Starting phenix.real_space_refine on Wed Sep 17 16:29:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vqb_43437/09_2025/8vqb_43437.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vqb_43437/09_2025/8vqb_43437.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vqb_43437/09_2025/8vqb_43437.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vqb_43437/09_2025/8vqb_43437.map" model { file = "/net/cci-nas-00/data/ceres_data/8vqb_43437/09_2025/8vqb_43437.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vqb_43437/09_2025/8vqb_43437.cif" } 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= 0.001 sd= 0.092 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 66 5.16 5 C 6204 2.51 5 N 1626 2.21 5 O 1782 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 63 residue(s): 0.01s 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: 9678 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 3086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3086 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 97} Link IDs: {'PTRANS': 22, 'TRANS': 409} Chain breaks: 2 Unresolved non-hydrogen bonds: 250 Unresolved non-hydrogen angles: 310 Unresolved non-hydrogen dihedrals: 190 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'ASP:plan': 13, 'GLU:plan': 8, 'GLN:plan1': 6, 'ASN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 106 Chain: "B" Number of atoms: 3086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3086 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 97} Link IDs: {'PTRANS': 22, 'TRANS': 409} Chain breaks: 2 Unresolved non-hydrogen bonds: 250 Unresolved non-hydrogen angles: 310 Unresolved non-hydrogen dihedrals: 190 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'ASP:plan': 13, 'GLU:plan': 8, 'GLN:plan1': 6, 'ASN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 106 Chain: "C" Number of atoms: 3086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3086 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 97} Link IDs: {'PTRANS': 22, 'TRANS': 409} Chain breaks: 2 Unresolved non-hydrogen bonds: 250 Unresolved non-hydrogen angles: 310 Unresolved non-hydrogen dihedrals: 190 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'ASP:plan': 13, 'GLU:plan': 8, 'GLN:plan1': 6, 'ASN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 106 Chain: "D" 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: "E" 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: "F" 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: "G" 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: "H" 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: "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: "L" 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: "M" 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: "N" 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: "O" 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: 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: "B" 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: "C" 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 Time building chain proxies: 2.30, per 1000 atoms: 0.24 Number of scatterers: 9678 At special positions: 0 Unit cell: (87.672, 88.515, 134.037, 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 66 16.00 O 1782 8.00 N 1626 7.00 C 6204 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 707 " - pdb=" SG CYS B 883 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.17 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.08 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.03 Simple disulfide: pdb=" SG CYS A 883 " - pdb=" SG CYS C 707 " distance=2.04 Simple disulfide: pdb=" SG CYS A 970 " - pdb=" SG CYS A 999 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 707 " - pdb=" SG CYS C 883 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.17 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.08 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B 970 " - pdb=" SG CYS B 999 " distance=2.02 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.17 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.08 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C 970 " - pdb=" SG CYS C 999 " distance=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 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 D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A1301 " - " ASN A 709 " " NAG A1302 " - " ASN A1074 " " NAG B1301 " - " ASN B 709 " " NAG B1302 " - " ASN B1074 " " NAG C1301 " - " ASN C 709 " " NAG C1302 " - " ASN C1074 " " NAG D 1 " - " ASN A 717 " " NAG E 1 " - " ASN A 801 " " NAG F 1 " - " ASN A1098 " " NAG G 1 " - " ASN A1134 " " NAG H 1 " - " ASN B 717 " " NAG I 1 " - " ASN B 801 " " NAG J 1 " - " ASN B1098 " " NAG K 1 " - " ASN B1134 " " NAG L 1 " - " ASN C 717 " " NAG M 1 " - " ASN C 801 " " NAG N 1 " - " ASN C1098 " " NAG O 1 " - " ASN C1134 " Time building additional restraints: 0.84 Conformation dependent library (CDL) restraints added in 342.2 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2442 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 12 sheets defined 51.9% alpha, 14.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.540A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.853A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 815 Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 834 through 841 Processing helix chain 'A' and resid 849 through 853 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 907 Processing helix chain 'A' and resid 908 through 910 No H-bonds generated for 'chain 'A' and resid 908 through 910' Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.556A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.778A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 966 removed outlier: 4.071A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.112A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.539A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.853A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 811 through 815 Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 834 through 841 Processing helix chain 'B' and resid 849 through 853 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 907 Processing helix chain 'B' and resid 908 through 910 No H-bonds generated for 'chain 'B' and resid 908 through 910' Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.557A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.778A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 966 removed outlier: 4.072A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.112A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.539A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.853A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 811 through 815 Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 834 through 841 Processing helix chain 'C' and resid 849 through 853 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 907 Processing helix chain 'C' and resid 908 through 910 No H-bonds generated for 'chain 'C' and resid 908 through 910' Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.557A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.778A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 966 removed outlier: 4.072A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.112A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1146 Processing sheet with id=AA1, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.574A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.069A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.427A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.588A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.573A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.069A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.428A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.588A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.573A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.069A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.427A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.588A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 555 hydrogen bonds defined for protein. 1602 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: 1.65 Time building geometry restraints manager: 1.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1671 1.32 - 1.44: 2472 1.44 - 1.57: 5625 1.57 - 1.70: 18 1.70 - 1.82: 90 Bond restraints: 9876 Sorted by residual: bond pdb=" CG ASP B 737 " pdb=" OD1 ASP B 737 " ideal model delta sigma weight residual 1.249 1.190 0.059 1.90e-02 2.77e+03 9.56e+00 bond pdb=" CG ASP A 737 " pdb=" OD1 ASP A 737 " ideal model delta sigma weight residual 1.249 1.191 0.058 1.90e-02 2.77e+03 9.45e+00 bond pdb=" CG ASP C 737 " pdb=" OD1 ASP C 737 " ideal model delta sigma weight residual 1.249 1.191 0.058 1.90e-02 2.77e+03 9.29e+00 bond pdb=" C5 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.413 1.471 -0.058 2.00e-02 2.50e+03 8.54e+00 bond pdb=" C5 NAG O 2 " pdb=" O5 NAG O 2 " ideal model delta sigma weight residual 1.413 1.471 -0.058 2.00e-02 2.50e+03 8.47e+00 ... (remaining 9871 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.69: 13275 3.69 - 7.38: 228 7.38 - 11.07: 6 11.07 - 14.76: 0 14.76 - 18.45: 3 Bond angle restraints: 13512 Sorted by residual: angle pdb=" C LEU B 861 " pdb=" N PRO B 862 " pdb=" CA PRO B 862 " ideal model delta sigma weight residual 119.66 126.16 -6.50 7.20e-01 1.93e+00 8.15e+01 angle pdb=" C LEU A 861 " pdb=" N PRO A 862 " pdb=" CA PRO A 862 " ideal model delta sigma weight residual 119.66 126.15 -6.49 7.20e-01 1.93e+00 8.12e+01 angle pdb=" C LEU C 861 " pdb=" N PRO C 862 " pdb=" CA PRO C 862 " ideal model delta sigma weight residual 119.66 126.15 -6.49 7.20e-01 1.93e+00 8.12e+01 angle pdb=" C PRO C 792 " pdb=" N PRO C 793 " pdb=" CA PRO C 793 " ideal model delta sigma weight residual 119.87 127.87 -8.00 1.04e+00 9.25e-01 5.91e+01 angle pdb=" C PRO B 792 " pdb=" N PRO B 793 " pdb=" CA PRO B 793 " ideal model delta sigma weight residual 119.87 127.85 -7.98 1.04e+00 9.25e-01 5.88e+01 ... (remaining 13507 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 5999 17.56 - 35.13: 198 35.13 - 52.69: 49 52.69 - 70.25: 15 70.25 - 87.82: 12 Dihedral angle restraints: 6273 sinusoidal: 2505 harmonic: 3768 Sorted by residual: dihedral pdb=" CB CYS A 840 " pdb=" SG CYS A 840 " pdb=" SG CYS A 851 " pdb=" CB CYS A 851 " ideal model delta sinusoidal sigma weight residual 93.00 133.19 -40.19 1 1.00e+01 1.00e-02 2.27e+01 dihedral pdb=" CB CYS C 840 " pdb=" SG CYS C 840 " pdb=" SG CYS C 851 " pdb=" CB CYS C 851 " ideal model delta sinusoidal sigma weight residual 93.00 133.19 -40.19 1 1.00e+01 1.00e-02 2.27e+01 dihedral pdb=" CB CYS B 840 " pdb=" SG CYS B 840 " pdb=" SG CYS B 851 " pdb=" CB CYS B 851 " ideal model delta sinusoidal sigma weight residual 93.00 133.18 -40.18 1 1.00e+01 1.00e-02 2.27e+01 ... (remaining 6270 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 1450 0.120 - 0.240: 191 0.240 - 0.360: 36 0.360 - 0.480: 0 0.480 - 0.601: 3 Chirality restraints: 1680 Sorted by residual: chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.51 0.11 2.00e-02 2.50e+03 3.16e+01 chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.51 0.11 2.00e-02 2.50e+03 2.87e+01 chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.51 0.11 2.00e-02 2.50e+03 2.83e+01 ... (remaining 1677 not shown) Planarity restraints: 1755 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 709 " -0.063 2.00e-02 2.50e+03 6.39e-02 5.10e+01 pdb=" CG ASN C 709 " 0.034 2.00e-02 2.50e+03 pdb=" OD1 ASN C 709 " 0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN C 709 " 0.097 2.00e-02 2.50e+03 pdb=" C1 NAG C1301 " -0.077 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 709 " 0.063 2.00e-02 2.50e+03 6.38e-02 5.09e+01 pdb=" CG ASN A 709 " -0.035 2.00e-02 2.50e+03 pdb=" OD1 ASN A 709 " -0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN A 709 " -0.096 2.00e-02 2.50e+03 pdb=" C1 NAG A1301 " 0.076 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 709 " -0.063 2.00e-02 2.50e+03 6.37e-02 5.08e+01 pdb=" CG ASN B 709 " 0.034 2.00e-02 2.50e+03 pdb=" OD1 ASN B 709 " 0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN B 709 " 0.097 2.00e-02 2.50e+03 pdb=" C1 NAG B1301 " -0.076 2.00e-02 2.50e+03 ... (remaining 1752 not shown) Histogram of nonbonded interaction distances: 2.56 - 3.02: 5658 3.02 - 3.49: 9468 3.49 - 3.96: 15085 3.96 - 4.43: 18290 4.43 - 4.90: 27819 Nonbonded interactions: 76320 Sorted by model distance: nonbonded pdb=" O SER A 975 " pdb=" OG SER A 975 " model vdw 2.555 3.040 nonbonded pdb=" O SER B 975 " pdb=" OG SER B 975 " model vdw 2.555 3.040 nonbonded pdb=" O SER C 975 " pdb=" OG SER C 975 " model vdw 2.556 3.040 nonbonded pdb=" OE1 GLN A 957 " pdb=" NH2 ARG B 765 " model vdw 2.564 3.120 nonbonded pdb=" NH2 ARG A 765 " pdb=" OE1 GLN C 957 " model vdw 2.565 3.120 ... (remaining 76315 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.900 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: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.020 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 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 : 0.012 0.136 9927 Z= 0.651 Angle : 1.306 18.449 13644 Z= 0.863 Chirality : 0.091 0.601 1680 Planarity : 0.005 0.032 1737 Dihedral : 10.783 87.817 3768 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 0.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.71 % Allowed : 1.07 % Favored : 98.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.40 (0.21), residues: 1278 helix: 0.74 (0.20), residues: 582 sheet: 1.52 (0.34), residues: 153 loop : -0.55 (0.23), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 765 TYR 0.042 0.005 TYR B 904 PHE 0.009 0.002 PHE C 888 TRP 0.017 0.005 TRP C 886 HIS 0.003 0.001 HIS B1083 Details of bonding type rmsd covalent geometry : bond 0.01105 ( 9876) covalent geometry : angle 1.28574 (13512) SS BOND : bond 0.05594 ( 21) SS BOND : angle 3.18132 ( 42) hydrogen bonds : bond 0.18658 ( 555) hydrogen bonds : angle 7.40341 ( 1602) link_BETA1-4 : bond 0.06038 ( 12) link_BETA1-4 : angle 2.56810 ( 36) link_NAG-ASN : bond 0.05975 ( 18) link_NAG-ASN : angle 2.21489 ( 54) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 169 time to evaluate : 0.246 Fit side-chains REVERT: A 751 ASN cc_start: 0.7572 (m-40) cc_final: 0.7212 (m110) REVERT: A 836 GLN cc_start: 0.6720 (mt0) cc_final: 0.6471 (mt0) REVERT: A 860 VAL cc_start: 0.6548 (t) cc_final: 0.6338 (p) REVERT: B 836 GLN cc_start: 0.6891 (mt0) cc_final: 0.6625 (mt0) REVERT: B 860 VAL cc_start: 0.6643 (t) cc_final: 0.6327 (p) REVERT: C 751 ASN cc_start: 0.7395 (m-40) cc_final: 0.7129 (m-40) REVERT: C 836 GLN cc_start: 0.6618 (mt0) cc_final: 0.6416 (mt0) REVERT: C 860 VAL cc_start: 0.6645 (t) cc_final: 0.6349 (p) outliers start: 6 outliers final: 5 residues processed: 175 average time/residue: 0.6540 time to fit residues: 121.3020 Evaluate side-chains 118 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 113 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 1098 ASN Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 1098 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 755 GLN A 872 GLN A 901 GLN A1088 HIS ** A1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1113 GLN B 755 GLN B1005 GLN C 755 GLN C 994 GLN ** C1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.173612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.139682 restraints weight = 9164.450| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 1.88 r_work: 0.3436 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3296 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9927 Z= 0.171 Angle : 0.702 8.588 13644 Z= 0.349 Chirality : 0.047 0.231 1680 Planarity : 0.006 0.095 1737 Dihedral : 5.650 49.983 1996 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 3.45 % Allowed : 7.62 % Favored : 88.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.45 (0.23), residues: 1278 helix: 2.12 (0.22), residues: 594 sheet: 0.90 (0.32), residues: 183 loop : -0.43 (0.26), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B1107 TYR 0.018 0.002 TYR B1067 PHE 0.014 0.002 PHE C1121 TRP 0.009 0.002 TRP C1102 HIS 0.005 0.002 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 9876) covalent geometry : angle 0.63923 (13512) SS BOND : bond 0.00556 ( 21) SS BOND : angle 2.32415 ( 42) hydrogen bonds : bond 0.05799 ( 555) hydrogen bonds : angle 5.29187 ( 1602) link_BETA1-4 : bond 0.00536 ( 12) link_BETA1-4 : angle 2.13018 ( 36) link_NAG-ASN : bond 0.00917 ( 18) link_NAG-ASN : angle 3.89125 ( 54) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 122 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 823 PHE cc_start: 0.6695 (m-80) cc_final: 0.6485 (m-80) REVERT: A 836 GLN cc_start: 0.6387 (mt0) cc_final: 0.6011 (mt0) REVERT: A 860 VAL cc_start: 0.6994 (t) cc_final: 0.6683 (p) REVERT: A 869 MET cc_start: 0.7622 (OUTLIER) cc_final: 0.7245 (mtp) REVERT: B 725 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7784 (tt0) REVERT: B 804 GLN cc_start: 0.8001 (mm-40) cc_final: 0.6647 (mp10) REVERT: B 823 PHE cc_start: 0.6580 (m-80) cc_final: 0.6324 (m-80) REVERT: B 836 GLN cc_start: 0.6386 (mt0) cc_final: 0.5926 (mt0) REVERT: B 860 VAL cc_start: 0.6986 (t) cc_final: 0.6633 (p) REVERT: B 1001 LEU cc_start: 0.7118 (OUTLIER) cc_final: 0.6772 (tt) REVERT: C 836 GLN cc_start: 0.6477 (mt0) cc_final: 0.6097 (mt0) REVERT: C 860 VAL cc_start: 0.7002 (t) cc_final: 0.6685 (p) REVERT: C 869 MET cc_start: 0.7548 (OUTLIER) cc_final: 0.7178 (mtp) REVERT: C 907 GLU cc_start: 0.7593 (pt0) cc_final: 0.7238 (mm-30) REVERT: C 1071 GLN cc_start: 0.8959 (OUTLIER) cc_final: 0.8535 (mp10) outliers start: 29 outliers final: 9 residues processed: 141 average time/residue: 0.6088 time to fit residues: 91.6350 Evaluate side-chains 123 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 109 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain B residue 725 GLU Chi-restraints excluded: chain B residue 840 CYS Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1098 ASN Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain C residue 840 CYS Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1071 GLN Chi-restraints excluded: chain C residue 1098 ASN Chi-restraints excluded: chain C residue 1117 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 0 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 chunk 117 optimal weight: 0.5980 chunk 123 optimal weight: 0.9980 chunk 74 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 GLN A 774 GLN A 901 GLN B 774 GLN B 779 GLN B1005 GLN C 762 GLN C 774 GLN C 992 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.170406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.134789 restraints weight = 9231.703| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 1.99 r_work: 0.3390 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 9927 Z= 0.156 Angle : 0.660 10.864 13644 Z= 0.319 Chirality : 0.046 0.238 1680 Planarity : 0.005 0.040 1737 Dihedral : 5.625 49.462 1992 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 4.76 % Allowed : 7.62 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.44 (0.23), residues: 1278 helix: 2.37 (0.21), residues: 576 sheet: 0.44 (0.30), residues: 213 loop : -0.54 (0.26), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 765 TYR 0.017 0.002 TYR B1067 PHE 0.017 0.002 PHE C 927 TRP 0.009 0.002 TRP B 886 HIS 0.004 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 9876) covalent geometry : angle 0.58217 (13512) SS BOND : bond 0.00331 ( 21) SS BOND : angle 1.49948 ( 42) hydrogen bonds : bond 0.05275 ( 555) hydrogen bonds : angle 5.00153 ( 1602) link_BETA1-4 : bond 0.00518 ( 12) link_BETA1-4 : angle 1.78864 ( 36) link_NAG-ASN : bond 0.00869 ( 18) link_NAG-ASN : angle 4.60965 ( 54) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 123 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 804 GLN cc_start: 0.8179 (mm-40) cc_final: 0.6548 (mp10) REVERT: A 820 ASP cc_start: 0.7399 (OUTLIER) cc_final: 0.7170 (t0) REVERT: A 823 PHE cc_start: 0.6726 (m-80) cc_final: 0.6506 (m-80) REVERT: A 836 GLN cc_start: 0.6445 (mt0) cc_final: 0.6158 (mt0) REVERT: A 860 VAL cc_start: 0.6929 (t) cc_final: 0.6617 (p) REVERT: A 1001 LEU cc_start: 0.7087 (OUTLIER) cc_final: 0.6133 (mp) REVERT: B 725 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.7923 (tt0) REVERT: B 804 GLN cc_start: 0.8101 (mm-40) cc_final: 0.6664 (mp10) REVERT: B 823 PHE cc_start: 0.6531 (m-80) cc_final: 0.6277 (m-80) REVERT: B 836 GLN cc_start: 0.6486 (mt0) cc_final: 0.5485 (mp10) REVERT: B 860 VAL cc_start: 0.6956 (t) cc_final: 0.6564 (p) REVERT: B 869 MET cc_start: 0.7598 (OUTLIER) cc_final: 0.7294 (mtp) REVERT: B 1001 LEU cc_start: 0.7023 (OUTLIER) cc_final: 0.6209 (mp) REVERT: B 1014 ARG cc_start: 0.7030 (mtt180) cc_final: 0.6782 (ttm-80) REVERT: C 804 GLN cc_start: 0.8122 (mm-40) cc_final: 0.6704 (mp10) REVERT: C 836 GLN cc_start: 0.6631 (mt0) cc_final: 0.6218 (mt0) REVERT: C 860 VAL cc_start: 0.6961 (t) cc_final: 0.6641 (p) REVERT: C 907 GLU cc_start: 0.7652 (pt0) cc_final: 0.7249 (mm-30) REVERT: C 954 GLN cc_start: 0.6602 (OUTLIER) cc_final: 0.6145 (mt0) REVERT: C 995 ARG cc_start: 0.6574 (ttm170) cc_final: 0.4919 (ttt180) REVERT: C 1001 LEU cc_start: 0.7233 (OUTLIER) cc_final: 0.6507 (mp) REVERT: C 1071 GLN cc_start: 0.8916 (OUTLIER) cc_final: 0.8376 (mp10) outliers start: 40 outliers final: 9 residues processed: 145 average time/residue: 0.6755 time to fit residues: 103.7535 Evaluate side-chains 136 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 119 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 840 CYS Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain B residue 725 GLU Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1098 ASN Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 954 GLN Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1071 GLN Chi-restraints excluded: chain C residue 1098 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 9 optimal weight: 0.9980 chunk 14 optimal weight: 0.0980 chunk 27 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 116 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 113 optimal weight: 0.7980 chunk 65 optimal weight: 0.6980 chunk 71 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 774 GLN A 992 GLN A1088 HIS B 762 GLN B 774 GLN B1005 GLN B1071 GLN B1119 ASN C 774 GLN C1048 HIS C1119 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.187921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.175141 restraints weight = 9289.260| |-----------------------------------------------------------------------------| r_work (start): 0.3978 rms_B_bonded: 0.69 r_work: 0.3726 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9927 Z= 0.134 Angle : 0.622 12.136 13644 Z= 0.297 Chirality : 0.045 0.282 1680 Planarity : 0.005 0.039 1737 Dihedral : 5.385 49.173 1992 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 4.40 % Allowed : 10.83 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.18 (0.22), residues: 1278 helix: 2.18 (0.21), residues: 594 sheet: 0.28 (0.30), residues: 213 loop : -0.79 (0.25), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 765 TYR 0.016 0.002 TYR B1067 PHE 0.017 0.002 PHE C 927 TRP 0.007 0.002 TRP A 886 HIS 0.003 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 9876) covalent geometry : angle 0.54264 (13512) SS BOND : bond 0.00324 ( 21) SS BOND : angle 1.19050 ( 42) hydrogen bonds : bond 0.04750 ( 555) hydrogen bonds : angle 4.85227 ( 1602) link_BETA1-4 : bond 0.00449 ( 12) link_BETA1-4 : angle 1.82770 ( 36) link_NAG-ASN : bond 0.00807 ( 18) link_NAG-ASN : angle 4.54337 ( 54) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 126 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 804 GLN cc_start: 0.8176 (mm-40) cc_final: 0.7370 (mp10) REVERT: A 869 MET cc_start: 0.7880 (OUTLIER) cc_final: 0.7503 (mtp) REVERT: A 995 ARG cc_start: 0.6971 (ttm170) cc_final: 0.5765 (mtp85) REVERT: B 804 GLN cc_start: 0.8147 (mm-40) cc_final: 0.7446 (mp10) REVERT: B 869 MET cc_start: 0.7865 (OUTLIER) cc_final: 0.7485 (mtp) REVERT: B 995 ARG cc_start: 0.7118 (ttm170) cc_final: 0.5931 (mtp85) REVERT: B 1001 LEU cc_start: 0.8071 (OUTLIER) cc_final: 0.7397 (mp) REVERT: C 804 GLN cc_start: 0.8081 (mm-40) cc_final: 0.7271 (mp10) REVERT: C 954 GLN cc_start: 0.7322 (OUTLIER) cc_final: 0.6852 (mt0) REVERT: C 1071 GLN cc_start: 0.8936 (OUTLIER) cc_final: 0.8600 (mp10) outliers start: 37 outliers final: 13 residues processed: 143 average time/residue: 0.6698 time to fit residues: 101.6247 Evaluate side-chains 133 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 115 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 840 CYS Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1071 GLN Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain B residue 840 CYS Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1011 MET Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1098 ASN Chi-restraints excluded: chain C residue 840 CYS Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 954 GLN Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1071 GLN Chi-restraints excluded: chain C residue 1098 ASN Chi-restraints excluded: chain C residue 1117 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 68 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 34 optimal weight: 0.5980 chunk 107 optimal weight: 3.9990 chunk 13 optimal weight: 7.9990 chunk 49 optimal weight: 1.9990 chunk 125 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 774 GLN A1048 HIS A1071 GLN B 774 GLN B1005 GLN B1048 HIS B1071 GLN C 755 GLN C 774 GLN C 994 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.185730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.161092 restraints weight = 9219.631| |-----------------------------------------------------------------------------| r_work (start): 0.3862 rms_B_bonded: 1.45 r_work: 0.3547 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9927 Z= 0.155 Angle : 0.648 12.017 13644 Z= 0.311 Chirality : 0.046 0.279 1680 Planarity : 0.005 0.043 1737 Dihedral : 5.528 48.185 1992 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 4.76 % Allowed : 11.43 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.22), residues: 1278 helix: 2.11 (0.21), residues: 597 sheet: -0.05 (0.32), residues: 183 loop : -0.95 (0.24), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B1014 TYR 0.016 0.002 TYR B1067 PHE 0.018 0.002 PHE C 927 TRP 0.008 0.002 TRP C 886 HIS 0.004 0.002 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 9876) covalent geometry : angle 0.57284 (13512) SS BOND : bond 0.00367 ( 21) SS BOND : angle 1.22993 ( 42) hydrogen bonds : bond 0.04918 ( 555) hydrogen bonds : angle 4.90838 ( 1602) link_BETA1-4 : bond 0.00463 ( 12) link_BETA1-4 : angle 1.74043 ( 36) link_NAG-ASN : bond 0.00834 ( 18) link_NAG-ASN : angle 4.57459 ( 54) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 116 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 804 GLN cc_start: 0.8372 (mm-40) cc_final: 0.7229 (mp10) REVERT: A 820 ASP cc_start: 0.7441 (OUTLIER) cc_final: 0.7231 (t0) REVERT: A 869 MET cc_start: 0.7943 (OUTLIER) cc_final: 0.7545 (mtp) REVERT: A 995 ARG cc_start: 0.6765 (ttm170) cc_final: 0.5211 (mtp85) REVERT: A 1001 LEU cc_start: 0.7865 (OUTLIER) cc_final: 0.7004 (mp) REVERT: B 725 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.7995 (tt0) REVERT: B 804 GLN cc_start: 0.8303 (mm-40) cc_final: 0.7307 (mp10) REVERT: B 869 MET cc_start: 0.7979 (OUTLIER) cc_final: 0.7639 (mtp) REVERT: B 995 ARG cc_start: 0.6934 (ttm170) cc_final: 0.5465 (mtp85) REVERT: B 1001 LEU cc_start: 0.7784 (OUTLIER) cc_final: 0.7041 (mp) REVERT: B 1050 MET cc_start: 0.8478 (mtp) cc_final: 0.8135 (mtt) REVERT: C 804 GLN cc_start: 0.8273 (mm-40) cc_final: 0.7215 (mp10) REVERT: C 954 GLN cc_start: 0.7108 (OUTLIER) cc_final: 0.6649 (mt0) REVERT: C 1001 LEU cc_start: 0.7858 (OUTLIER) cc_final: 0.7190 (mp) REVERT: C 1071 GLN cc_start: 0.9016 (OUTLIER) cc_final: 0.8785 (mp10) outliers start: 40 outliers final: 11 residues processed: 138 average time/residue: 0.6410 time to fit residues: 93.9573 Evaluate side-chains 137 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 117 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 840 CYS Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain B residue 725 GLU Chi-restraints excluded: chain B residue 840 CYS Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1098 ASN Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain C residue 840 CYS Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 954 GLN Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1071 GLN Chi-restraints excluded: chain C residue 1098 ASN Chi-restraints excluded: chain C residue 1117 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 0 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 14 optimal weight: 0.0970 chunk 60 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 111 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 774 GLN A 836 GLN A1071 GLN B 774 GLN B1005 GLN B1071 GLN C 755 GLN C 774 GLN C 836 GLN C 994 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.185524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.160212 restraints weight = 9218.409| |-----------------------------------------------------------------------------| r_work (start): 0.3828 rms_B_bonded: 1.51 r_work: 0.3485 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9927 Z= 0.154 Angle : 0.643 12.200 13644 Z= 0.307 Chirality : 0.046 0.271 1680 Planarity : 0.005 0.056 1737 Dihedral : 5.627 48.224 1992 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 4.64 % Allowed : 11.79 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.89 (0.22), residues: 1278 helix: 2.12 (0.21), residues: 600 sheet: -0.22 (0.32), residues: 183 loop : -1.03 (0.24), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B1014 TYR 0.016 0.002 TYR B1067 PHE 0.017 0.002 PHE C 927 TRP 0.009 0.002 TRP B 886 HIS 0.003 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 9876) covalent geometry : angle 0.56105 (13512) SS BOND : bond 0.00288 ( 21) SS BOND : angle 1.14664 ( 42) hydrogen bonds : bond 0.04830 ( 555) hydrogen bonds : angle 4.91651 ( 1602) link_BETA1-4 : bond 0.00455 ( 12) link_BETA1-4 : angle 1.67314 ( 36) link_NAG-ASN : bond 0.00937 ( 18) link_NAG-ASN : angle 4.75923 ( 54) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 116 time to evaluate : 0.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 804 GLN cc_start: 0.8475 (mm-40) cc_final: 0.7288 (mp10) REVERT: A 820 ASP cc_start: 0.7553 (OUTLIER) cc_final: 0.7346 (t0) REVERT: A 995 ARG cc_start: 0.6743 (ttm170) cc_final: 0.5197 (mtp85) REVERT: A 1001 LEU cc_start: 0.7870 (OUTLIER) cc_final: 0.7000 (mp) REVERT: B 725 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.8040 (tt0) REVERT: B 804 GLN cc_start: 0.8325 (mm-40) cc_final: 0.7360 (mp10) REVERT: B 869 MET cc_start: 0.8007 (OUTLIER) cc_final: 0.7667 (mtp) REVERT: B 995 ARG cc_start: 0.6947 (ttm170) cc_final: 0.5452 (mtp85) REVERT: B 1001 LEU cc_start: 0.7809 (OUTLIER) cc_final: 0.7072 (mp) REVERT: B 1050 MET cc_start: 0.8505 (mtp) cc_final: 0.8165 (mtt) REVERT: C 779 GLN cc_start: 0.7686 (OUTLIER) cc_final: 0.7322 (tp40) REVERT: C 804 GLN cc_start: 0.8313 (mm-40) cc_final: 0.7227 (mp10) REVERT: C 954 GLN cc_start: 0.7134 (OUTLIER) cc_final: 0.6673 (mt0) REVERT: C 1001 LEU cc_start: 0.7867 (OUTLIER) cc_final: 0.7215 (mp) REVERT: C 1071 GLN cc_start: 0.9020 (OUTLIER) cc_final: 0.8716 (mp10) outliers start: 39 outliers final: 14 residues processed: 136 average time/residue: 0.6139 time to fit residues: 88.8594 Evaluate side-chains 136 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 113 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 840 CYS Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain B residue 725 GLU Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 840 CYS Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1011 MET Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1098 ASN Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 840 CYS Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 954 GLN Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1029 MET Chi-restraints excluded: chain C residue 1071 GLN Chi-restraints excluded: chain C residue 1098 ASN Chi-restraints excluded: chain C residue 1117 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 36 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 120 optimal weight: 0.7980 chunk 18 optimal weight: 0.2980 chunk 40 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 13 optimal weight: 7.9990 chunk 108 optimal weight: 3.9990 chunk 2 optimal weight: 0.6980 chunk 65 optimal weight: 0.5980 chunk 81 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 774 GLN A1071 GLN B 774 GLN B1005 GLN B1071 GLN C 755 GLN C 774 GLN C 836 GLN C 994 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.186137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.161983 restraints weight = 9236.455| |-----------------------------------------------------------------------------| r_work (start): 0.3869 rms_B_bonded: 1.39 r_work: 0.3534 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9927 Z= 0.132 Angle : 0.616 12.712 13644 Z= 0.296 Chirality : 0.045 0.289 1680 Planarity : 0.005 0.055 1737 Dihedral : 5.624 47.269 1992 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 4.40 % Allowed : 13.10 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.00 (0.22), residues: 1278 helix: 2.26 (0.21), residues: 600 sheet: -0.22 (0.32), residues: 183 loop : -1.03 (0.24), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B1014 TYR 0.015 0.002 TYR B1067 PHE 0.018 0.002 PHE C 927 TRP 0.007 0.001 TRP B 886 HIS 0.002 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 9876) covalent geometry : angle 0.53300 (13512) SS BOND : bond 0.00257 ( 21) SS BOND : angle 1.03580 ( 42) hydrogen bonds : bond 0.04526 ( 555) hydrogen bonds : angle 4.84686 ( 1602) link_BETA1-4 : bond 0.00512 ( 12) link_BETA1-4 : angle 1.56176 ( 36) link_NAG-ASN : bond 0.00940 ( 18) link_NAG-ASN : angle 4.72546 ( 54) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 110 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 804 GLN cc_start: 0.8441 (mm-40) cc_final: 0.7273 (mp10) REVERT: A 820 ASP cc_start: 0.7493 (OUTLIER) cc_final: 0.7278 (t0) REVERT: A 954 GLN cc_start: 0.7081 (OUTLIER) cc_final: 0.6618 (mt0) REVERT: A 995 ARG cc_start: 0.6800 (ttm170) cc_final: 0.5248 (mtp85) REVERT: A 1001 LEU cc_start: 0.7843 (OUTLIER) cc_final: 0.6999 (mp) REVERT: B 725 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.8061 (tt0) REVERT: B 804 GLN cc_start: 0.8296 (mm-40) cc_final: 0.7313 (mp10) REVERT: B 869 MET cc_start: 0.7986 (OUTLIER) cc_final: 0.7642 (mtp) REVERT: B 995 ARG cc_start: 0.6944 (ttm170) cc_final: 0.5484 (mtp85) REVERT: B 1001 LEU cc_start: 0.7794 (OUTLIER) cc_final: 0.7068 (mp) REVERT: B 1050 MET cc_start: 0.8471 (mtp) cc_final: 0.8124 (mtt) REVERT: C 779 GLN cc_start: 0.7604 (OUTLIER) cc_final: 0.7286 (tp40) REVERT: C 804 GLN cc_start: 0.8285 (mm-40) cc_final: 0.7226 (mp10) REVERT: C 954 GLN cc_start: 0.7021 (OUTLIER) cc_final: 0.6592 (mt0) REVERT: C 1001 LEU cc_start: 0.7855 (OUTLIER) cc_final: 0.7203 (mp) REVERT: C 1071 GLN cc_start: 0.8995 (OUTLIER) cc_final: 0.8707 (mp10) REVERT: C 1119 ASN cc_start: 0.6915 (m110) cc_final: 0.6655 (m-40) outliers start: 37 outliers final: 11 residues processed: 131 average time/residue: 0.5832 time to fit residues: 81.5672 Evaluate side-chains 129 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 840 CYS Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 954 GLN Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain B residue 725 GLU Chi-restraints excluded: chain B residue 840 CYS Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1011 MET Chi-restraints excluded: chain B residue 1098 ASN Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 840 CYS Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 954 GLN Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1029 MET Chi-restraints excluded: chain C residue 1071 GLN Chi-restraints excluded: chain C residue 1098 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 90 optimal weight: 5.9990 chunk 57 optimal weight: 0.0170 chunk 10 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 45 optimal weight: 0.5980 chunk 99 optimal weight: 0.2980 chunk 37 optimal weight: 2.9990 chunk 6 optimal weight: 0.2980 chunk 69 optimal weight: 4.9990 overall best weight: 0.4018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 774 GLN B 774 GLN C 774 GLN C 836 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.186994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 110)---------------| | r_work = 0.3799 r_free = 0.3799 target = 0.158110 restraints weight = 9272.671| |-----------------------------------------------------------------------------| r_work (start): 0.3815 rms_B_bonded: 2.13 r_work: 0.3589 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.3526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9927 Z= 0.114 Angle : 0.585 12.663 13644 Z= 0.282 Chirality : 0.045 0.394 1680 Planarity : 0.005 0.056 1737 Dihedral : 5.607 46.158 1992 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.21 % Allowed : 14.29 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.20 (0.23), residues: 1278 helix: 2.43 (0.21), residues: 600 sheet: -0.16 (0.32), residues: 183 loop : -0.91 (0.24), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B1014 TYR 0.014 0.001 TYR B1067 PHE 0.020 0.001 PHE C 927 TRP 0.006 0.001 TRP B 886 HIS 0.002 0.001 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 9876) covalent geometry : angle 0.50487 (13512) SS BOND : bond 0.00211 ( 21) SS BOND : angle 0.93571 ( 42) hydrogen bonds : bond 0.04180 ( 555) hydrogen bonds : angle 4.75193 ( 1602) link_BETA1-4 : bond 0.00552 ( 12) link_BETA1-4 : angle 1.45319 ( 36) link_NAG-ASN : bond 0.01091 ( 18) link_NAG-ASN : angle 4.54606 ( 54) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 118 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 804 GLN cc_start: 0.8378 (mm-40) cc_final: 0.7173 (mp10) REVERT: A 820 ASP cc_start: 0.7400 (OUTLIER) cc_final: 0.7183 (t0) REVERT: A 995 ARG cc_start: 0.6676 (ttm170) cc_final: 0.5055 (mtp85) REVERT: A 1001 LEU cc_start: 0.7664 (OUTLIER) cc_final: 0.6812 (mp) REVERT: B 804 GLN cc_start: 0.8194 (mm-40) cc_final: 0.7222 (mp10) REVERT: B 869 MET cc_start: 0.7886 (OUTLIER) cc_final: 0.7540 (mtp) REVERT: B 995 ARG cc_start: 0.6831 (ttm170) cc_final: 0.5364 (mtp85) REVERT: B 1001 LEU cc_start: 0.7667 (OUTLIER) cc_final: 0.6869 (mp) REVERT: B 1050 MET cc_start: 0.8382 (mtp) cc_final: 0.7959 (mtt) REVERT: C 779 GLN cc_start: 0.7471 (OUTLIER) cc_final: 0.7163 (tp40) REVERT: C 804 GLN cc_start: 0.8165 (mm-40) cc_final: 0.7083 (mp10) REVERT: C 954 GLN cc_start: 0.6966 (OUTLIER) cc_final: 0.6529 (mt0) REVERT: C 1001 LEU cc_start: 0.7682 (OUTLIER) cc_final: 0.7033 (mp) REVERT: C 1071 GLN cc_start: 0.8924 (OUTLIER) cc_final: 0.8679 (mp10) outliers start: 27 outliers final: 11 residues processed: 135 average time/residue: 0.6252 time to fit residues: 89.9812 Evaluate side-chains 128 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 109 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 840 CYS Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1011 MET Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain B residue 840 CYS Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1011 MET Chi-restraints excluded: chain B residue 1098 ASN Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 840 CYS Chi-restraints excluded: chain C residue 954 GLN Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1071 GLN Chi-restraints excluded: chain C residue 1098 ASN Chi-restraints excluded: chain C residue 1117 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 95 optimal weight: 0.9980 chunk 77 optimal weight: 0.5980 chunk 51 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 81 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 124 optimal weight: 0.0980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 774 GLN B 774 GLN B 992 GLN C 774 GLN C 836 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.186433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.164154 restraints weight = 9131.496| |-----------------------------------------------------------------------------| r_work (start): 0.3891 rms_B_bonded: 1.20 r_work: 0.3542 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.3600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9927 Z= 0.141 Angle : 0.621 12.655 13644 Z= 0.300 Chirality : 0.047 0.525 1680 Planarity : 0.005 0.067 1737 Dihedral : 5.787 47.188 1992 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.98 % Allowed : 15.24 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 1.04 (0.23), residues: 1278 helix: 2.31 (0.21), residues: 600 sheet: -0.27 (0.32), residues: 183 loop : -0.99 (0.24), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 765 TYR 0.016 0.002 TYR B1067 PHE 0.019 0.002 PHE C 927 TRP 0.008 0.002 TRP B 886 HIS 0.003 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 9876) covalent geometry : angle 0.54717 (13512) SS BOND : bond 0.00245 ( 21) SS BOND : angle 1.01665 ( 42) hydrogen bonds : bond 0.04528 ( 555) hydrogen bonds : angle 4.89246 ( 1602) link_BETA1-4 : bond 0.00479 ( 12) link_BETA1-4 : angle 1.51409 ( 36) link_NAG-ASN : bond 0.01092 ( 18) link_NAG-ASN : angle 4.49670 ( 54) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 109 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 804 GLN cc_start: 0.8374 (mm-40) cc_final: 0.7226 (mp10) REVERT: A 820 ASP cc_start: 0.7418 (OUTLIER) cc_final: 0.7186 (t0) REVERT: A 995 ARG cc_start: 0.6737 (ttm170) cc_final: 0.5105 (mtp85) REVERT: A 1001 LEU cc_start: 0.7811 (OUTLIER) cc_final: 0.6991 (mp) REVERT: B 804 GLN cc_start: 0.8300 (mm-40) cc_final: 0.7959 (mt0) REVERT: B 869 MET cc_start: 0.7969 (OUTLIER) cc_final: 0.7636 (mtp) REVERT: B 995 ARG cc_start: 0.6945 (ttm170) cc_final: 0.5461 (mtp85) REVERT: B 1001 LEU cc_start: 0.7758 (OUTLIER) cc_final: 0.7007 (mp) REVERT: B 1050 MET cc_start: 0.8487 (mtp) cc_final: 0.8134 (mtt) REVERT: C 779 GLN cc_start: 0.7560 (OUTLIER) cc_final: 0.7279 (tp40) REVERT: C 804 GLN cc_start: 0.8291 (mm-40) cc_final: 0.7300 (mp10) REVERT: C 954 GLN cc_start: 0.7026 (OUTLIER) cc_final: 0.6601 (mt0) REVERT: C 1001 LEU cc_start: 0.7850 (OUTLIER) cc_final: 0.7186 (mp) REVERT: C 1071 GLN cc_start: 0.8962 (OUTLIER) cc_final: 0.8703 (mp10) outliers start: 25 outliers final: 11 residues processed: 126 average time/residue: 0.5932 time to fit residues: 79.8037 Evaluate side-chains 128 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 109 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 774 GLN Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 840 CYS Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain B residue 840 CYS Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1011 MET Chi-restraints excluded: chain B residue 1098 ASN Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 840 CYS Chi-restraints excluded: chain C residue 954 GLN Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1071 GLN Chi-restraints excluded: chain C residue 1098 ASN Chi-restraints excluded: chain C residue 1117 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 66 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 chunk 70 optimal weight: 0.4980 chunk 100 optimal weight: 0.0070 chunk 61 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 774 GLN B 774 GLN C 774 GLN C 836 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.185208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.157518 restraints weight = 9178.928| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 1.95 r_work: 0.3567 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.3611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 9927 Z= 0.157 Angle : 0.903 59.047 13644 Z= 0.501 Chirality : 0.048 0.726 1680 Planarity : 0.005 0.069 1737 Dihedral : 5.767 47.191 1992 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.98 % Allowed : 15.24 % Favored : 81.79 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 1.03 (0.23), residues: 1278 helix: 2.31 (0.21), residues: 600 sheet: -0.31 (0.32), residues: 183 loop : -1.00 (0.24), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 765 TYR 0.016 0.002 TYR B1067 PHE 0.018 0.002 PHE C 927 TRP 0.007 0.001 TRP B 886 HIS 0.003 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 9876) covalent geometry : angle 0.85375 (13512) SS BOND : bond 0.00255 ( 21) SS BOND : angle 0.98726 ( 42) hydrogen bonds : bond 0.04558 ( 555) hydrogen bonds : angle 4.90098 ( 1602) link_BETA1-4 : bond 0.00424 ( 12) link_BETA1-4 : angle 1.53116 ( 36) link_NAG-ASN : bond 0.01199 ( 18) link_NAG-ASN : angle 4.59874 ( 54) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 108 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 804 GLN cc_start: 0.8239 (mm-40) cc_final: 0.7061 (mp10) REVERT: A 820 ASP cc_start: 0.7326 (OUTLIER) cc_final: 0.7079 (t0) REVERT: A 995 ARG cc_start: 0.6653 (ttm170) cc_final: 0.4984 (mtp85) REVERT: A 1001 LEU cc_start: 0.7633 (OUTLIER) cc_final: 0.6786 (mp) REVERT: B 725 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.8010 (tt0) REVERT: B 804 GLN cc_start: 0.8178 (mm-40) cc_final: 0.7815 (mt0) REVERT: B 869 MET cc_start: 0.7869 (OUTLIER) cc_final: 0.7537 (mtp) REVERT: B 995 ARG cc_start: 0.6841 (ttm170) cc_final: 0.5324 (mtp85) REVERT: B 1001 LEU cc_start: 0.7576 (OUTLIER) cc_final: 0.6804 (mp) REVERT: B 1050 MET cc_start: 0.8430 (mtp) cc_final: 0.8053 (mtt) REVERT: C 779 GLN cc_start: 0.7472 (OUTLIER) cc_final: 0.7185 (tp40) REVERT: C 804 GLN cc_start: 0.8142 (mm-40) cc_final: 0.7144 (mp10) REVERT: C 954 GLN cc_start: 0.6944 (OUTLIER) cc_final: 0.6495 (mt0) REVERT: C 1001 LEU cc_start: 0.7668 (OUTLIER) cc_final: 0.6977 (mp) REVERT: C 1071 GLN cc_start: 0.8920 (OUTLIER) cc_final: 0.8649 (mp10) outliers start: 25 outliers final: 10 residues processed: 126 average time/residue: 0.6240 time to fit residues: 83.6492 Evaluate side-chains 127 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 108 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 840 CYS Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain B residue 725 GLU Chi-restraints excluded: chain B residue 840 CYS Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1011 MET Chi-restraints excluded: chain B residue 1098 ASN Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 840 CYS Chi-restraints excluded: chain C residue 954 GLN Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1071 GLN Chi-restraints excluded: chain C residue 1098 ASN Chi-restraints excluded: chain C residue 1117 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 81 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 56 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 755 GLN A 994 GLN B 774 GLN C 774 GLN C 836 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.182928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.169298 restraints weight = 9173.507| |-----------------------------------------------------------------------------| r_work (start): 0.3924 rms_B_bonded: 0.66 r_work: 0.3673 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.3626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 9927 Z= 0.253 Angle : 0.739 12.221 13644 Z= 0.360 Chirality : 0.052 0.489 1680 Planarity : 0.006 0.073 1737 Dihedral : 6.107 50.035 1992 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.57 % Allowed : 15.00 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.57 (0.22), residues: 1278 helix: 1.97 (0.21), residues: 594 sheet: -0.51 (0.32), residues: 183 loop : -1.25 (0.23), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B1014 TYR 0.021 0.003 TYR C1018 PHE 0.019 0.003 PHE C 927 TRP 0.012 0.003 TRP B 886 HIS 0.005 0.002 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00619 ( 9876) covalent geometry : angle 0.67264 (13512) SS BOND : bond 0.00312 ( 21) SS BOND : angle 1.30362 ( 42) hydrogen bonds : bond 0.05501 ( 555) hydrogen bonds : angle 5.18963 ( 1602) link_BETA1-4 : bond 0.00404 ( 12) link_BETA1-4 : angle 1.73326 ( 36) link_NAG-ASN : bond 0.01202 ( 18) link_NAG-ASN : angle 4.64856 ( 54) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2942.26 seconds wall clock time: 50 minutes 51.50 seconds (3051.50 seconds total)