Starting phenix.real_space_refine on Sun Jun 8 16:08:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vqb_43437/06_2025/8vqb_43437.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vqb_43437/06_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_43437/06_2025/8vqb_43437.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vqb_43437/06_2025/8vqb_43437.map" model { file = "/net/cci-nas-00/data/ceres_data/8vqb_43437/06_2025/8vqb_43437.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vqb_43437/06_2025/8vqb_43437.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 6, 'GLU:plan': 8, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 13} 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: {'GLN:plan1': 6, 'GLU:plan': 8, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 13} 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: {'GLN:plan1': 6, 'GLU:plan': 8, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 13} 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: 6.79, per 1000 atoms: 0.70 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: 2.80 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 1.26 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: 2.80 Time building geometry restraints manager: 3.26 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: 0.07 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: 3.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 26.000 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.900 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (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 TRP 0.017 0.005 TRP C 886 HIS 0.003 0.001 HIS B1083 PHE 0.009 0.002 PHE C 888 TYR 0.042 0.005 TYR B 904 ARG 0.003 0.001 ARG C 765 Details of bonding type rmsd link_NAG-ASN : bond 0.05975 ( 18) link_NAG-ASN : angle 2.21489 ( 54) link_BETA1-4 : bond 0.06038 ( 12) link_BETA1-4 : angle 2.56810 ( 36) hydrogen bonds : bond 0.18658 ( 555) hydrogen bonds : angle 7.40341 ( 1602) SS BOND : bond 0.05594 ( 21) SS BOND : angle 3.18132 ( 42) covalent geometry : bond 0.01105 ( 9876) covalent geometry : angle 1.28574 (13512) *********************** 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 : 0.969 Fit side-chains REVERT: A 751 ASN cc_start: 0.7572 (m-40) cc_final: 0.7213 (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: 1.3284 time to fit residues: 247.3096 Evaluate side-chains 119 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 114 time to evaluate : 1.012 ------------------------------------------------------------------------------- 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 108 optimal weight: 0.6980 chunk 97 optimal weight: 0.5980 chunk 54 optimal weight: 0.9990 chunk 33 optimal weight: 0.1980 chunk 65 optimal weight: 3.9990 chunk 52 optimal weight: 0.7980 chunk 101 optimal weight: 1.9990 chunk 39 optimal weight: 0.4980 chunk 61 optimal weight: 0.5980 chunk 75 optimal weight: 0.8980 chunk 117 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3950 r_free = 0.3950 target = 0.175949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.141306 restraints weight = 9147.883| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 1.94 r_work: 0.3464 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3321 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9927 Z= 0.154 Angle : 0.675 8.535 13644 Z= 0.337 Chirality : 0.045 0.221 1680 Planarity : 0.006 0.091 1737 Dihedral : 5.584 49.843 1996 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 3.10 % Allowed : 7.98 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.23), residues: 1278 helix: 2.23 (0.22), residues: 594 sheet: 0.96 (0.32), residues: 183 loop : -0.39 (0.26), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C1102 HIS 0.004 0.001 HIS C1048 PHE 0.012 0.002 PHE C1121 TYR 0.017 0.002 TYR C1067 ARG 0.008 0.001 ARG B1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00861 ( 18) link_NAG-ASN : angle 3.86166 ( 54) link_BETA1-4 : bond 0.00752 ( 12) link_BETA1-4 : angle 2.06485 ( 36) hydrogen bonds : bond 0.05814 ( 555) hydrogen bonds : angle 5.29621 ( 1602) SS BOND : bond 0.00257 ( 21) SS BOND : angle 2.25420 ( 42) covalent geometry : bond 0.00325 ( 9876) covalent geometry : angle 0.61122 (13512) *********************** 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 149 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 123 time to evaluate : 1.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 836 GLN cc_start: 0.6413 (mt0) cc_final: 0.6034 (mt0) REVERT: A 860 VAL cc_start: 0.6901 (t) cc_final: 0.6576 (p) REVERT: A 869 MET cc_start: 0.7548 (OUTLIER) cc_final: 0.7160 (mtp) REVERT: B 725 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7777 (tt0) REVERT: B 804 GLN cc_start: 0.7903 (mm-40) cc_final: 0.6519 (mp10) REVERT: B 823 PHE cc_start: 0.6513 (m-80) cc_final: 0.6264 (m-80) REVERT: B 836 GLN cc_start: 0.6279 (mt0) cc_final: 0.5549 (mp10) REVERT: B 860 VAL cc_start: 0.6950 (t) cc_final: 0.6594 (p) REVERT: B 1001 LEU cc_start: 0.7010 (OUTLIER) cc_final: 0.6671 (tt) REVERT: B 1050 MET cc_start: 0.8465 (mtp) cc_final: 0.8056 (mtt) REVERT: C 836 GLN cc_start: 0.6428 (mt0) cc_final: 0.6035 (mt0) REVERT: C 860 VAL cc_start: 0.6928 (t) cc_final: 0.6609 (p) REVERT: C 869 MET cc_start: 0.7475 (OUTLIER) cc_final: 0.7128 (mtp) REVERT: C 907 GLU cc_start: 0.7622 (pt0) cc_final: 0.7204 (mm-30) REVERT: C 918 GLU cc_start: 0.7464 (mt-10) cc_final: 0.7199 (mm-30) REVERT: C 1071 GLN cc_start: 0.8902 (OUTLIER) cc_final: 0.8467 (mp10) outliers start: 26 outliers final: 8 residues processed: 141 average time/residue: 1.2986 time to fit residues: 196.3208 Evaluate side-chains 126 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 113 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 900 MET 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 1001 LEU Chi-restraints excluded: chain B residue 1098 ASN Chi-restraints excluded: chain C residue 840 CYS Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 900 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 124 optimal weight: 0.8980 chunk 81 optimal weight: 0.6980 chunk 51 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 57 optimal weight: 0.0000 chunk 23 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 103 optimal weight: 0.4980 overall best weight: 0.4784 ------------------------------------------------------------------------------- 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 ** A1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 774 GLN B 779 GLN B1005 GLN B1101 HIS C 762 GLN C 774 GLN C 992 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 = 0.3928 r_free = 0.3928 target = 0.173626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.138820 restraints weight = 9271.385| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 1.92 r_work: 0.3431 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9927 Z= 0.130 Angle : 0.611 9.999 13644 Z= 0.298 Chirality : 0.045 0.242 1680 Planarity : 0.005 0.037 1737 Dihedral : 5.479 49.617 1992 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 1.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 4.17 % Allowed : 8.57 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.23), residues: 1278 helix: 2.64 (0.21), residues: 576 sheet: 0.57 (0.29), residues: 213 loop : -0.36 (0.26), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 886 HIS 0.003 0.001 HIS A1064 PHE 0.017 0.002 PHE C 927 TYR 0.015 0.002 TYR B1067 ARG 0.008 0.001 ARG A 765 Details of bonding type rmsd link_NAG-ASN : bond 0.00877 ( 18) link_NAG-ASN : angle 4.31887 ( 54) link_BETA1-4 : bond 0.00552 ( 12) link_BETA1-4 : angle 1.64587 ( 36) hydrogen bonds : bond 0.04936 ( 555) hydrogen bonds : angle 4.86138 ( 1602) SS BOND : bond 0.00310 ( 21) SS BOND : angle 1.36276 ( 42) covalent geometry : bond 0.00273 ( 9876) covalent geometry : angle 0.53766 (13512) *********************** 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 159 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 124 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 804 GLN cc_start: 0.8130 (mm-40) cc_final: 0.6632 (mp10) REVERT: A 836 GLN cc_start: 0.6618 (mt0) cc_final: 0.6286 (mt0) REVERT: A 860 VAL cc_start: 0.6981 (t) cc_final: 0.6706 (p) REVERT: A 954 GLN cc_start: 0.6653 (OUTLIER) cc_final: 0.6233 (mm-40) REVERT: A 1001 LEU cc_start: 0.7254 (OUTLIER) cc_final: 0.6311 (mp) REVERT: B 804 GLN cc_start: 0.8074 (mm-40) cc_final: 0.6736 (mp10) REVERT: B 823 PHE cc_start: 0.6596 (m-80) cc_final: 0.6334 (m-80) REVERT: B 836 GLN cc_start: 0.6607 (mt0) cc_final: 0.5660 (mp10) REVERT: B 860 VAL cc_start: 0.7035 (t) cc_final: 0.6669 (p) REVERT: B 869 MET cc_start: 0.7706 (OUTLIER) cc_final: 0.7366 (mtp) REVERT: B 954 GLN cc_start: 0.6617 (mt0) cc_final: 0.6174 (mm-40) REVERT: B 1001 LEU cc_start: 0.7186 (OUTLIER) cc_final: 0.6382 (mp) REVERT: C 804 GLN cc_start: 0.8114 (mm-40) cc_final: 0.6690 (mp10) REVERT: C 814 LYS cc_start: 0.7137 (tttm) cc_final: 0.6908 (tttm) REVERT: C 836 GLN cc_start: 0.6555 (mt0) cc_final: 0.6173 (mt0) REVERT: C 860 VAL cc_start: 0.7021 (t) cc_final: 0.6713 (p) REVERT: C 907 GLU cc_start: 0.7542 (pt0) cc_final: 0.7339 (mm-30) REVERT: C 995 ARG cc_start: 0.6585 (ttm170) cc_final: 0.4914 (ttt180) REVERT: C 1001 LEU cc_start: 0.7395 (OUTLIER) cc_final: 0.6701 (mp) REVERT: C 1071 GLN cc_start: 0.8965 (OUTLIER) cc_final: 0.8495 (mp10) outliers start: 35 outliers final: 7 residues processed: 144 average time/residue: 1.2711 time to fit residues: 195.8113 Evaluate side-chains 132 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 119 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 1098 ASN Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 1001 LEU 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 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 28 optimal weight: 0.5980 chunk 121 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 774 GLN A 901 GLN A 992 GLN A1048 HIS A1071 GLN A1113 GLN B 762 GLN B 774 GLN B1005 GLN B1048 HIS B1071 GLN C 774 GLN C1048 HIS C1119 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.186195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.171905 restraints weight = 9180.711| |-----------------------------------------------------------------------------| r_work (start): 0.3950 rms_B_bonded: 0.71 r_work: 0.3648 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9927 Z= 0.169 Angle : 0.676 10.643 13644 Z= 0.324 Chirality : 0.047 0.244 1680 Planarity : 0.005 0.054 1737 Dihedral : 5.493 48.447 1992 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 5.00 % Allowed : 10.12 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.22), residues: 1278 helix: 2.44 (0.21), residues: 558 sheet: 0.27 (0.30), residues: 213 loop : -0.79 (0.24), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 886 HIS 0.004 0.002 HIS A1064 PHE 0.016 0.002 PHE C 927 TYR 0.018 0.002 TYR B1067 ARG 0.009 0.001 ARG C1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00853 ( 18) link_NAG-ASN : angle 4.61123 ( 54) link_BETA1-4 : bond 0.00415 ( 12) link_BETA1-4 : angle 2.00498 ( 36) hydrogen bonds : bond 0.05156 ( 555) hydrogen bonds : angle 4.95570 ( 1602) SS BOND : bond 0.00300 ( 21) SS BOND : angle 1.40105 ( 42) covalent geometry : bond 0.00396 ( 9876) covalent geometry : angle 0.60009 (13512) *********************** 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 177 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 135 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 804 GLN cc_start: 0.8292 (mm-40) cc_final: 0.7388 (mp10) REVERT: A 869 MET cc_start: 0.7993 (OUTLIER) cc_final: 0.7640 (mtp) REVERT: A 995 ARG cc_start: 0.7016 (ttm170) cc_final: 0.5759 (mtp85) REVERT: A 1014 ARG cc_start: 0.7683 (mtt180) cc_final: 0.7470 (ttm-80) REVERT: B 725 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7850 (tt0) REVERT: B 804 GLN cc_start: 0.8277 (mm-40) cc_final: 0.7499 (mp10) REVERT: B 860 VAL cc_start: 0.7605 (t) cc_final: 0.7396 (p) REVERT: B 869 MET cc_start: 0.7988 (OUTLIER) cc_final: 0.7630 (mtp) REVERT: B 995 ARG cc_start: 0.7186 (ttm170) cc_final: 0.5976 (mtp85) REVERT: B 1001 LEU cc_start: 0.8127 (OUTLIER) cc_final: 0.7440 (mp) REVERT: B 1050 MET cc_start: 0.8287 (mtp) cc_final: 0.7971 (mtt) REVERT: C 804 GLN cc_start: 0.8207 (mm-40) cc_final: 0.7298 (mp10) REVERT: C 869 MET cc_start: 0.7880 (OUTLIER) cc_final: 0.7537 (mtp) REVERT: C 954 GLN cc_start: 0.7411 (OUTLIER) cc_final: 0.6971 (mt0) REVERT: C 1001 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7583 (mp) REVERT: C 1071 GLN cc_start: 0.8968 (OUTLIER) cc_final: 0.8603 (mp10) outliers start: 42 outliers final: 10 residues processed: 154 average time/residue: 1.3916 time to fit residues: 227.6599 Evaluate side-chains 142 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 124 time to evaluate : 1.037 ------------------------------------------------------------------------------- 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 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 869 MET 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 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 27 optimal weight: 0.9980 chunk 100 optimal weight: 0.0000 chunk 33 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 53 optimal weight: 0.0170 chunk 82 optimal weight: 0.0470 chunk 60 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 overall best weight: 0.3720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 774 GLN A1071 GLN A1088 HIS B 774 GLN B1005 GLN B1071 GLN C 774 GLN C1119 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.188010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.161436 restraints weight = 9190.337| |-----------------------------------------------------------------------------| r_work (start): 0.3841 rms_B_bonded: 1.80 r_work: 0.3565 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9927 Z= 0.112 Angle : 0.590 12.267 13644 Z= 0.283 Chirality : 0.044 0.292 1680 Planarity : 0.005 0.046 1737 Dihedral : 5.328 48.209 1992 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 3.33 % Allowed : 12.86 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.22), residues: 1278 helix: 2.56 (0.21), residues: 582 sheet: 0.18 (0.30), residues: 213 loop : -0.72 (0.25), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 886 HIS 0.002 0.001 HIS B1088 PHE 0.016 0.001 PHE C 927 TYR 0.014 0.001 TYR B1067 ARG 0.007 0.001 ARG B1014 Details of bonding type rmsd link_NAG-ASN : bond 0.00784 ( 18) link_NAG-ASN : angle 4.53850 ( 54) link_BETA1-4 : bond 0.00499 ( 12) link_BETA1-4 : angle 1.59741 ( 36) hydrogen bonds : bond 0.04397 ( 555) hydrogen bonds : angle 4.76257 ( 1602) SS BOND : bond 0.00289 ( 21) SS BOND : angle 1.05938 ( 42) covalent geometry : bond 0.00236 ( 9876) covalent geometry : angle 0.50940 (13512) *********************** 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: 28 poor density : 128 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 804 GLN cc_start: 0.8254 (mm-40) cc_final: 0.7096 (mp10) REVERT: A 869 MET cc_start: 0.7854 (OUTLIER) cc_final: 0.7432 (mtp) REVERT: A 995 ARG cc_start: 0.6658 (ttm170) cc_final: 0.5116 (mtp85) REVERT: A 1001 LEU cc_start: 0.7643 (OUTLIER) cc_final: 0.6777 (mp) REVERT: A 1014 ARG cc_start: 0.7535 (mtt180) cc_final: 0.7304 (ttm-80) REVERT: A 1091 ARG cc_start: 0.7799 (ttm-80) cc_final: 0.7407 (mmt-90) REVERT: B 804 GLN cc_start: 0.8233 (mm-40) cc_final: 0.7195 (mp10) REVERT: B 860 VAL cc_start: 0.7266 (t) cc_final: 0.6943 (p) REVERT: B 869 MET cc_start: 0.7876 (OUTLIER) cc_final: 0.7533 (mtp) REVERT: B 995 ARG cc_start: 0.6827 (ttm170) cc_final: 0.5343 (mtp85) REVERT: B 1001 LEU cc_start: 0.7579 (OUTLIER) cc_final: 0.6809 (mp) REVERT: B 1050 MET cc_start: 0.8407 (mtp) cc_final: 0.8022 (mtt) REVERT: C 804 GLN cc_start: 0.8181 (mm-40) cc_final: 0.6984 (mp10) REVERT: C 869 MET cc_start: 0.7773 (OUTLIER) cc_final: 0.7382 (mtp) REVERT: C 1071 GLN cc_start: 0.8960 (OUTLIER) cc_final: 0.8552 (mp10) outliers start: 28 outliers final: 7 residues processed: 145 average time/residue: 1.4220 time to fit residues: 219.0285 Evaluate side-chains 136 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 123 time to evaluate : 1.057 ------------------------------------------------------------------------------- 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 1001 LEU 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 1098 ASN 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 50 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 111 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- 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 B 774 GLN B1005 GLN B1071 GLN ** B1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 755 GLN C 774 GLN C 994 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.183311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 117)---------------| | r_work = 0.3759 r_free = 0.3759 target = 0.154321 restraints weight = 9164.200| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 1.75 r_work: 0.3546 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.3344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 9927 Z= 0.221 Angle : 0.742 11.969 13644 Z= 0.356 Chirality : 0.049 0.274 1680 Planarity : 0.006 0.072 1737 Dihedral : 5.888 50.923 1992 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.22), residues: 1278 helix: 1.96 (0.21), residues: 576 sheet: -0.21 (0.32), residues: 183 loop : -1.17 (0.23), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP C 886 HIS 0.006 0.002 HIS A1064 PHE 0.019 0.003 PHE C 927 TYR 0.020 0.003 TYR A 741 ARG 0.008 0.001 ARG B1014 Details of bonding type rmsd link_NAG-ASN : bond 0.00932 ( 18) link_NAG-ASN : angle 4.87928 ( 54) link_BETA1-4 : bond 0.00411 ( 12) link_BETA1-4 : angle 1.88434 ( 36) hydrogen bonds : bond 0.05617 ( 555) hydrogen bonds : angle 5.13742 ( 1602) SS BOND : bond 0.00370 ( 21) SS BOND : angle 1.37837 ( 42) covalent geometry : bond 0.00544 ( 9876) covalent geometry : angle 0.66749 (13512) *********************** 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: 37 poor density : 118 time to evaluate : 1.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 804 GLN cc_start: 0.8276 (mm-40) cc_final: 0.7072 (mp10) REVERT: A 995 ARG cc_start: 0.6776 (ttm170) cc_final: 0.5191 (mtp85) REVERT: A 1001 LEU cc_start: 0.7750 (OUTLIER) cc_final: 0.6852 (mp) REVERT: A 1014 ARG cc_start: 0.7705 (mtt180) cc_final: 0.7442 (ttm-80) REVERT: B 725 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.8051 (tt0) REVERT: B 804 GLN cc_start: 0.8244 (mm-40) cc_final: 0.7845 (mt0) REVERT: B 860 VAL cc_start: 0.7422 (t) cc_final: 0.7092 (p) REVERT: B 869 MET cc_start: 0.7905 (OUTLIER) cc_final: 0.7637 (mtp) REVERT: B 995 ARG cc_start: 0.6883 (ttm170) cc_final: 0.5336 (mtp85) REVERT: B 1001 LEU cc_start: 0.7692 (OUTLIER) cc_final: 0.6923 (mp) REVERT: B 1050 MET cc_start: 0.8436 (mtp) cc_final: 0.8084 (mtt) REVERT: C 804 GLN cc_start: 0.8218 (mm-40) cc_final: 0.7173 (mp10) REVERT: C 869 MET cc_start: 0.7850 (OUTLIER) cc_final: 0.7577 (mtp) REVERT: C 954 GLN cc_start: 0.7007 (OUTLIER) cc_final: 0.6580 (mt0) REVERT: C 1001 LEU cc_start: 0.7717 (OUTLIER) cc_final: 0.7022 (mp) REVERT: C 1071 GLN cc_start: 0.8972 (OUTLIER) cc_final: 0.8713 (mp10) outliers start: 37 outliers final: 10 residues processed: 138 average time/residue: 2.0801 time to fit residues: 306.1146 Evaluate side-chains 132 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 114 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 774 GLN Chi-restraints excluded: chain A residue 840 CYS Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1050 MET 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 124 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 78 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 1 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 95 optimal weight: 0.0980 chunk 32 optimal weight: 0.0470 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 836 GLN B 774 GLN B 992 GLN B1005 GLN B1071 GLN C 755 GLN C 774 GLN C 994 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.185484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.154980 restraints weight = 9279.689| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 2.76 r_work: 0.3589 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.3411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9927 Z= 0.125 Angle : 0.621 12.923 13644 Z= 0.298 Chirality : 0.045 0.299 1680 Planarity : 0.005 0.064 1737 Dihedral : 5.675 47.564 1992 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.10 % Allowed : 14.88 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.22), residues: 1278 helix: 2.15 (0.21), residues: 600 sheet: -0.22 (0.33), residues: 183 loop : -1.06 (0.24), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 886 HIS 0.002 0.001 HIS A1064 PHE 0.018 0.001 PHE C 927 TYR 0.015 0.002 TYR A 741 ARG 0.006 0.001 ARG B 765 Details of bonding type rmsd link_NAG-ASN : bond 0.01077 ( 18) link_NAG-ASN : angle 4.88720 ( 54) link_BETA1-4 : bond 0.00500 ( 12) link_BETA1-4 : angle 1.58900 ( 36) hydrogen bonds : bond 0.04557 ( 555) hydrogen bonds : angle 4.87583 ( 1602) SS BOND : bond 0.00265 ( 21) SS BOND : angle 1.05071 ( 42) covalent geometry : bond 0.00267 ( 9876) covalent geometry : angle 0.53304 (13512) *********************** 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 145 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 119 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 804 GLN cc_start: 0.8230 (mm-40) cc_final: 0.7030 (mp10) REVERT: A 869 MET cc_start: 0.7805 (OUTLIER) cc_final: 0.7440 (mtp) REVERT: A 995 ARG cc_start: 0.6686 (ttm170) cc_final: 0.5108 (mtp85) REVERT: A 1001 LEU cc_start: 0.7627 (OUTLIER) cc_final: 0.6733 (mp) REVERT: A 1014 ARG cc_start: 0.7603 (mtt180) cc_final: 0.7336 (ttm-80) REVERT: B 804 GLN cc_start: 0.8141 (mm-40) cc_final: 0.7149 (mp10) REVERT: B 860 VAL cc_start: 0.7287 (t) cc_final: 0.6951 (p) REVERT: B 869 MET cc_start: 0.7818 (OUTLIER) cc_final: 0.7492 (mtp) REVERT: B 995 ARG cc_start: 0.6788 (ttm170) cc_final: 0.5298 (mtp85) REVERT: B 1001 LEU cc_start: 0.7559 (OUTLIER) cc_final: 0.6803 (mp) REVERT: B 1050 MET cc_start: 0.8366 (mtp) cc_final: 0.7943 (mtt) REVERT: C 740 MET cc_start: 0.8245 (ttp) cc_final: 0.8027 (ttp) REVERT: C 804 GLN cc_start: 0.8156 (mm-40) cc_final: 0.7070 (mp10) REVERT: C 869 MET cc_start: 0.7765 (OUTLIER) cc_final: 0.7413 (mtp) REVERT: C 954 GLN cc_start: 0.6901 (OUTLIER) cc_final: 0.6505 (mt0) REVERT: C 957 GLN cc_start: 0.6339 (pt0) cc_final: 0.6126 (tp-100) REVERT: C 1001 LEU cc_start: 0.7599 (OUTLIER) cc_final: 0.6936 (mp) REVERT: C 1071 GLN cc_start: 0.8969 (OUTLIER) cc_final: 0.8648 (mp10) outliers start: 26 outliers final: 8 residues processed: 133 average time/residue: 1.2837 time to fit residues: 182.4467 Evaluate side-chains 132 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 0.985 ------------------------------------------------------------------------------- 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 1001 LEU 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 840 CYS Chi-restraints excluded: chain C residue 869 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 41 optimal weight: 0.5980 chunk 118 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 chunk 110 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 83 optimal weight: 0.4980 chunk 107 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 774 GLN B 992 GLN C 755 GLN C 774 GLN C 994 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.184686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 99)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.154604 restraints weight = 9319.295| |-----------------------------------------------------------------------------| r_work (start): 0.3783 rms_B_bonded: 2.16 r_work: 0.3544 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.3516 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= 0.144 Angle : 0.643 12.423 13644 Z= 0.309 Chirality : 0.046 0.390 1680 Planarity : 0.005 0.065 1737 Dihedral : 5.799 48.105 1992 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.21 % Allowed : 15.12 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.22), residues: 1278 helix: 2.21 (0.21), residues: 597 sheet: -0.27 (0.33), residues: 183 loop : -1.15 (0.23), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 886 HIS 0.003 0.001 HIS B1088 PHE 0.020 0.002 PHE A 961 TYR 0.017 0.002 TYR B 741 ARG 0.007 0.001 ARG A1091 Details of bonding type rmsd link_NAG-ASN : bond 0.00957 ( 18) link_NAG-ASN : angle 4.74401 ( 54) link_BETA1-4 : bond 0.00448 ( 12) link_BETA1-4 : angle 1.59662 ( 36) hydrogen bonds : bond 0.04704 ( 555) hydrogen bonds : angle 4.91272 ( 1602) SS BOND : bond 0.00269 ( 21) SS BOND : angle 1.10390 ( 42) covalent geometry : bond 0.00331 ( 9876) covalent geometry : angle 0.56307 (13512) *********************** 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 141 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 114 time to evaluate : 1.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 804 GLN cc_start: 0.8306 (mm-40) cc_final: 0.7111 (mp10) REVERT: A 995 ARG cc_start: 0.6704 (ttm170) cc_final: 0.5106 (mtp85) REVERT: A 1001 LEU cc_start: 0.7748 (OUTLIER) cc_final: 0.6895 (mp) REVERT: A 1014 ARG cc_start: 0.7691 (mtt180) cc_final: 0.7424 (ttm-80) REVERT: B 725 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.8084 (tt0) REVERT: B 804 GLN cc_start: 0.8306 (mm-40) cc_final: 0.7234 (mp10) REVERT: B 860 VAL cc_start: 0.7398 (t) cc_final: 0.7053 (p) REVERT: B 869 MET cc_start: 0.7913 (OUTLIER) cc_final: 0.7608 (mtp) REVERT: B 995 ARG cc_start: 0.6867 (ttm170) cc_final: 0.5384 (mtp85) REVERT: B 1001 LEU cc_start: 0.7720 (OUTLIER) cc_final: 0.6925 (mp) REVERT: B 1050 MET cc_start: 0.8433 (mtp) cc_final: 0.8069 (mtt) REVERT: C 804 GLN cc_start: 0.8241 (mm-40) cc_final: 0.7209 (mp10) REVERT: C 869 MET cc_start: 0.7850 (OUTLIER) cc_final: 0.7520 (mtp) REVERT: C 954 GLN cc_start: 0.6971 (OUTLIER) cc_final: 0.6544 (mt0) REVERT: C 1001 LEU cc_start: 0.7745 (OUTLIER) cc_final: 0.7077 (mp) REVERT: C 1071 GLN cc_start: 0.8973 (OUTLIER) cc_final: 0.8739 (mp10) outliers start: 27 outliers final: 9 residues processed: 129 average time/residue: 1.3249 time to fit residues: 182.4978 Evaluate side-chains 129 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 112 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 840 CYS 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 1098 ASN Chi-restraints excluded: chain C residue 840 CYS Chi-restraints excluded: chain C residue 869 MET 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 78 optimal weight: 0.9980 chunk 76 optimal weight: 0.6980 chunk 82 optimal weight: 0.1980 chunk 39 optimal weight: 1.9990 chunk 95 optimal weight: 0.0070 chunk 79 optimal weight: 0.5980 chunk 88 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 774 GLN B 992 GLN C 774 GLN C 992 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.186501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.157953 restraints weight = 9193.698| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 2.26 r_work: 0.3585 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.3574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9927 Z= 0.120 Angle : 0.597 12.856 13644 Z= 0.287 Chirality : 0.046 0.532 1680 Planarity : 0.005 0.064 1737 Dihedral : 5.777 46.015 1992 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.23), residues: 1278 helix: 2.31 (0.21), residues: 600 sheet: -0.19 (0.33), residues: 183 loop : -1.01 (0.24), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 886 HIS 0.002 0.001 HIS B1088 PHE 0.020 0.001 PHE C 927 TYR 0.014 0.002 TYR B1067 ARG 0.007 0.001 ARG A1091 Details of bonding type rmsd link_NAG-ASN : bond 0.01103 ( 18) link_NAG-ASN : angle 4.52629 ( 54) link_BETA1-4 : bond 0.00545 ( 12) link_BETA1-4 : angle 1.48802 ( 36) hydrogen bonds : bond 0.04284 ( 555) hydrogen bonds : angle 4.81720 ( 1602) SS BOND : bond 0.00224 ( 21) SS BOND : angle 0.96366 ( 42) covalent geometry : bond 0.00258 ( 9876) covalent geometry : angle 0.51830 (13512) *********************** 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 139 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 114 time to evaluate : 1.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 804 GLN cc_start: 0.8281 (mm-40) cc_final: 0.7076 (mp10) REVERT: A 954 GLN cc_start: 0.6829 (OUTLIER) cc_final: 0.6398 (mt0) REVERT: A 995 ARG cc_start: 0.6663 (ttm170) cc_final: 0.5014 (mtp85) REVERT: A 1001 LEU cc_start: 0.7580 (OUTLIER) cc_final: 0.6728 (mp) REVERT: A 1014 ARG cc_start: 0.7618 (mtt180) cc_final: 0.7318 (ttm-80) REVERT: B 804 GLN cc_start: 0.8200 (mm-40) cc_final: 0.7145 (mp10) REVERT: B 860 VAL cc_start: 0.7331 (t) cc_final: 0.6973 (p) REVERT: B 869 MET cc_start: 0.7836 (OUTLIER) cc_final: 0.7509 (mtp) REVERT: B 995 ARG cc_start: 0.6770 (ttm170) cc_final: 0.5269 (mtp85) REVERT: B 1001 LEU cc_start: 0.7567 (OUTLIER) cc_final: 0.6780 (mp) REVERT: B 1050 MET cc_start: 0.8370 (mtp) cc_final: 0.7938 (mtt) REVERT: C 804 GLN cc_start: 0.8173 (mm-40) cc_final: 0.7167 (mp10) REVERT: C 869 MET cc_start: 0.7777 (OUTLIER) cc_final: 0.7409 (mtp) REVERT: C 954 GLN cc_start: 0.6873 (OUTLIER) cc_final: 0.6435 (mt0) REVERT: C 1001 LEU cc_start: 0.7610 (OUTLIER) cc_final: 0.6925 (mp) REVERT: C 1071 GLN cc_start: 0.8922 (OUTLIER) cc_final: 0.8643 (mp10) REVERT: C 1119 ASN cc_start: 0.6741 (m110) cc_final: 0.6539 (m-40) outliers start: 25 outliers final: 8 residues processed: 129 average time/residue: 1.3278 time to fit residues: 183.0215 Evaluate side-chains 128 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 112 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 840 CYS Chi-restraints excluded: chain A residue 954 GLN Chi-restraints excluded: chain A residue 1001 LEU 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 840 CYS Chi-restraints excluded: chain C residue 869 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 63 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 81 optimal weight: 0.8980 chunk 41 optimal weight: 0.1980 chunk 91 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 24 optimal weight: 0.0070 chunk 52 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 26 optimal weight: 6.9990 chunk 74 optimal weight: 0.5980 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 774 GLN B 992 GLN C 774 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.186529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.164923 restraints weight = 9194.140| |-----------------------------------------------------------------------------| r_work (start): 0.3894 rms_B_bonded: 1.20 r_work: 0.3563 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.3641 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= 0.120 Angle : 0.598 12.866 13644 Z= 0.289 Chirality : 0.046 0.528 1680 Planarity : 0.005 0.062 1737 Dihedral : 5.751 45.986 1992 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.38 % Allowed : 15.71 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.23), residues: 1278 helix: 2.39 (0.21), residues: 597 sheet: -0.21 (0.33), residues: 183 loop : -1.04 (0.24), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 886 HIS 0.002 0.001 HIS B1088 PHE 0.018 0.001 PHE C 927 TYR 0.015 0.002 TYR B1067 ARG 0.005 0.001 ARG A 765 Details of bonding type rmsd link_NAG-ASN : bond 0.01038 ( 18) link_NAG-ASN : angle 4.47001 ( 54) link_BETA1-4 : bond 0.00495 ( 12) link_BETA1-4 : angle 1.44350 ( 36) hydrogen bonds : bond 0.04249 ( 555) hydrogen bonds : angle 4.80953 ( 1602) SS BOND : bond 0.00232 ( 21) SS BOND : angle 0.95538 ( 42) covalent geometry : bond 0.00261 ( 9876) covalent geometry : angle 0.52193 (13512) ********************** 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 137 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 117 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 804 GLN cc_start: 0.8322 (mm-40) cc_final: 0.7170 (mp10) REVERT: A 954 GLN cc_start: 0.6889 (OUTLIER) cc_final: 0.6467 (mt0) REVERT: A 995 ARG cc_start: 0.6706 (ttm170) cc_final: 0.5074 (mtp85) REVERT: A 1001 LEU cc_start: 0.7769 (OUTLIER) cc_final: 0.6969 (mp) REVERT: A 1014 ARG cc_start: 0.7729 (mtt180) cc_final: 0.7452 (ttm-80) REVERT: B 804 GLN cc_start: 0.8259 (mm-40) cc_final: 0.7926 (mt0) REVERT: B 860 VAL cc_start: 0.7456 (t) cc_final: 0.7105 (p) REVERT: B 869 MET cc_start: 0.7931 (OUTLIER) cc_final: 0.7580 (mtp) REVERT: B 995 ARG cc_start: 0.6867 (ttm170) cc_final: 0.5365 (mtp85) REVERT: B 1001 LEU cc_start: 0.7746 (OUTLIER) cc_final: 0.6992 (mp) REVERT: B 1050 MET cc_start: 0.8408 (mtp) cc_final: 0.8003 (mtt) REVERT: C 804 GLN cc_start: 0.8254 (mm-40) cc_final: 0.7324 (mp10) REVERT: C 869 MET cc_start: 0.7878 (OUTLIER) cc_final: 0.7500 (mtp) REVERT: C 954 GLN cc_start: 0.6966 (OUTLIER) cc_final: 0.6530 (mt0) REVERT: C 1001 LEU cc_start: 0.7768 (OUTLIER) cc_final: 0.7126 (mp) REVERT: C 1071 GLN cc_start: 0.8920 (OUTLIER) cc_final: 0.8671 (mp10) REVERT: C 1119 ASN cc_start: 0.6886 (m110) cc_final: 0.6649 (m-40) outliers start: 20 outliers final: 8 residues processed: 130 average time/residue: 1.2251 time to fit residues: 170.7986 Evaluate side-chains 130 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 114 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 840 CYS Chi-restraints excluded: chain A residue 954 GLN Chi-restraints excluded: chain A residue 1001 LEU 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 840 CYS Chi-restraints excluded: chain C residue 869 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 68 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 23 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 97 optimal weight: 0.9990 chunk 96 optimal weight: 0.8980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 774 GLN B 992 GLN C 774 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.182911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.166638 restraints weight = 9142.633| |-----------------------------------------------------------------------------| r_work (start): 0.3913 rms_B_bonded: 0.78 r_work: 0.3615 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.3678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 9927 Z= 0.192 Angle : 0.694 12.628 13644 Z= 0.336 Chirality : 0.050 0.553 1680 Planarity : 0.006 0.072 1737 Dihedral : 6.101 49.493 1992 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.62 % Allowed : 15.83 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.22), residues: 1278 helix: 1.99 (0.21), residues: 600 sheet: -0.41 (0.32), residues: 183 loop : -1.24 (0.23), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 886 HIS 0.004 0.002 HIS C1048 PHE 0.021 0.002 PHE C 927 TYR 0.020 0.003 TYR C 741 ARG 0.005 0.001 ARG B1014 Details of bonding type rmsd link_NAG-ASN : bond 0.01154 ( 18) link_NAG-ASN : angle 4.67604 ( 54) link_BETA1-4 : bond 0.00455 ( 12) link_BETA1-4 : angle 1.65120 ( 36) hydrogen bonds : bond 0.05107 ( 555) hydrogen bonds : angle 5.10906 ( 1602) SS BOND : bond 0.00309 ( 21) SS BOND : angle 1.20881 ( 42) covalent geometry : bond 0.00464 ( 9876) covalent geometry : angle 0.62172 (13512) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6732.15 seconds wall clock time: 117 minutes 24.29 seconds (7044.29 seconds total)