Starting phenix.real_space_refine on Wed Sep 17 15:53:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vqa_43436/09_2025/8vqa_43436.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vqa_43436/09_2025/8vqa_43436.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vqa_43436/09_2025/8vqa_43436.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vqa_43436/09_2025/8vqa_43436.map" model { file = "/net/cci-nas-00/data/ceres_data/8vqa_43436/09_2025/8vqa_43436.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vqa_43436/09_2025/8vqa_43436.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.080 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 69 5.16 5 C 6093 2.51 5 N 1620 2.21 5 O 1713 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9495 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 3025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3025 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 116} Link IDs: {'PTRANS': 23, 'TRANS': 406} Chain breaks: 3 Unresolved non-hydrogen bonds: 301 Unresolved non-hydrogen angles: 381 Unresolved non-hydrogen dihedrals: 223 Unresolved non-hydrogen chiralities: 37 Planarities with less than four sites: {'GLU:plan': 9, 'ASP:plan': 19, 'ASN:plan1': 7, 'GLN:plan1': 5, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 144 Chain: "B" Number of atoms: 3025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3025 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 116} Link IDs: {'PTRANS': 23, 'TRANS': 406} Chain breaks: 3 Unresolved non-hydrogen bonds: 301 Unresolved non-hydrogen angles: 381 Unresolved non-hydrogen dihedrals: 223 Unresolved non-hydrogen chiralities: 37 Planarities with less than four sites: {'GLU:plan': 9, 'ASP:plan': 19, 'ASN:plan1': 7, 'GLN:plan1': 5, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 144 Chain: "C" Number of atoms: 3025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3025 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 116} Link IDs: {'PTRANS': 23, 'TRANS': 406} Chain breaks: 3 Unresolved non-hydrogen bonds: 301 Unresolved non-hydrogen angles: 381 Unresolved non-hydrogen dihedrals: 223 Unresolved non-hydrogen chiralities: 37 Planarities with less than four sites: {'GLU:plan': 9, 'ASP:plan': 19, 'ASN:plan1': 7, 'GLN:plan1': 5, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 144 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 2.21, per 1000 atoms: 0.23 Number of scatterers: 9495 At special positions: 0 Unit cell: (90, 90, 134, 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 69 16.00 O 1713 8.00 N 1620 7.00 C 6093 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=2.02 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.02 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=2.02 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=2.03 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=2.02 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 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=2.03 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=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A1301 " - " ASN A 709 " " NAG A1302 " - " ASN A1074 " " NAG B1301 " - " ASN B 709 " " NAG B1302 " - " ASN B1074 " " NAG C1301 " - " ASN C 709 " " NAG C1302 " - " ASN C1074 " " NAG D 1 " - " ASN A 717 " " NAG E 1 " - " ASN A 801 " " NAG F 1 " - " ASN A1098 " " NAG G 1 " - " ASN A1134 " " NAG H 1 " - " ASN B 717 " " NAG I 1 " - " ASN B 801 " " NAG J 1 " - " ASN B1098 " " NAG K 1 " - " ASN B1134 " " NAG L 1 " - " ASN C 717 " " NAG M 1 " - " ASN C 801 " " NAG N 1 " - " ASN C1098 " " NAG O 1 " - " ASN C1134 " Time building additional restraints: 0.82 Conformation dependent library (CDL) restraints added in 340.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2424 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 12 sheets defined 47.7% alpha, 22.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 755 Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.846A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 834 through 841 Processing helix chain 'A' and resid 848 through 855 Processing helix chain 'A' and resid 866 through 879 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 918 Processing helix chain 'A' and resid 919 through 938 Processing helix chain 'A' and resid 945 through 966 removed outlier: 4.173A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 982 Processing helix chain 'A' and resid 985 through 1033 Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 755 Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.846A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 834 through 841 Processing helix chain 'B' and resid 848 through 855 Processing helix chain 'B' and resid 866 through 879 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 918 Processing helix chain 'B' and resid 919 through 938 Processing helix chain 'B' and resid 945 through 966 removed outlier: 4.173A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 977 through 982 Processing helix chain 'B' and resid 985 through 1033 Processing helix chain 'B' and resid 1141 through 1146 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 755 Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.846A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 834 through 841 Processing helix chain 'C' and resid 848 through 855 Processing helix chain 'C' and resid 866 through 879 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 918 Processing helix chain 'C' and resid 919 through 938 Processing helix chain 'C' and resid 945 through 966 removed outlier: 4.173A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 977 through 982 Processing helix chain 'C' and resid 985 through 1033 Processing helix chain 'C' and resid 1141 through 1146 Processing sheet with id=AA1, first strand: chain 'A' and resid 711 through 727 removed outlier: 6.642A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 711 through 727 removed outlier: 6.642A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AA4, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AA5, first strand: chain 'B' and resid 711 through 727 removed outlier: 6.642A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 711 through 727 removed outlier: 6.642A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AA8, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AA9, first strand: chain 'C' and resid 711 through 727 removed outlier: 6.642A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 711 through 727 removed outlier: 6.642A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AB3, first strand: chain 'C' and resid 1120 through 1122 561 hydrogen bonds defined for protein. 1665 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.57 Time building geometry restraints manager: 1.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2783 1.33 - 1.46: 2271 1.46 - 1.58: 4537 1.58 - 1.71: 0 1.71 - 1.84: 96 Bond restraints: 9687 Sorted by residual: bond pdb=" NE ARG A 847 " pdb=" CZ ARG A 847 " ideal model delta sigma weight residual 1.326 1.371 -0.045 1.10e-02 8.26e+03 1.65e+01 bond pdb=" NE ARG C 847 " pdb=" CZ ARG C 847 " ideal model delta sigma weight residual 1.326 1.370 -0.044 1.10e-02 8.26e+03 1.61e+01 bond pdb=" NE ARG B 847 " pdb=" CZ ARG B 847 " ideal model delta sigma weight residual 1.326 1.370 -0.044 1.10e-02 8.26e+03 1.59e+01 bond pdb=" C5 NAG K 2 " pdb=" O5 NAG K 2 " ideal model delta sigma weight residual 1.413 1.477 -0.064 2.00e-02 2.50e+03 1.03e+01 bond pdb=" C5 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.413 1.477 -0.064 2.00e-02 2.50e+03 1.03e+01 ... (remaining 9682 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.52: 12934 3.52 - 7.05: 257 7.05 - 10.57: 42 10.57 - 14.10: 0 14.10 - 17.62: 3 Bond angle restraints: 13236 Sorted by residual: angle pdb=" C LEU C 861 " pdb=" N PRO C 862 " pdb=" CA PRO C 862 " ideal model delta sigma weight residual 119.66 126.03 -6.37 7.20e-01 1.93e+00 7.84e+01 angle pdb=" C LEU A 861 " pdb=" N PRO A 862 " pdb=" CA PRO A 862 " ideal model delta sigma weight residual 119.66 126.02 -6.36 7.20e-01 1.93e+00 7.80e+01 angle pdb=" C LEU B 861 " pdb=" N PRO B 862 " pdb=" CA PRO B 862 " ideal model delta sigma weight residual 119.66 126.00 -6.34 7.20e-01 1.93e+00 7.75e+01 angle pdb=" C ALA C1078 " pdb=" N PRO C1079 " pdb=" CA PRO C1079 " ideal model delta sigma weight residual 119.24 127.76 -8.52 1.04e+00 9.25e-01 6.71e+01 angle pdb=" C ALA B1078 " pdb=" N PRO B1079 " pdb=" CA PRO B1079 " ideal model delta sigma weight residual 119.24 127.73 -8.49 1.04e+00 9.25e-01 6.67e+01 ... (remaining 13231 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.88: 5940 16.88 - 33.76: 162 33.76 - 50.63: 48 50.63 - 67.51: 24 67.51 - 84.39: 6 Dihedral angle restraints: 6180 sinusoidal: 2439 harmonic: 3741 Sorted by residual: 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 93.00 135.86 -42.86 1 1.00e+01 1.00e-02 2.56e+01 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 93.00 135.85 -42.85 1 1.00e+01 1.00e-02 2.56e+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 93.00 135.83 -42.83 1 1.00e+01 1.00e-02 2.56e+01 ... (remaining 6177 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 1316 0.099 - 0.199: 255 0.199 - 0.298: 46 0.298 - 0.397: 21 0.397 - 0.496: 3 Chirality restraints: 1641 Sorted by residual: chirality pdb=" C1 NAG L 2 " pdb=" O4 NAG L 1 " pdb=" C2 NAG L 2 " pdb=" O5 NAG L 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.53 0.13 2.00e-02 2.50e+03 4.51e+01 chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.53 0.13 2.00e-02 2.50e+03 4.41e+01 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.53 0.13 2.00e-02 2.50e+03 4.39e+01 ... (remaining 1638 not shown) Planarity restraints: 1713 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C1134 " -0.033 2.00e-02 2.50e+03 3.35e-02 1.41e+01 pdb=" CG ASN C1134 " 0.014 2.00e-02 2.50e+03 pdb=" OD1 ASN C1134 " 0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN C1134 " 0.052 2.00e-02 2.50e+03 pdb=" C1 NAG O 1 " -0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B1134 " 0.032 2.00e-02 2.50e+03 3.34e-02 1.40e+01 pdb=" CG ASN B1134 " -0.013 2.00e-02 2.50e+03 pdb=" OD1 ASN B1134 " -0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN B1134 " -0.052 2.00e-02 2.50e+03 pdb=" C1 NAG K 1 " 0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A1134 " 0.032 2.00e-02 2.50e+03 3.34e-02 1.39e+01 pdb=" CG ASN A1134 " -0.014 2.00e-02 2.50e+03 pdb=" OD1 ASN A1134 " -0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN A1134 " -0.051 2.00e-02 2.50e+03 pdb=" C1 NAG G 1 " 0.040 2.00e-02 2.50e+03 ... (remaining 1710 not shown) Histogram of nonbonded interaction distances: 2.44 - 2.93: 4194 2.93 - 3.43: 8891 3.43 - 3.92: 15011 3.92 - 4.41: 16898 4.41 - 4.90: 27061 Nonbonded interactions: 72055 Sorted by model distance: nonbonded pdb=" OD1 ASN B 709 " pdb=" O5 NAG B1301 " model vdw 2.443 3.040 nonbonded pdb=" OD1 ASN A 709 " pdb=" O5 NAG A1301 " model vdw 2.443 3.040 nonbonded pdb=" OD1 ASN C 709 " pdb=" O5 NAG C1301 " model vdw 2.443 3.040 nonbonded pdb=" O ASN C 969 " pdb=" N GLY C 971 " model vdw 2.547 3.120 nonbonded pdb=" O ASN B 969 " pdb=" N GLY B 971 " model vdw 2.547 3.120 ... (remaining 72050 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 3.330 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.080 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6618 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 : 0.011 0.064 9738 Z= 0.629 Angle : 1.370 17.624 13368 Z= 0.893 Chirality : 0.089 0.496 1641 Planarity : 0.005 0.019 1695 Dihedral : 9.894 84.391 3693 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 0.78 Ramachandran Plot: Outliers : 0.71 % Allowed : 2.61 % Favored : 96.68 % Rotamer: Outliers : 0.77 % Allowed : 0.77 % Favored : 98.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.22), residues: 1266 helix: 0.94 (0.19), residues: 585 sheet: 1.14 (0.47), residues: 120 loop : -1.15 (0.25), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C1000 TYR 0.018 0.003 TYR B 789 PHE 0.018 0.003 PHE C 833 TRP 0.006 0.002 TRP B 886 HIS 0.002 0.001 HIS C1088 Details of bonding type rmsd covalent geometry : bond 0.01070 ( 9687) covalent geometry : angle 1.33680 (13236) SS BOND : bond 0.00713 ( 21) SS BOND : angle 4.80710 ( 42) hydrogen bonds : bond 0.21244 ( 525) hydrogen bonds : angle 7.79885 ( 1665) link_BETA1-4 : bond 0.05072 ( 12) link_BETA1-4 : angle 2.43284 ( 36) link_NAG-ASN : bond 0.05750 ( 18) link_NAG-ASN : angle 2.19239 ( 54) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 137 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1011 MET cc_start: 0.7020 (mmp) cc_final: 0.6790 (mmt) REVERT: A 1014 ARG cc_start: 0.6479 (ttm170) cc_final: 0.6219 (ttm170) REVERT: B 752 LEU cc_start: 0.8281 (mt) cc_final: 0.8060 (mt) REVERT: B 854 LYS cc_start: 0.6885 (ttmt) cc_final: 0.6582 (ttpp) REVERT: B 1011 MET cc_start: 0.7021 (mmp) cc_final: 0.6800 (mmt) REVERT: B 1019 ARG cc_start: 0.7963 (tpt170) cc_final: 0.7708 (tpt170) REVERT: C 1011 MET cc_start: 0.6987 (mmp) cc_final: 0.6757 (mmt) REVERT: C 1019 ARG cc_start: 0.8009 (tpt170) cc_final: 0.7727 (tpt170) outliers start: 6 outliers final: 3 residues processed: 143 average time/residue: 0.1543 time to fit residues: 27.3206 Evaluate side-chains 71 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 68 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain C residue 1074 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 935 GLN A1101 HIS B 935 GLN C 935 GLN C1113 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.175954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.144775 restraints weight = 10099.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.148620 restraints weight = 6996.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.151041 restraints weight = 5463.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.152818 restraints weight = 4611.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.153802 restraints weight = 4109.141| |-----------------------------------------------------------------------------| r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9738 Z= 0.190 Angle : 0.660 7.492 13368 Z= 0.344 Chirality : 0.046 0.249 1641 Planarity : 0.005 0.050 1695 Dihedral : 4.840 43.244 1986 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.51 % Allowed : 6.05 % Favored : 93.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.81 (0.23), residues: 1266 helix: 1.96 (0.21), residues: 594 sheet: 0.43 (0.38), residues: 165 loop : -1.20 (0.26), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 995 TYR 0.021 0.002 TYR A1067 PHE 0.014 0.002 PHE B1121 TRP 0.006 0.001 TRP B 886 HIS 0.006 0.002 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00437 ( 9687) covalent geometry : angle 0.63540 (13236) SS BOND : bond 0.00339 ( 21) SS BOND : angle 1.76240 ( 42) hydrogen bonds : bond 0.06392 ( 525) hydrogen bonds : angle 5.28388 ( 1665) link_BETA1-4 : bond 0.00365 ( 12) link_BETA1-4 : angle 1.51901 ( 36) link_NAG-ASN : bond 0.00441 ( 18) link_NAG-ASN : angle 2.18506 ( 54) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 89 time to evaluate : 0.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 752 LEU cc_start: 0.8776 (mt) cc_final: 0.8491 (mt) REVERT: C 752 LEU cc_start: 0.8697 (mt) cc_final: 0.8243 (mp) outliers start: 4 outliers final: 3 residues processed: 93 average time/residue: 0.1335 time to fit residues: 15.6941 Evaluate side-chains 81 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 78 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain C residue 1074 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 87 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 69 optimal weight: 0.0980 chunk 15 optimal weight: 1.9990 chunk 8 optimal weight: 0.0070 chunk 103 optimal weight: 1.9990 chunk 89 optimal weight: 0.2980 chunk 1 optimal weight: 0.7980 chunk 120 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 overall best weight: 0.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 779 GLN C1101 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.176245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.145528 restraints weight = 10024.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.149330 restraints weight = 6939.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.151778 restraints weight = 5427.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.153397 restraints weight = 4590.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.154572 restraints weight = 4080.683| |-----------------------------------------------------------------------------| r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9738 Z= 0.130 Angle : 0.548 5.699 13368 Z= 0.279 Chirality : 0.044 0.263 1641 Planarity : 0.005 0.051 1695 Dihedral : 4.278 40.553 1986 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.16 % Allowed : 6.95 % Favored : 91.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.11 (0.23), residues: 1266 helix: 2.50 (0.21), residues: 582 sheet: 0.08 (0.37), residues: 165 loop : -1.18 (0.26), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1039 TYR 0.019 0.001 TYR C1067 PHE 0.012 0.001 PHE C1121 TRP 0.004 0.001 TRP C1102 HIS 0.003 0.001 HIS C1101 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 9687) covalent geometry : angle 0.52566 (13236) SS BOND : bond 0.00322 ( 21) SS BOND : angle 1.15343 ( 42) hydrogen bonds : bond 0.05328 ( 525) hydrogen bonds : angle 4.63198 ( 1665) link_BETA1-4 : bond 0.00461 ( 12) link_BETA1-4 : angle 1.29346 ( 36) link_NAG-ASN : bond 0.00488 ( 18) link_NAG-ASN : angle 2.11304 ( 54) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 90 time to evaluate : 0.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 752 LEU cc_start: 0.8646 (mt) cc_final: 0.8394 (mt) REVERT: B 895 GLN cc_start: 0.6961 (OUTLIER) cc_final: 0.6320 (mt0) REVERT: B 1011 MET cc_start: 0.6315 (mmt) cc_final: 0.6092 (mmt) REVERT: C 752 LEU cc_start: 0.8574 (mt) cc_final: 0.8280 (mt) REVERT: C 815 ARG cc_start: 0.7009 (mtt90) cc_final: 0.5871 (mtt180) outliers start: 9 outliers final: 3 residues processed: 98 average time/residue: 0.1341 time to fit residues: 16.6769 Evaluate side-chains 75 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 71 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain C residue 1074 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 5 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1101 HIS B 779 GLN C1101 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.176485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.149688 restraints weight = 10416.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.152025 restraints weight = 8088.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.153614 restraints weight = 6844.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.154443 restraints weight = 6142.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.155318 restraints weight = 5729.183| |-----------------------------------------------------------------------------| r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.3396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 9738 Z= 0.231 Angle : 0.711 14.483 13368 Z= 0.361 Chirality : 0.049 0.279 1641 Planarity : 0.005 0.051 1695 Dihedral : 4.741 32.916 1986 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.93 % Allowed : 8.49 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.29 (0.23), residues: 1266 helix: 1.83 (0.21), residues: 597 sheet: -0.24 (0.34), residues: 195 loop : -1.84 (0.25), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1019 TYR 0.022 0.002 TYR A1067 PHE 0.016 0.003 PHE A 802 TRP 0.004 0.002 TRP C 886 HIS 0.007 0.002 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00583 ( 9687) covalent geometry : angle 0.66114 (13236) SS BOND : bond 0.00536 ( 21) SS BOND : angle 3.73303 ( 42) hydrogen bonds : bond 0.05938 ( 525) hydrogen bonds : angle 5.10675 ( 1665) link_BETA1-4 : bond 0.00242 ( 12) link_BETA1-4 : angle 1.32841 ( 36) link_NAG-ASN : bond 0.00320 ( 18) link_NAG-ASN : angle 2.48069 ( 54) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 815 ARG cc_start: 0.6659 (OUTLIER) cc_final: 0.5651 (mtt180) REVERT: A 1031 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7475 (mt-10) REVERT: A 1091 ARG cc_start: 0.8394 (tpp-160) cc_final: 0.8192 (tpp80) REVERT: A 1115 ILE cc_start: 0.7943 (mt) cc_final: 0.7683 (mt) REVERT: B 752 LEU cc_start: 0.8927 (mt) cc_final: 0.8661 (mt) REVERT: B 815 ARG cc_start: 0.6751 (OUTLIER) cc_final: 0.5753 (mtt180) REVERT: C 752 LEU cc_start: 0.8904 (mt) cc_final: 0.8599 (mt) outliers start: 15 outliers final: 12 residues processed: 94 average time/residue: 0.0972 time to fit residues: 12.6446 Evaluate side-chains 89 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 815 ARG Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 815 ARG Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 12 optimal weight: 0.0770 chunk 33 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 chunk 41 optimal weight: 0.2980 chunk 23 optimal weight: 0.9990 chunk 105 optimal weight: 0.9980 chunk 71 optimal weight: 0.8980 chunk 98 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 38 optimal weight: 0.4980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 779 GLN ** C1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.179543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.152404 restraints weight = 10114.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.155414 restraints weight = 7345.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.157054 restraints weight = 5929.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.158655 restraints weight = 5170.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.159216 restraints weight = 4679.092| |-----------------------------------------------------------------------------| r_work (final): 0.3857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9738 Z= 0.135 Angle : 0.553 8.381 13368 Z= 0.277 Chirality : 0.044 0.285 1641 Planarity : 0.004 0.046 1695 Dihedral : 4.252 32.575 1986 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.93 % Allowed : 9.78 % Favored : 88.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.60 (0.23), residues: 1266 helix: 2.13 (0.21), residues: 594 sheet: -0.36 (0.37), residues: 165 loop : -1.50 (0.25), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1039 TYR 0.020 0.001 TYR A1067 PHE 0.015 0.001 PHE C1121 TRP 0.002 0.001 TRP A1102 HIS 0.003 0.001 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 9687) covalent geometry : angle 0.52090 (13236) SS BOND : bond 0.00240 ( 21) SS BOND : angle 2.27017 ( 42) hydrogen bonds : bond 0.04803 ( 525) hydrogen bonds : angle 4.54995 ( 1665) link_BETA1-4 : bond 0.00369 ( 12) link_BETA1-4 : angle 0.99595 ( 36) link_NAG-ASN : bond 0.00435 ( 18) link_NAG-ASN : angle 2.12675 ( 54) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 756 TYR cc_start: 0.8370 (m-80) cc_final: 0.8137 (m-80) REVERT: B 752 LEU cc_start: 0.8854 (mt) cc_final: 0.8484 (mt) REVERT: B 756 TYR cc_start: 0.8435 (m-80) cc_final: 0.8126 (m-80) REVERT: C 752 LEU cc_start: 0.8794 (mt) cc_final: 0.8466 (mt) REVERT: C 1014 ARG cc_start: 0.5878 (OUTLIER) cc_final: 0.5096 (mtm180) outliers start: 15 outliers final: 8 residues processed: 96 average time/residue: 0.0954 time to fit residues: 13.0306 Evaluate side-chains 87 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 78 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 1014 ARG Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 46 optimal weight: 0.2980 chunk 0 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 chunk 86 optimal weight: 0.7980 chunk 117 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1101 HIS C 779 GLN C1101 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.179568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.153414 restraints weight = 10181.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.155828 restraints weight = 7901.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.157584 restraints weight = 6609.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.158430 restraints weight = 5891.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.159376 restraints weight = 5473.954| |-----------------------------------------------------------------------------| r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.3737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 9738 Z= 0.167 Angle : 0.598 14.024 13368 Z= 0.301 Chirality : 0.044 0.275 1641 Planarity : 0.004 0.045 1695 Dihedral : 4.229 29.997 1986 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.93 % Allowed : 9.52 % Favored : 88.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.54 (0.23), residues: 1266 helix: 2.11 (0.21), residues: 594 sheet: -0.43 (0.39), residues: 165 loop : -1.57 (0.24), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1091 TYR 0.021 0.002 TYR A1067 PHE 0.015 0.001 PHE C1121 TRP 0.003 0.001 TRP A 886 HIS 0.004 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00415 ( 9687) covalent geometry : angle 0.55051 (13236) SS BOND : bond 0.00459 ( 21) SS BOND : angle 3.42911 ( 42) hydrogen bonds : bond 0.04931 ( 525) hydrogen bonds : angle 4.64362 ( 1665) link_BETA1-4 : bond 0.00320 ( 12) link_BETA1-4 : angle 1.01731 ( 36) link_NAG-ASN : bond 0.00347 ( 18) link_NAG-ASN : angle 2.12085 ( 54) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 82 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 756 TYR cc_start: 0.8385 (m-80) cc_final: 0.8045 (m-80) REVERT: A 815 ARG cc_start: 0.6581 (OUTLIER) cc_final: 0.5687 (mtt180) REVERT: A 934 ILE cc_start: 0.8343 (tp) cc_final: 0.8049 (tp) REVERT: A 1011 MET cc_start: 0.6564 (mmt) cc_final: 0.6161 (mmt) REVERT: A 1091 ARG cc_start: 0.8363 (tpp80) cc_final: 0.8136 (ttm-80) REVERT: B 752 LEU cc_start: 0.8921 (mt) cc_final: 0.8572 (mt) REVERT: B 756 TYR cc_start: 0.8468 (m-80) cc_final: 0.8115 (m-80) REVERT: B 815 ARG cc_start: 0.6875 (OUTLIER) cc_final: 0.5762 (mtt180) REVERT: C 752 LEU cc_start: 0.8840 (mt) cc_final: 0.8544 (mt) REVERT: C 1011 MET cc_start: 0.6432 (mmt) cc_final: 0.6026 (mmt) REVERT: C 1014 ARG cc_start: 0.5992 (OUTLIER) cc_final: 0.5243 (mtm180) outliers start: 15 outliers final: 7 residues processed: 96 average time/residue: 0.1082 time to fit residues: 14.2546 Evaluate side-chains 92 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 82 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 815 ARG Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 815 ARG Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain C residue 1014 ARG Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 27 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 chunk 88 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 96 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 56 optimal weight: 10.0000 chunk 7 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 779 GLN C1101 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.191807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.169839 restraints weight = 9863.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.171165 restraints weight = 8113.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.172617 restraints weight = 7123.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.173026 restraints weight = 6518.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.173885 restraints weight = 6204.256| |-----------------------------------------------------------------------------| r_work (final): 0.4023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.4015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 9738 Z= 0.211 Angle : 0.640 10.325 13368 Z= 0.323 Chirality : 0.046 0.270 1641 Planarity : 0.005 0.044 1695 Dihedral : 4.467 29.835 1986 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.54 % Allowed : 9.78 % Favored : 88.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.23), residues: 1266 helix: 2.02 (0.21), residues: 588 sheet: -0.72 (0.37), residues: 165 loop : -1.77 (0.24), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1091 TYR 0.022 0.002 TYR A1067 PHE 0.017 0.002 PHE C1121 TRP 0.005 0.002 TRP A 886 HIS 0.005 0.002 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00531 ( 9687) covalent geometry : angle 0.60227 (13236) SS BOND : bond 0.00492 ( 21) SS BOND : angle 2.97267 ( 42) hydrogen bonds : bond 0.05372 ( 525) hydrogen bonds : angle 4.88936 ( 1665) link_BETA1-4 : bond 0.00299 ( 12) link_BETA1-4 : angle 1.04868 ( 36) link_NAG-ASN : bond 0.00307 ( 18) link_NAG-ASN : angle 2.22511 ( 54) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 0.332 Fit side-chains REVERT: A 756 TYR cc_start: 0.8476 (m-80) cc_final: 0.8163 (m-80) REVERT: A 815 ARG cc_start: 0.6551 (OUTLIER) cc_final: 0.5680 (mtt180) REVERT: A 934 ILE cc_start: 0.8458 (tp) cc_final: 0.8210 (tp) REVERT: A 1011 MET cc_start: 0.6559 (mmt) cc_final: 0.6177 (mmt) REVERT: A 1091 ARG cc_start: 0.8423 (tpp80) cc_final: 0.8145 (ttm-80) REVERT: B 752 LEU cc_start: 0.8947 (mt) cc_final: 0.8674 (mt) REVERT: B 756 TYR cc_start: 0.8543 (m-80) cc_final: 0.8186 (m-80) REVERT: B 815 ARG cc_start: 0.6861 (OUTLIER) cc_final: 0.5889 (mtt180) REVERT: B 1011 MET cc_start: 0.6414 (mmt) cc_final: 0.6037 (mmt) REVERT: C 752 LEU cc_start: 0.8939 (mt) cc_final: 0.8657 (mt) outliers start: 12 outliers final: 9 residues processed: 100 average time/residue: 0.1084 time to fit residues: 14.9277 Evaluate side-chains 96 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 815 ARG Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 815 ARG Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 76 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 35 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 70 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 106 optimal weight: 0.3980 chunk 55 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 779 GLN C1101 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.169096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.139390 restraints weight = 10501.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.142919 restraints weight = 7227.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.145284 restraints weight = 5635.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.146804 restraints weight = 4758.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.147889 restraints weight = 4228.321| |-----------------------------------------------------------------------------| r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.4130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 9738 Z= 0.151 Angle : 0.562 8.102 13368 Z= 0.283 Chirality : 0.044 0.275 1641 Planarity : 0.004 0.045 1695 Dihedral : 4.040 26.640 1980 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.29 % Allowed : 11.20 % Favored : 87.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.23), residues: 1266 helix: 2.15 (0.21), residues: 591 sheet: -0.62 (0.33), residues: 195 loop : -1.79 (0.24), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1091 TYR 0.021 0.001 TYR A1067 PHE 0.022 0.001 PHE B 823 TRP 0.005 0.001 TRP C 886 HIS 0.003 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 9687) covalent geometry : angle 0.53149 (13236) SS BOND : bond 0.00391 ( 21) SS BOND : angle 2.29239 ( 42) hydrogen bonds : bond 0.04699 ( 525) hydrogen bonds : angle 4.62341 ( 1665) link_BETA1-4 : bond 0.00380 ( 12) link_BETA1-4 : angle 0.92044 ( 36) link_NAG-ASN : bond 0.00359 ( 18) link_NAG-ASN : angle 2.04968 ( 54) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.276 Fit side-chains REVERT: A 756 TYR cc_start: 0.8314 (m-80) cc_final: 0.7938 (m-80) REVERT: A 815 ARG cc_start: 0.6696 (OUTLIER) cc_final: 0.5595 (mtt180) REVERT: A 934 ILE cc_start: 0.8171 (tp) cc_final: 0.7850 (tp) REVERT: A 1091 ARG cc_start: 0.8403 (tpp80) cc_final: 0.8198 (ttm-80) REVERT: B 752 LEU cc_start: 0.8736 (mt) cc_final: 0.8501 (mt) REVERT: B 815 ARG cc_start: 0.6867 (OUTLIER) cc_final: 0.5710 (mtt180) REVERT: C 752 LEU cc_start: 0.8749 (mt) cc_final: 0.8395 (mt) REVERT: C 1014 ARG cc_start: 0.5879 (OUTLIER) cc_final: 0.5064 (mtm180) outliers start: 10 outliers final: 6 residues processed: 90 average time/residue: 0.0993 time to fit residues: 12.4733 Evaluate side-chains 89 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 815 ARG Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 815 ARG Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 1014 ARG Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 82 optimal weight: 0.0470 chunk 101 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 69 optimal weight: 4.9990 chunk 28 optimal weight: 0.5980 chunk 27 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 779 GLN C1101 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.168602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.138731 restraints weight = 10557.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.142362 restraints weight = 7162.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.144683 restraints weight = 5533.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.146327 restraints weight = 4650.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.147448 restraints weight = 4128.435| |-----------------------------------------------------------------------------| r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.4184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9738 Z= 0.153 Angle : 0.563 7.132 13368 Z= 0.282 Chirality : 0.044 0.273 1641 Planarity : 0.005 0.045 1695 Dihedral : 4.019 25.929 1980 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.54 % Allowed : 10.81 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.23), residues: 1266 helix: 2.18 (0.21), residues: 591 sheet: -0.64 (0.33), residues: 195 loop : -1.82 (0.25), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1091 TYR 0.021 0.002 TYR A1067 PHE 0.022 0.001 PHE B 823 TRP 0.004 0.001 TRP C 886 HIS 0.004 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 9687) covalent geometry : angle 0.53553 (13236) SS BOND : bond 0.00406 ( 21) SS BOND : angle 2.08422 ( 42) hydrogen bonds : bond 0.04680 ( 525) hydrogen bonds : angle 4.60840 ( 1665) link_BETA1-4 : bond 0.00347 ( 12) link_BETA1-4 : angle 0.93949 ( 36) link_NAG-ASN : bond 0.00356 ( 18) link_NAG-ASN : angle 2.02989 ( 54) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.359 Fit side-chains REVERT: A 756 TYR cc_start: 0.8325 (m-80) cc_final: 0.7936 (m-80) REVERT: A 815 ARG cc_start: 0.6743 (OUTLIER) cc_final: 0.5626 (mtt180) REVERT: A 934 ILE cc_start: 0.8174 (tp) cc_final: 0.7908 (tp) REVERT: A 1091 ARG cc_start: 0.8418 (tpp80) cc_final: 0.8210 (ttm-80) REVERT: B 752 LEU cc_start: 0.8734 (mt) cc_final: 0.8497 (mt) REVERT: B 789 TYR cc_start: 0.6382 (t80) cc_final: 0.6072 (t80) REVERT: B 815 ARG cc_start: 0.6878 (OUTLIER) cc_final: 0.5721 (mtt180) REVERT: B 1011 MET cc_start: 0.6558 (mmt) cc_final: 0.6152 (mmt) REVERT: C 752 LEU cc_start: 0.8747 (mt) cc_final: 0.8419 (mt) REVERT: C 1014 ARG cc_start: 0.5894 (OUTLIER) cc_final: 0.5084 (mtm180) outliers start: 12 outliers final: 8 residues processed: 90 average time/residue: 0.1051 time to fit residues: 13.1654 Evaluate side-chains 91 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 815 ARG Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 815 ARG Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1014 ARG Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 85 optimal weight: 0.0870 chunk 128 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 chunk 3 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 779 GLN ** A1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.168785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.139158 restraints weight = 10404.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.142773 restraints weight = 7094.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.144855 restraints weight = 5497.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.146694 restraints weight = 4641.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.147599 restraints weight = 4120.495| |-----------------------------------------------------------------------------| r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.4226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9738 Z= 0.147 Angle : 0.556 6.535 13368 Z= 0.279 Chirality : 0.044 0.272 1641 Planarity : 0.004 0.044 1695 Dihedral : 3.976 25.111 1980 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.42 % Allowed : 10.94 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.23), residues: 1266 helix: 2.21 (0.21), residues: 591 sheet: -0.63 (0.33), residues: 195 loop : -1.82 (0.24), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1091 TYR 0.021 0.001 TYR A1067 PHE 0.021 0.001 PHE B 823 TRP 0.004 0.001 TRP C 886 HIS 0.003 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 9687) covalent geometry : angle 0.53040 (13236) SS BOND : bond 0.00418 ( 21) SS BOND : angle 1.98309 ( 42) hydrogen bonds : bond 0.04594 ( 525) hydrogen bonds : angle 4.57355 ( 1665) link_BETA1-4 : bond 0.00345 ( 12) link_BETA1-4 : angle 0.93911 ( 36) link_NAG-ASN : bond 0.00378 ( 18) link_NAG-ASN : angle 2.00829 ( 54) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 0.319 Fit side-chains REVERT: A 756 TYR cc_start: 0.8349 (m-80) cc_final: 0.7969 (m-80) REVERT: A 815 ARG cc_start: 0.6742 (OUTLIER) cc_final: 0.5640 (mtt180) REVERT: A 934 ILE cc_start: 0.8159 (tp) cc_final: 0.7844 (tp) REVERT: B 752 LEU cc_start: 0.8725 (mt) cc_final: 0.8488 (mt) REVERT: B 789 TYR cc_start: 0.6349 (t80) cc_final: 0.5999 (t80) REVERT: B 815 ARG cc_start: 0.6900 (OUTLIER) cc_final: 0.5747 (mtt180) REVERT: B 1011 MET cc_start: 0.6559 (mmt) cc_final: 0.6165 (mmt) REVERT: C 752 LEU cc_start: 0.8744 (mt) cc_final: 0.8391 (mt) REVERT: C 1014 ARG cc_start: 0.5868 (OUTLIER) cc_final: 0.5055 (mtm180) outliers start: 11 outliers final: 7 residues processed: 92 average time/residue: 0.1039 time to fit residues: 13.2895 Evaluate side-chains 91 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 815 ARG Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 815 ARG Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1014 ARG Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 126 optimal weight: 3.9990 chunk 62 optimal weight: 0.1980 chunk 40 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 115 optimal weight: 0.8980 chunk 120 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 101 optimal weight: 0.0370 overall best weight: 0.8060 ------------------------------------------------------------------------------- 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** C1101 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.166982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.137695 restraints weight = 10465.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.141238 restraints weight = 7096.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.143641 restraints weight = 5485.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.145252 restraints weight = 4575.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.146150 restraints weight = 4067.840| |-----------------------------------------------------------------------------| r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.4289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9738 Z= 0.170 Angle : 0.575 6.489 13368 Z= 0.288 Chirality : 0.044 0.270 1641 Planarity : 0.005 0.045 1695 Dihedral : 4.057 24.591 1980 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 1.42 % Allowed : 10.81 % Favored : 87.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.39 (0.23), residues: 1266 helix: 2.17 (0.21), residues: 591 sheet: -0.66 (0.33), residues: 195 loop : -1.87 (0.24), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1091 TYR 0.021 0.002 TYR A1067 PHE 0.021 0.002 PHE B 823 TRP 0.004 0.001 TRP C 886 HIS 0.004 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00420 ( 9687) covalent geometry : angle 0.54960 (13236) SS BOND : bond 0.00394 ( 21) SS BOND : angle 2.00623 ( 42) hydrogen bonds : bond 0.04738 ( 525) hydrogen bonds : angle 4.64461 ( 1665) link_BETA1-4 : bond 0.00335 ( 12) link_BETA1-4 : angle 0.96093 ( 36) link_NAG-ASN : bond 0.00318 ( 18) link_NAG-ASN : angle 1.98872 ( 54) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1445.09 seconds wall clock time: 25 minutes 34.30 seconds (1534.30 seconds total)