5 THR cc_start: 0.8599 (OUTLIER) cc_final: 0.8214 (p) REVERT: B 739 THR cc_start: 0.8623 (m) cc_final: 0.8389 (t) REVERT: B 773 GLU cc_start: 0.7796 (mm-30) cc_final: 0.7377 (tm-30) REVERT: B 866 THR cc_start: 0.8501 (p) cc_final: 0.8206 (t) REVERT: B 873 TYR cc_start: 0.8015 (m-10) cc_final: 0.7730 (m-10) REVERT: B 1010 GLN cc_start: 0.8222 (OUTLIER) cc_final: 0.7632 (mp10) REVERT: B 1031 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.7991 (mt-10) REVERT: B 1092 GLU cc_start: 0.7697 (mt-10) cc_final: 0.7467 (mt-10) REVERT: C 731 MET cc_start: 0.8472 (OUTLIER) cc_final: 0.8243 (ptm) REVERT: C 855 PHE cc_start: 0.7871 (m-80) cc_final: 0.7480 (m-80) REVERT: C 860 VAL cc_start: 0.8812 (m) cc_final: 0.8556 (t) REVERT: C 957 GLU cc_start: 0.8130 (tp30) cc_final: 0.7518 (tp30) REVERT: C 967 SER cc_start: 0.8583 (m) cc_final: 0.8362 (p) REVERT: C 994 ASP cc_start: 0.7949 (m-30) cc_final: 0.7682 (m-30) REVERT: C 1031 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7935 (mt-10) outliers start: 45 outliers final: 15 residues processed: 366 average time/residue: 0.5257 time to fit residues: 215.4287 Evaluate side-chains 373 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 351 time to evaluate : 0.592 ------------------------------------------------------------------------------- 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 1072 GLU Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain H residue 11 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 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 C residue 731 MET Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1031 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 131 optimal weight: 0.2980 chunk 25 optimal weight: 1.9990 chunk 10 optimal weight: 0.3980 chunk 154 optimal weight: 0.8980 chunk 120 optimal weight: 0.1980 chunk 35 optimal weight: 0.6980 chunk 147 optimal weight: 0.5980 chunk 26 optimal weight: 0.3980 chunk 51 optimal weight: 0.9980 chunk 165 optimal weight: 0.4980 chunk 174 optimal weight: 0.2980 overall best weight: 0.3180 ------------------------------------------------------------------------------- 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 954 GLN B1002 GLN C 804 GLN C 824 ASN C 872 GLN C1002 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.119305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.101976 restraints weight = 22747.283| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 2.13 r_work: 0.3092 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16386 Z= 0.148 Angle : 0.564 11.001 22362 Z= 0.284 Chirality : 0.042 0.159 2598 Planarity : 0.004 0.055 2841 Dihedral : 5.087 47.131 2625 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.40 % Allowed : 12.24 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.94 (0.18), residues: 2022 helix: 2.04 (0.21), residues: 618 sheet: 0.78 (0.23), residues: 483 loop : -0.42 (0.20), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C1019 TYR 0.018 0.001 TYR B1067 PHE 0.015 0.001 PHE C 927 TRP 0.009 0.001 TRP D 103 HIS 0.004 0.001 HIS G 49 Details of bonding type rmsd covalent geometry : bond 0.00340 (16338) covalent geometry : angle 0.55297 (22245) SS BOND : bond 0.00289 ( 27) SS BOND : angle 1.65853 ( 54) hydrogen bonds : bond 0.04960 ( 786) hydrogen bonds : angle 5.11770 ( 2394) link_BETA1-4 : bond 0.00260 ( 3) link_BETA1-4 : angle 1.34180 ( 9) link_NAG-ASN : bond 0.00158 ( 18) link_NAG-ASN : angle 1.61828 ( 54) *********************** 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 389 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 347 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 773 GLU cc_start: 0.7766 (mm-30) cc_final: 0.7387 (tm-30) REVERT: A 833 PHE cc_start: 0.7068 (m-10) cc_final: 0.6159 (t80) REVERT: A 837 TYR cc_start: 0.7852 (t80) cc_final: 0.7416 (t80) REVERT: A 866 THR cc_start: 0.8503 (p) cc_final: 0.8172 (t) REVERT: A 952 VAL cc_start: 0.8370 (t) cc_final: 0.7985 (p) REVERT: A 957 GLU cc_start: 0.8109 (tp30) cc_final: 0.7687 (tp30) REVERT: A 994 ASP cc_start: 0.7799 (m-30) cc_final: 0.7426 (m-30) REVERT: A 1010 GLN cc_start: 0.8316 (OUTLIER) cc_final: 0.8056 (mm110) REVERT: A 1138 TYR cc_start: 0.7341 (t80) cc_final: 0.7050 (t80) REVERT: F 5 THR cc_start: 0.8594 (OUTLIER) cc_final: 0.8237 (p) REVERT: G 5 THR cc_start: 0.8523 (m) cc_final: 0.8229 (p) REVERT: B 773 GLU cc_start: 0.7794 (mm-30) cc_final: 0.7111 (tm-30) REVERT: B 833 PHE cc_start: 0.7151 (m-10) cc_final: 0.6460 (t80) REVERT: B 866 THR cc_start: 0.8371 (p) cc_final: 0.8041 (t) REVERT: B 1031 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.7935 (mt-10) REVERT: C 855 PHE cc_start: 0.7812 (m-80) cc_final: 0.7472 (m-80) REVERT: C 860 VAL cc_start: 0.8779 (m) cc_final: 0.8505 (t) REVERT: C 957 GLU cc_start: 0.8140 (tp30) cc_final: 0.7507 (tp30) REVERT: C 967 SER cc_start: 0.8615 (m) cc_final: 0.8393 (p) REVERT: C 994 ASP cc_start: 0.7924 (m-30) cc_final: 0.7653 (m-30) REVERT: C 1031 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7918 (mt-10) outliers start: 42 outliers final: 23 residues processed: 357 average time/residue: 0.4973 time to fit residues: 198.7790 Evaluate side-chains 369 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 342 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 747 THR 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 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 37 ILE 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 122 optimal weight: 0.0770 chunk 102 optimal weight: 0.2980 chunk 78 optimal weight: 0.9980 chunk 100 optimal weight: 0.4980 chunk 69 optimal weight: 0.8980 chunk 111 optimal weight: 0.0020 chunk 99 optimal weight: 0.5980 chunk 2 optimal weight: 0.0870 chunk 4 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 overall best weight: 0.1924 ------------------------------------------------------------------------------- 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 B1010 GLN C 824 ASN C 872 GLN C 901 GLN C1002 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.119552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.102367 restraints weight = 22495.275| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.03 r_work: 0.3149 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16386 Z= 0.117 Angle : 0.543 11.507 22362 Z= 0.272 Chirality : 0.041 0.155 2598 Planarity : 0.004 0.050 2841 Dihedral : 4.710 38.517 2625 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.86 % Allowed : 12.41 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.08 (0.19), residues: 2022 helix: 2.21 (0.21), residues: 618 sheet: 0.84 (0.23), residues: 483 loop : -0.36 (0.20), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1014 TYR 0.019 0.001 TYR C1067 PHE 0.016 0.001 PHE B 823 TRP 0.007 0.001 TRP H 35A HIS 0.003 0.001 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00260 (16338) covalent geometry : angle 0.53252 (22245) SS BOND : bond 0.00246 ( 27) SS BOND : angle 1.68324 ( 54) hydrogen bonds : bond 0.04495 ( 786) hydrogen bonds : angle 4.93199 ( 2394) link_BETA1-4 : bond 0.00280 ( 3) link_BETA1-4 : angle 1.32923 ( 9) link_NAG-ASN : bond 0.00121 ( 18) link_NAG-ASN : angle 1.53054 ( 54) *********************** 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 396 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 346 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 773 GLU cc_start: 0.7700 (mm-30) cc_final: 0.7409 (tm-30) REVERT: A 833 PHE cc_start: 0.7052 (m-10) cc_final: 0.6244 (t80) REVERT: A 837 TYR cc_start: 0.7848 (t80) cc_final: 0.7467 (t80) REVERT: A 855 PHE cc_start: 0.7899 (m-80) cc_final: 0.7460 (m-80) REVERT: A 866 THR cc_start: 0.8589 (p) cc_final: 0.8262 (t) REVERT: A 952 VAL cc_start: 0.8468 (t) cc_final: 0.8090 (p) REVERT: A 957 GLU cc_start: 0.8088 (tp30) cc_final: 0.7726 (tp30) REVERT: A 994 ASP cc_start: 0.7792 (m-30) cc_final: 0.7451 (m-30) REVERT: A 1010 GLN cc_start: 0.8314 (OUTLIER) cc_final: 0.8101 (mm110) REVERT: A 1028 LYS cc_start: 0.8519 (mtpp) cc_final: 0.8291 (mttt) REVERT: A 1031 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7892 (mt-10) REVERT: A 1138 TYR cc_start: 0.7301 (t80) cc_final: 0.7032 (t80) REVERT: D 78 PHE cc_start: 0.8768 (p90) cc_final: 0.8489 (p90) REVERT: F 5 THR cc_start: 0.8599 (OUTLIER) cc_final: 0.8305 (p) REVERT: G 5 THR cc_start: 0.8488 (m) cc_final: 0.8248 (p) REVERT: B 773 GLU cc_start: 0.7738 (mm-30) cc_final: 0.7101 (tm-30) REVERT: B 821 LEU cc_start: 0.8041 (mp) cc_final: 0.7827 (tp) REVERT: B 833 PHE cc_start: 0.7120 (m-10) cc_final: 0.6552 (t80) REVERT: B 858 LEU cc_start: 0.8076 (mt) cc_final: 0.7857 (mm) REVERT: B 866 THR cc_start: 0.8605 (p) cc_final: 0.8288 (t) REVERT: B 905 ARG cc_start: 0.8563 (mmt180) cc_final: 0.8235 (mmt180) REVERT: B 953 ASN cc_start: 0.8331 (m-40) cc_final: 0.8128 (m-40) REVERT: B 1010 GLN cc_start: 0.8305 (OUTLIER) cc_final: 0.8018 (mm-40) REVERT: B 1031 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7911 (mt-10) REVERT: B 1098 ASN cc_start: 0.8052 (p0) cc_final: 0.7779 (p0) REVERT: C 855 PHE cc_start: 0.7871 (m-80) cc_final: 0.7529 (m-80) REVERT: C 860 VAL cc_start: 0.8819 (m) cc_final: 0.8524 (t) REVERT: C 957 GLU cc_start: 0.8087 (tp30) cc_final: 0.7551 (tp30) REVERT: C 994 ASP cc_start: 0.7826 (m-30) cc_final: 0.7584 (m-30) REVERT: C 1031 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7886 (mt-10) REVERT: C 1073 LYS cc_start: 0.8414 (OUTLIER) cc_final: 0.8055 (mtmm) outliers start: 50 outliers final: 29 residues processed: 364 average time/residue: 0.4723 time to fit residues: 193.8642 Evaluate side-chains 379 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 343 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 861 LEU 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 1038 LYS Chi-restraints excluded: chain A residue 1072 GLU 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 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 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 C residue 815 ARG Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1073 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 25 optimal weight: 0.6980 chunk 127 optimal weight: 0.9990 chunk 128 optimal weight: 0.9990 chunk 148 optimal weight: 0.9990 chunk 109 optimal weight: 0.4980 chunk 104 optimal weight: 0.6980 chunk 106 optimal weight: 0.0770 chunk 9 optimal weight: 0.9990 chunk 114 optimal weight: 0.5980 chunk 47 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- 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 B 935 GLN B 954 GLN B1010 GLN ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3500 r_free = 0.3500 target = 0.118461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.101030 restraints weight = 22409.227| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 2.07 r_work: 0.3114 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 16386 Z= 0.210 Angle : 0.593 11.318 22362 Z= 0.299 Chirality : 0.044 0.170 2598 Planarity : 0.005 0.055 2841 Dihedral : 4.693 35.948 2625 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.14 % Allowed : 13.21 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.96 (0.18), residues: 2022 helix: 2.05 (0.20), residues: 618 sheet: 0.86 (0.23), residues: 483 loop : -0.44 (0.20), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1014 TYR 0.020 0.002 TYR D 50 PHE 0.021 0.002 PHE B 823 TRP 0.013 0.002 TRP D 103 HIS 0.005 0.002 HIS H 77 Details of bonding type rmsd covalent geometry : bond 0.00498 (16338) covalent geometry : angle 0.58198 (22245) SS BOND : bond 0.00294 ( 27) SS BOND : angle 1.78990 ( 54) hydrogen bonds : bond 0.05234 ( 786) hydrogen bonds : angle 5.11161 ( 2394) link_BETA1-4 : bond 0.00288 ( 3) link_BETA1-4 : angle 1.47885 ( 9) link_NAG-ASN : bond 0.00268 ( 18) link_NAG-ASN : angle 1.63789 ( 54) *********************** 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 406 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 351 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 773 GLU cc_start: 0.7819 (mm-30) cc_final: 0.7534 (tm-30) REVERT: A 833 PHE cc_start: 0.7053 (m-10) cc_final: 0.6340 (t80) REVERT: A 837 TYR cc_start: 0.8024 (t80) cc_final: 0.7568 (t80) REVERT: A 855 PHE cc_start: 0.8060 (m-80) cc_final: 0.7571 (m-80) REVERT: A 866 THR cc_start: 0.8647 (p) cc_final: 0.8329 (t) REVERT: A 952 VAL cc_start: 0.8551 (t) cc_final: 0.8179 (p) REVERT: A 957 GLU cc_start: 0.8113 (tp30) cc_final: 0.7769 (tp30) REVERT: A 994 ASP cc_start: 0.7859 (m-30) cc_final: 0.7532 (m-30) REVERT: A 1010 GLN cc_start: 0.8280 (OUTLIER) cc_final: 0.8055 (mm110) REVERT: A 1028 LYS cc_start: 0.8610 (mtpp) cc_final: 0.8378 (mttt) REVERT: A 1031 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.7985 (mt-10) REVERT: A 1138 TYR cc_start: 0.7399 (t80) cc_final: 0.7105 (t80) REVERT: D 78 PHE cc_start: 0.8828 (p90) cc_final: 0.8551 (p90) REVERT: F 4 MET cc_start: 0.8811 (mmm) cc_final: 0.8584 (mmt) REVERT: F 5 THR cc_start: 0.8655 (m) cc_final: 0.8323 (p) REVERT: G 5 THR cc_start: 0.8555 (m) cc_final: 0.8279 (p) REVERT: B 773 GLU cc_start: 0.7887 (mm-30) cc_final: 0.7234 (tm-30) REVERT: B 821 LEU cc_start: 0.8112 (mp) cc_final: 0.7910 (tp) REVERT: B 866 THR cc_start: 0.8710 (p) cc_final: 0.8393 (t) REVERT: B 1031 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7998 (mt-10) REVERT: B 1098 ASN cc_start: 0.8068 (p0) cc_final: 0.7791 (p0) REVERT: C 773 GLU cc_start: 0.7825 (mm-30) cc_final: 0.7453 (tm-30) REVERT: C 855 PHE cc_start: 0.7977 (m-80) cc_final: 0.7706 (m-80) REVERT: C 860 VAL cc_start: 0.8843 (m) cc_final: 0.8571 (t) REVERT: C 957 GLU cc_start: 0.8104 (tp30) cc_final: 0.7605 (tp30) REVERT: C 994 ASP cc_start: 0.7907 (m-30) cc_final: 0.7669 (m-30) REVERT: C 1031 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7944 (mt-10) REVERT: C 1073 LYS cc_start: 0.8463 (OUTLIER) cc_final: 0.8133 (mtmm) outliers start: 55 outliers final: 30 residues processed: 370 average time/residue: 0.5177 time to fit residues: 215.1492 Evaluate side-chains 379 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 344 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 945 LEU 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 1038 LYS Chi-restraints excluded: chain A residue 1072 GLU 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 96 LEU Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 933 LYS 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 878 LEU Chi-restraints excluded: chain C residue 947 LYS 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 169 optimal weight: 1.9990 chunk 183 optimal weight: 0.4980 chunk 184 optimal weight: 0.3980 chunk 51 optimal weight: 0.6980 chunk 84 optimal weight: 0.9980 chunk 112 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 75 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 144 optimal weight: 0.5980 chunk 33 optimal weight: 0.4980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 A1113 GLN B 935 GLN B 954 GLN B1010 GLN ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN C 824 ASN C 872 GLN C1113 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.118302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.100794 restraints weight = 22538.265| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.08 r_work: 0.3105 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 16386 Z= 0.210 Angle : 0.601 11.279 22362 Z= 0.303 Chirality : 0.044 0.171 2598 Planarity : 0.005 0.056 2841 Dihedral : 4.642 37.233 2625 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.80 % Allowed : 13.61 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.91 (0.18), residues: 2022 helix: 2.01 (0.20), residues: 618 sheet: 0.86 (0.23), residues: 483 loop : -0.50 (0.19), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1014 TYR 0.019 0.002 TYR D 50 PHE 0.020 0.002 PHE B 823 TRP 0.013 0.002 TRP D 103 HIS 0.005 0.002 HIS H 77 Details of bonding type rmsd covalent geometry : bond 0.00499 (16338) covalent geometry : angle 0.58999 (22245) SS BOND : bond 0.00298 ( 27) SS BOND : angle 1.77861 ( 54) hydrogen bonds : bond 0.05368 ( 786) hydrogen bonds : angle 5.17427 ( 2394) link_BETA1-4 : bond 0.00283 ( 3) link_BETA1-4 : angle 1.58727 ( 9) link_NAG-ASN : bond 0.00272 ( 18) link_NAG-ASN : angle 1.68719 ( 54) *********************** 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 399 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 350 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 773 GLU cc_start: 0.7777 (mm-30) cc_final: 0.7482 (tm-30) REVERT: A 837 TYR cc_start: 0.8039 (t80) cc_final: 0.7496 (t80) REVERT: A 866 THR cc_start: 0.8653 (p) cc_final: 0.8349 (t) REVERT: A 952 VAL cc_start: 0.8550 (t) cc_final: 0.8195 (p) REVERT: A 957 GLU cc_start: 0.8143 (tp30) cc_final: 0.7897 (tp30) REVERT: A 994 ASP cc_start: 0.7882 (m-30) cc_final: 0.7548 (m-30) REVERT: A 1010 GLN cc_start: 0.8310 (OUTLIER) cc_final: 0.8083 (mm110) REVERT: A 1028 LYS cc_start: 0.8652 (mtpp) cc_final: 0.8450 (mttt) REVERT: A 1031 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.7995 (mt-10) REVERT: A 1138 TYR cc_start: 0.7440 (t80) cc_final: 0.7120 (t80) REVERT: D 78 PHE cc_start: 0.8835 (p90) cc_final: 0.8566 (p90) REVERT: F 5 THR cc_start: 0.8655 (m) cc_final: 0.8328 (p) REVERT: B 773 GLU cc_start: 0.7886 (mm-30) cc_final: 0.7220 (tm-30) REVERT: B 815 ARG cc_start: 0.8134 (OUTLIER) cc_final: 0.7495 (ttp-170) REVERT: B 866 THR cc_start: 0.8723 (p) cc_final: 0.8443 (t) REVERT: B 1031 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.7995 (mt-10) REVERT: B 1098 ASN cc_start: 0.8054 (p0) cc_final: 0.7777 (p0) REVERT: C 773 GLU cc_start: 0.7811 (mm-30) cc_final: 0.7449 (tm-30) REVERT: C 855 PHE cc_start: 0.7954 (m-80) cc_final: 0.7685 (m-80) REVERT: C 860 VAL cc_start: 0.8837 (m) cc_final: 0.8573 (t) REVERT: C 957 GLU cc_start: 0.8100 (tp30) cc_final: 0.7618 (tp30) REVERT: C 994 ASP cc_start: 0.7946 (m-30) cc_final: 0.7702 (m-30) REVERT: C 1031 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7916 (mt-10) REVERT: C 1073 LYS cc_start: 0.8468 (OUTLIER) cc_final: 0.8138 (mtmm) outliers start: 49 outliers final: 32 residues processed: 365 average time/residue: 0.4933 time to fit residues: 202.0052 Evaluate side-chains 383 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 345 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 907 ASN 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 1072 GLU 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 96 LEU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 815 ARG Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 933 LYS 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 1072 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 947 LYS 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 29 optimal weight: 0.9990 chunk 188 optimal weight: 0.0670 chunk 110 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 108 optimal weight: 0.9980 chunk 100 optimal weight: 0.3980 chunk 186 optimal weight: 0.8980 chunk 197 optimal weight: 0.1980 chunk 36 optimal weight: 0.5980 chunk 31 optimal weight: 0.2980 chunk 71 optimal weight: 0.8980 overall best weight: 0.3118 ------------------------------------------------------------------------------- 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 B 935 GLN B1010 GLN ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3512 r_free = 0.3512 target = 0.119032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.101638 restraints weight = 22343.280| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.06 r_work: 0.3125 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16386 Z= 0.149 Angle : 0.574 11.614 22362 Z= 0.287 Chirality : 0.042 0.160 2598 Planarity : 0.004 0.055 2841 Dihedral : 4.502 36.345 2625 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.63 % Allowed : 14.35 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.01 (0.18), residues: 2022 helix: 2.09 (0.20), residues: 618 sheet: 1.00 (0.24), residues: 453 loop : -0.44 (0.19), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1014 TYR 0.020 0.001 TYR D 50 PHE 0.016 0.002 PHE B 823 TRP 0.009 0.001 TRP D 103 HIS 0.004 0.001 HIS H 77 Details of bonding type rmsd covalent geometry : bond 0.00342 (16338) covalent geometry : angle 0.56308 (22245) SS BOND : bond 0.00247 ( 27) SS BOND : angle 1.67146 ( 54) hydrogen bonds : bond 0.04934 ( 786) hydrogen bonds : angle 5.05064 ( 2394) link_BETA1-4 : bond 0.00249 ( 3) link_BETA1-4 : angle 1.49090 ( 9) link_NAG-ASN : bond 0.00171 ( 18) link_NAG-ASN : angle 1.60401 ( 54) *********************** 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 388 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 342 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 773 GLU cc_start: 0.7733 (mm-30) cc_final: 0.7423 (tm-30) REVERT: A 833 PHE cc_start: 0.7187 (m-10) cc_final: 0.6274 (t80) REVERT: A 837 TYR cc_start: 0.7922 (t80) cc_final: 0.7400 (t80) REVERT: A 855 PHE cc_start: 0.8043 (m-80) cc_final: 0.7510 (m-80) REVERT: A 866 THR cc_start: 0.8643 (p) cc_final: 0.8310 (t) REVERT: A 952 VAL cc_start: 0.8492 (t) cc_final: 0.8131 (p) REVERT: A 957 GLU cc_start: 0.8085 (tp30) cc_final: 0.7847 (tp30) REVERT: A 994 ASP cc_start: 0.7850 (m-30) cc_final: 0.7512 (m-30) REVERT: A 1010 GLN cc_start: 0.8284 (OUTLIER) cc_final: 0.8067 (mm110) REVERT: A 1028 LYS cc_start: 0.8601 (mtpp) cc_final: 0.8392 (mttt) REVERT: A 1031 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.7963 (mt-10) REVERT: A 1138 TYR cc_start: 0.7386 (t80) cc_final: 0.7067 (t80) REVERT: D 78 PHE cc_start: 0.8801 (p90) cc_final: 0.8530 (p90) REVERT: D 111 VAL cc_start: 0.8438 (t) cc_final: 0.8190 (m) REVERT: F 4 MET cc_start: 0.8819 (mmm) cc_final: 0.8603 (mmt) REVERT: F 5 THR cc_start: 0.8641 (m) cc_final: 0.8314 (p) REVERT: B 773 GLU cc_start: 0.7827 (mm-30) cc_final: 0.7144 (tm-30) REVERT: B 815 ARG cc_start: 0.8099 (OUTLIER) cc_final: 0.7488 (ttp-170) REVERT: B 833 PHE cc_start: 0.7120 (m-10) cc_final: 0.6489 (t80) REVERT: B 866 THR cc_start: 0.8737 (p) cc_final: 0.8483 (t) REVERT: B 1031 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7963 (mt-10) REVERT: B 1098 ASN cc_start: 0.8046 (p0) cc_final: 0.7767 (p0) REVERT: C 773 GLU cc_start: 0.7769 (mm-30) cc_final: 0.7379 (tm-30) REVERT: C 855 PHE cc_start: 0.7909 (m-80) cc_final: 0.7634 (m-80) REVERT: C 860 VAL cc_start: 0.8817 (m) cc_final: 0.8544 (t) REVERT: C 945 LEU cc_start: 0.8001 (mm) cc_final: 0.7786 (mt) REVERT: C 957 GLU cc_start: 0.8094 (tp30) cc_final: 0.7633 (tp30) REVERT: C 994 ASP cc_start: 0.7904 (m-30) cc_final: 0.7657 (m-30) REVERT: C 1073 LYS cc_start: 0.8455 (OUTLIER) cc_final: 0.8121 (mtmm) outliers start: 46 outliers final: 31 residues processed: 356 average time/residue: 0.4933 time to fit residues: 197.9146 Evaluate side-chains 378 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 342 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 861 LEU 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 1038 LYS Chi-restraints excluded: chain A residue 1072 GLU 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 33 LEU Chi-restraints excluded: chain H residue 11 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 96 LEU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 815 ARG Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 878 LEU 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 878 LEU Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 959 LEU 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 17 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 125 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 19 optimal weight: 0.3980 chunk 113 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 chunk 15 optimal weight: 0.3980 chunk 106 optimal weight: 0.9990 chunk 58 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 824 ASN B 935 GLN B1010 GLN B1135 ASN C 762 GLN C 804 GLN C 824 ASN C 872 GLN C 954 GLN C 969 ASN C1135 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.117083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.099569 restraints weight = 22491.075| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.07 r_work: 0.3080 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 16386 Z= 0.292 Angle : 0.662 11.007 22362 Z= 0.333 Chirality : 0.047 0.182 2598 Planarity : 0.005 0.064 2841 Dihedral : 4.809 39.023 2625 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.12 % Allowed : 14.87 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.74 (0.18), residues: 2022 helix: 1.78 (0.20), residues: 615 sheet: 0.92 (0.24), residues: 453 loop : -0.56 (0.19), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1014 TYR 0.027 0.002 TYR D 50 PHE 0.026 0.002 PHE B1121 TRP 0.017 0.002 TRP D 103 HIS 0.007 0.002 HIS H 77 Details of bonding type rmsd covalent geometry : bond 0.00696 (16338) covalent geometry : angle 0.64954 (22245) SS BOND : bond 0.00327 ( 27) SS BOND : angle 1.91294 ( 54) hydrogen bonds : bond 0.05970 ( 786) hydrogen bonds : angle 5.37079 ( 2394) link_BETA1-4 : bond 0.00233 ( 3) link_BETA1-4 : angle 1.68501 ( 9) link_NAG-ASN : bond 0.00427 ( 18) link_NAG-ASN : angle 1.87772 ( 54) ********************** 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 392 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 355 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 773 GLU cc_start: 0.7780 (mm-30) cc_final: 0.7443 (tm-30) REVERT: A 833 PHE cc_start: 0.7298 (m-10) cc_final: 0.6318 (t80) REVERT: A 837 TYR cc_start: 0.8080 (t80) cc_final: 0.7753 (t80) REVERT: A 855 PHE cc_start: 0.8108 (m-80) cc_final: 0.7594 (m-80) REVERT: A 858 LEU cc_start: 0.8330 (mt) cc_final: 0.8106 (mm) REVERT: A 866 THR cc_start: 0.8673 (p) cc_final: 0.8361 (t) REVERT: A 952 VAL cc_start: 0.8554 (t) cc_final: 0.8196 (p) REVERT: A 957 GLU cc_start: 0.8082 (tp30) cc_final: 0.7845 (tp30) REVERT: A 994 ASP cc_start: 0.7916 (m-30) cc_final: 0.7533 (m-30) REVERT: A 1028 LYS cc_start: 0.8675 (mtpp) cc_final: 0.8474 (mttt) REVERT: A 1031 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.8018 (mt-10) REVERT: A 1122 VAL cc_start: 0.8406 (t) cc_final: 0.8178 (p) REVERT: A 1138 TYR cc_start: 0.7505 (t80) cc_final: 0.7140 (t80) REVERT: D 11 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8326 (mt) REVERT: F 4 MET cc_start: 0.8818 (mmm) cc_final: 0.8586 (mmt) REVERT: F 5 THR cc_start: 0.8666 (m) cc_final: 0.8273 (p) REVERT: B 773 GLU cc_start: 0.7893 (mm-30) cc_final: 0.7535 (tm-30) REVERT: B 866 THR cc_start: 0.8748 (p) cc_final: 0.8472 (t) REVERT: B 1031 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.8036 (mt-10) REVERT: B 1098 ASN cc_start: 0.8079 (p0) cc_final: 0.7802 (p0) REVERT: C 773 GLU cc_start: 0.7818 (mm-30) cc_final: 0.7469 (tm-30) REVERT: C 804 GLN cc_start: 0.8435 (mm110) cc_final: 0.8023 (mp-120) REVERT: C 855 PHE cc_start: 0.8022 (m-80) cc_final: 0.7757 (m-80) REVERT: C 860 VAL cc_start: 0.8845 (m) cc_final: 0.8601 (t) REVERT: C 945 LEU cc_start: 0.8077 (mm) cc_final: 0.7843 (mt) REVERT: C 957 GLU cc_start: 0.8100 (tp30) cc_final: 0.7654 (tp30) REVERT: C 994 ASP cc_start: 0.7956 (m-30) cc_final: 0.7704 (m-30) REVERT: C 995 ARG cc_start: 0.8394 (mtp85) cc_final: 0.8166 (mtp85) REVERT: C 1073 LYS cc_start: 0.8473 (OUTLIER) cc_final: 0.8141 (mtmm) outliers start: 37 outliers final: 26 residues processed: 365 average time/residue: 0.5167 time to fit residues: 211.7586 Evaluate side-chains 381 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 351 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1072 GLU 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 96 LEU Chi-restraints excluded: chain B residue 723 THR 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 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 878 LEU Chi-restraints excluded: chain C residue 959 LEU 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 76 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 chunk 154 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 78 optimal weight: 0.9980 chunk 172 optimal weight: 0.9990 chunk 93 optimal weight: 0.3980 chunk 112 optimal weight: 0.4980 chunk 134 optimal weight: 0.2980 chunk 56 optimal weight: 1.9990 chunk 173 optimal weight: 0.0980 overall best weight: 0.3980 ------------------------------------------------------------------------------- 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 B 953 ASN B1010 GLN C 824 ASN C 872 GLN C 901 GLN C 954 GLN C 969 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.118629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.101174 restraints weight = 22353.351| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.07 r_work: 0.3123 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16386 Z= 0.175 Angle : 0.595 11.532 22362 Z= 0.298 Chirality : 0.043 0.162 2598 Planarity : 0.005 0.060 2841 Dihedral : 4.578 37.653 2625 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.06 % Allowed : 15.09 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.85 (0.18), residues: 2022 helix: 1.93 (0.20), residues: 618 sheet: 0.95 (0.24), residues: 453 loop : -0.55 (0.19), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1014 TYR 0.022 0.002 TYR D 50 PHE 0.016 0.002 PHE B1121 TRP 0.011 0.001 TRP D 103 HIS 0.005 0.001 HIS H 77 Details of bonding type rmsd covalent geometry : bond 0.00409 (16338) covalent geometry : angle 0.58194 (22245) SS BOND : bond 0.00283 ( 27) SS BOND : angle 1.94374 ( 54) hydrogen bonds : bond 0.05152 ( 786) hydrogen bonds : angle 5.13877 ( 2394) link_BETA1-4 : bond 0.00181 ( 3) link_BETA1-4 : angle 1.53019 ( 9) link_NAG-ASN : bond 0.00215 ( 18) link_NAG-ASN : angle 1.69174 ( 54) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6022.64 seconds wall clock time: 103 minutes 26.48 seconds (6206.48 seconds total)