Starting phenix.real_space_refine on Sun Jul 27 17:04:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vqa_43436/07_2025/8vqa_43436.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vqa_43436/07_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_43436/07_2025/8vqa_43436.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vqa_43436/07_2025/8vqa_43436.map" model { file = "/net/cci-nas-00/data/ceres_data/8vqa_43436/07_2025/8vqa_43436.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vqa_43436/07_2025/8vqa_43436.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.080 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 5, 'ASP:plan': 19, 'ASN:plan1': 7, 'HIS:plan': 1, 'GLU:plan': 9, 'ARG: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: {'GLN:plan1': 5, 'ASP:plan': 19, 'ASN:plan1': 7, 'HIS:plan': 1, 'GLU:plan': 9, 'ARG: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: {'GLN:plan1': 5, 'ASP:plan': 19, 'ASN:plan1': 7, 'HIS:plan': 1, 'GLU:plan': 9, 'ARG: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: 6.55, per 1000 atoms: 0.69 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: 2.87 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 1.12 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: 2.97 Time building geometry restraints manager: 3.36 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: 0.00 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: 2.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 25.890 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.480 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.22), 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 TRP 0.006 0.002 TRP B 886 HIS 0.002 0.001 HIS C1088 PHE 0.018 0.003 PHE C 833 TYR 0.018 0.003 TYR B 789 ARG 0.002 0.000 ARG C1000 Details of bonding type rmsd link_NAG-ASN : bond 0.05750 ( 18) link_NAG-ASN : angle 2.19239 ( 54) link_BETA1-4 : bond 0.05072 ( 12) link_BETA1-4 : angle 2.43284 ( 36) hydrogen bonds : bond 0.21244 ( 525) hydrogen bonds : angle 7.79885 ( 1665) SS BOND : bond 0.00713 ( 21) SS BOND : angle 4.80710 ( 42) covalent geometry : bond 0.01070 ( 9687) covalent geometry : angle 1.33680 (13236) *********************** 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 : 0.994 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: 0.6789 (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: 0.7709 (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: 0.7726 (tpt170) outliers start: 6 outliers final: 3 residues processed: 143 average time/residue: 0.3635 time to fit residues: 64.3263 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 : 0.961 ------------------------------------------------------------------------------- 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 108 optimal weight: 0.0670 chunk 97 optimal weight: 0.7980 chunk 54 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 101 optimal weight: 0.6980 chunk 39 optimal weight: 0.4980 chunk 61 optimal weight: 0.0970 chunk 75 optimal weight: 1.9990 chunk 117 optimal weight: 0.5980 overall best weight: 0.3716 ------------------------------------------------------------------------------- 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 = 0.4033 r_free = 0.4033 target = 0.179988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.149031 restraints weight = 9866.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.153014 restraints weight = 6682.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.155642 restraints weight = 5158.482| |-----------------------------------------------------------------------------| r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9738 Z= 0.156 Angle : 0.624 6.975 13368 Z= 0.328 Chirality : 0.044 0.234 1641 Planarity : 0.005 0.046 1695 Dihedral : 4.740 44.151 1986 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 1.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.51 % Allowed : 5.66 % Favored : 93.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.23), residues: 1266 helix: 2.10 (0.20), residues: 594 sheet: 0.60 (0.40), residues: 156 loop : -1.22 (0.26), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 886 HIS 0.003 0.001 HIS A1064 PHE 0.013 0.001 PHE B1121 TYR 0.019 0.002 TYR A1067 ARG 0.003 0.000 ARG B1039 Details of bonding type rmsd link_NAG-ASN : bond 0.00474 ( 18) link_NAG-ASN : angle 2.16476 ( 54) link_BETA1-4 : bond 0.00283 ( 12) link_BETA1-4 : angle 1.46937 ( 36) hydrogen bonds : bond 0.06525 ( 525) hydrogen bonds : angle 5.24465 ( 1665) SS BOND : bond 0.00455 ( 21) SS BOND : angle 1.84893 ( 42) covalent geometry : bond 0.00327 ( 9687) covalent geometry : angle 0.59780 (13236) *********************** 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 83 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 79 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 720 ILE cc_start: 0.8103 (mm) cc_final: 0.7675 (mm) REVERT: B 752 LEU cc_start: 0.8718 (mt) cc_final: 0.8443 (mt) REVERT: C 752 LEU cc_start: 0.8629 (mt) cc_final: 0.8127 (mp) outliers start: 4 outliers final: 3 residues processed: 83 average time/residue: 0.3009 time to fit residues: 33.0088 Evaluate side-chains 74 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 71 time to evaluate : 1.009 ------------------------------------------------------------------------------- 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 6 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 38 optimal weight: 0.0980 chunk 60 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 56 optimal weight: 0.0670 chunk 52 optimal weight: 0.0970 chunk 48 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 overall best weight: 0.3316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1101 HIS C1101 HIS C1106 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.178344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.147712 restraints weight = 9976.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.151570 restraints weight = 6773.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.154269 restraints weight = 5233.707| |-----------------------------------------------------------------------------| r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9738 Z= 0.122 Angle : 0.540 6.428 13368 Z= 0.274 Chirality : 0.043 0.257 1641 Planarity : 0.005 0.050 1695 Dihedral : 4.167 40.755 1986 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.16 % Allowed : 7.08 % Favored : 91.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.24), residues: 1266 helix: 2.59 (0.21), residues: 582 sheet: 0.11 (0.37), residues: 165 loop : -1.19 (0.26), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C1102 HIS 0.003 0.001 HIS C1101 PHE 0.010 0.001 PHE A1121 TYR 0.018 0.001 TYR C1067 ARG 0.003 0.000 ARG C1039 Details of bonding type rmsd link_NAG-ASN : bond 0.00483 ( 18) link_NAG-ASN : angle 2.04584 ( 54) link_BETA1-4 : bond 0.00442 ( 12) link_BETA1-4 : angle 1.30500 ( 36) hydrogen bonds : bond 0.04953 ( 525) hydrogen bonds : angle 4.48771 ( 1665) SS BOND : bond 0.00359 ( 21) SS BOND : angle 1.13867 ( 42) covalent geometry : bond 0.00259 ( 9687) covalent geometry : angle 0.51816 (13236) *********************** 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 105 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 96 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 815 ARG cc_start: 0.6523 (mtt90) cc_final: 0.5435 (mtt180) REVERT: A 917 TYR cc_start: 0.8024 (m-10) cc_final: 0.7803 (m-10) REVERT: B 752 LEU cc_start: 0.8612 (mt) cc_final: 0.8362 (mt) REVERT: B 895 GLN cc_start: 0.6798 (OUTLIER) cc_final: 0.6018 (mt0) REVERT: C 752 LEU cc_start: 0.8591 (mt) cc_final: 0.8265 (mt) REVERT: C 815 ARG cc_start: 0.6886 (mtt90) cc_final: 0.5825 (mtt180) outliers start: 9 outliers final: 3 residues processed: 104 average time/residue: 0.3219 time to fit residues: 42.7199 Evaluate side-chains 81 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 77 time to evaluate : 1.052 ------------------------------------------------------------------------------- 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 95 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 chunk 78 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 86 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 779 GLN B1088 HIS C1088 HIS C1101 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.181836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.154851 restraints weight = 10173.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.157344 restraints weight = 7900.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.159085 restraints weight = 6649.374| |-----------------------------------------------------------------------------| r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.114 9738 Z= 0.182 Angle : 0.641 14.383 13368 Z= 0.327 Chirality : 0.046 0.266 1641 Planarity : 0.005 0.053 1695 Dihedral : 4.320 35.909 1986 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.90 % Allowed : 8.24 % Favored : 90.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.23), residues: 1266 helix: 2.15 (0.21), residues: 597 sheet: 0.05 (0.33), residues: 195 loop : -1.70 (0.25), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 886 HIS 0.006 0.002 HIS A1064 PHE 0.011 0.002 PHE C 802 TYR 0.022 0.002 TYR A1067 ARG 0.003 0.000 ARG A1039 Details of bonding type rmsd link_NAG-ASN : bond 0.00341 ( 18) link_NAG-ASN : angle 2.12101 ( 54) link_BETA1-4 : bond 0.00305 ( 12) link_BETA1-4 : angle 1.23572 ( 36) hydrogen bonds : bond 0.05279 ( 525) hydrogen bonds : angle 4.78764 ( 1665) SS BOND : bond 0.00346 ( 21) SS BOND : angle 3.61143 ( 42) covalent geometry : bond 0.00453 ( 9687) covalent geometry : angle 0.59293 (13236) *********************** 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 90 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 83 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1011 MET cc_start: 0.6728 (mmt) cc_final: 0.6321 (mmt) REVERT: B 752 LEU cc_start: 0.8908 (mt) cc_final: 0.8582 (mt) REVERT: B 815 ARG cc_start: 0.6777 (OUTLIER) cc_final: 0.5567 (mtt180) REVERT: B 895 GLN cc_start: 0.7164 (OUTLIER) cc_final: 0.6864 (mt0) REVERT: C 752 LEU cc_start: 0.8847 (mt) cc_final: 0.8556 (mt) REVERT: C 1115 ILE cc_start: 0.7842 (mt) cc_final: 0.7611 (mt) outliers start: 7 outliers final: 4 residues processed: 90 average time/residue: 0.2709 time to fit residues: 32.5645 Evaluate side-chains 78 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 72 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain B residue 815 ARG 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 101 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 115 optimal weight: 0.9990 chunk 102 optimal weight: 0.5980 chunk 116 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 121 optimal weight: 0.5980 chunk 51 optimal weight: 0.0970 chunk 98 optimal weight: 4.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1101 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.181565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.154138 restraints weight = 10083.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.157157 restraints weight = 7297.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.159064 restraints weight = 5883.639| |-----------------------------------------------------------------------------| r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.3402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 9738 Z= 0.137 Angle : 0.545 8.697 13368 Z= 0.273 Chirality : 0.044 0.274 1641 Planarity : 0.004 0.051 1695 Dihedral : 4.051 33.792 1986 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.80 % Allowed : 8.88 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.23), residues: 1266 helix: 2.34 (0.21), residues: 597 sheet: -0.26 (0.37), residues: 165 loop : -1.51 (0.25), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP C1102 HIS 0.003 0.001 HIS A1088 PHE 0.013 0.001 PHE C1121 TYR 0.020 0.001 TYR A 789 ARG 0.003 0.000 ARG A1019 Details of bonding type rmsd link_NAG-ASN : bond 0.00418 ( 18) link_NAG-ASN : angle 2.12017 ( 54) link_BETA1-4 : bond 0.00401 ( 12) link_BETA1-4 : angle 1.06596 ( 36) hydrogen bonds : bond 0.04611 ( 525) hydrogen bonds : angle 4.41028 ( 1665) SS BOND : bond 0.00229 ( 21) SS BOND : angle 2.30032 ( 42) covalent geometry : bond 0.00324 ( 9687) covalent geometry : angle 0.51127 (13236) *********************** 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 100 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 756 TYR cc_start: 0.8210 (m-80) cc_final: 0.7983 (m-80) REVERT: A 815 ARG cc_start: 0.6702 (OUTLIER) cc_final: 0.5732 (mtt180) REVERT: A 917 TYR cc_start: 0.8053 (m-10) cc_final: 0.7772 (m-10) REVERT: A 1011 MET cc_start: 0.6603 (mmt) cc_final: 0.6239 (mmt) REVERT: B 752 LEU cc_start: 0.8838 (mt) cc_final: 0.8427 (mt) REVERT: B 756 TYR cc_start: 0.8449 (m-80) cc_final: 0.8129 (m-80) REVERT: C 752 LEU cc_start: 0.8780 (mt) cc_final: 0.8403 (mt) REVERT: C 789 TYR cc_start: 0.6036 (t80) cc_final: 0.5688 (t80) REVERT: C 1014 ARG cc_start: 0.5855 (OUTLIER) cc_final: 0.5070 (mtm180) REVERT: C 1115 ILE cc_start: 0.7726 (mt) cc_final: 0.7492 (mt) outliers start: 14 outliers final: 8 residues processed: 99 average time/residue: 0.2239 time to fit residues: 31.1912 Evaluate side-chains 93 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 83 time to evaluate : 0.925 ------------------------------------------------------------------------------- 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 882 ILE Chi-restraints excluded: chain B residue 1074 ASN 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 80 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 125 optimal weight: 0.4980 chunk 38 optimal weight: 0.9980 chunk 121 optimal weight: 0.6980 chunk 105 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1101 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.178907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.151745 restraints weight = 10160.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.154661 restraints weight = 7421.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.156568 restraints weight = 6015.287| |-----------------------------------------------------------------------------| r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.3671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 9738 Z= 0.166 Angle : 0.589 12.083 13368 Z= 0.298 Chirality : 0.044 0.268 1641 Planarity : 0.005 0.048 1695 Dihedral : 4.139 30.907 1986 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.80 % Allowed : 10.17 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.23), residues: 1266 helix: 2.22 (0.21), residues: 597 sheet: -0.32 (0.38), residues: 165 loop : -1.54 (0.25), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 886 HIS 0.004 0.001 HIS A1064 PHE 0.014 0.002 PHE C1121 TYR 0.020 0.002 TYR A1067 ARG 0.002 0.000 ARG A1019 Details of bonding type rmsd link_NAG-ASN : bond 0.00337 ( 18) link_NAG-ASN : angle 2.15725 ( 54) link_BETA1-4 : bond 0.00362 ( 12) link_BETA1-4 : angle 1.06883 ( 36) hydrogen bonds : bond 0.04892 ( 525) hydrogen bonds : angle 4.60972 ( 1665) SS BOND : bond 0.00591 ( 21) SS BOND : angle 2.84037 ( 42) covalent geometry : bond 0.00407 ( 9687) covalent geometry : angle 0.54990 (13236) *********************** 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 96 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 756 TYR cc_start: 0.8329 (m-80) cc_final: 0.7987 (m-80) REVERT: A 815 ARG cc_start: 0.6619 (OUTLIER) cc_final: 0.5693 (mtt180) REVERT: A 917 TYR cc_start: 0.8128 (m-10) cc_final: 0.7814 (m-10) REVERT: A 934 ILE cc_start: 0.8277 (tp) cc_final: 0.8028 (tp) REVERT: A 1031 GLU cc_start: 0.7723 (mt-10) cc_final: 0.7486 (mt-10) REVERT: A 1091 ARG cc_start: 0.8500 (tpp-160) cc_final: 0.8296 (tpp80) REVERT: B 752 LEU cc_start: 0.8897 (mt) cc_final: 0.8521 (mt) REVERT: B 756 TYR cc_start: 0.8450 (m-80) cc_final: 0.8102 (m-80) REVERT: B 815 ARG cc_start: 0.6887 (OUTLIER) cc_final: 0.5671 (mtt180) REVERT: B 934 ILE cc_start: 0.8198 (tp) cc_final: 0.7989 (tt) REVERT: C 752 LEU cc_start: 0.8868 (mt) cc_final: 0.8549 (mt) REVERT: C 789 TYR cc_start: 0.6217 (t80) cc_final: 0.6017 (t80) REVERT: C 1115 ILE cc_start: 0.7758 (mt) cc_final: 0.7526 (mt) outliers start: 14 outliers final: 9 residues processed: 95 average time/residue: 0.2294 time to fit residues: 30.6930 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 : 1.014 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 101 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 123 optimal weight: 0.0770 chunk 103 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 71 optimal weight: 0.5980 chunk 99 optimal weight: 9.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.179788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.153762 restraints weight = 10228.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.156228 restraints weight = 7878.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.157537 restraints weight = 6640.766| |-----------------------------------------------------------------------------| r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.3849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 9738 Z= 0.156 Angle : 0.563 9.014 13368 Z= 0.282 Chirality : 0.044 0.265 1641 Planarity : 0.004 0.045 1695 Dihedral : 4.086 28.856 1986 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.23), residues: 1266 helix: 2.29 (0.21), residues: 594 sheet: -0.41 (0.39), residues: 165 loop : -1.57 (0.25), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 886 HIS 0.004 0.001 HIS A1064 PHE 0.014 0.001 PHE C1121 TYR 0.020 0.002 TYR A1067 ARG 0.002 0.000 ARG A1019 Details of bonding type rmsd link_NAG-ASN : bond 0.00397 ( 18) link_NAG-ASN : angle 2.14261 ( 54) link_BETA1-4 : bond 0.00327 ( 12) link_BETA1-4 : angle 0.99978 ( 36) hydrogen bonds : bond 0.04692 ( 525) hydrogen bonds : angle 4.52277 ( 1665) SS BOND : bond 0.00292 ( 21) SS BOND : angle 2.36145 ( 42) covalent geometry : bond 0.00382 ( 9687) covalent geometry : angle 0.52974 (13236) *********************** 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 98 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 83 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 815 ARG cc_start: 0.6649 (OUTLIER) cc_final: 0.5718 (mtt180) REVERT: A 917 TYR cc_start: 0.8087 (m-10) cc_final: 0.7793 (m-10) REVERT: A 934 ILE cc_start: 0.8262 (tp) cc_final: 0.8011 (tp) REVERT: A 1091 ARG cc_start: 0.8517 (tpp-160) cc_final: 0.8248 (ttm-80) REVERT: B 752 LEU cc_start: 0.8881 (mt) cc_final: 0.8647 (mt) REVERT: B 756 TYR cc_start: 0.8430 (m-80) cc_final: 0.8043 (m-80) REVERT: B 815 ARG cc_start: 0.6857 (OUTLIER) cc_final: 0.5703 (mtt180) REVERT: C 752 LEU cc_start: 0.8825 (mt) cc_final: 0.8527 (mt) REVERT: C 1014 ARG cc_start: 0.5894 (OUTLIER) cc_final: 0.5078 (mtm180) REVERT: C 1115 ILE cc_start: 0.7747 (mt) cc_final: 0.7501 (mt) outliers start: 15 outliers final: 10 residues processed: 96 average time/residue: 0.2661 time to fit residues: 35.0283 Evaluate side-chains 95 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.981 ------------------------------------------------------------------------------- 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 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 772 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 113 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 48 optimal weight: 0.0970 chunk 19 optimal weight: 0.5980 chunk 67 optimal weight: 0.5980 chunk 102 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1101 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.178309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.151370 restraints weight = 10316.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.154372 restraints weight = 7458.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.156013 restraints weight = 6009.636| |-----------------------------------------------------------------------------| r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.3991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 9738 Z= 0.150 Angle : 0.559 9.227 13368 Z= 0.281 Chirality : 0.044 0.263 1641 Planarity : 0.004 0.043 1695 Dihedral : 4.031 27.599 1986 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.42 % Allowed : 10.17 % Favored : 88.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.23), residues: 1266 helix: 2.27 (0.21), residues: 594 sheet: -0.47 (0.39), residues: 165 loop : -1.56 (0.25), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 886 HIS 0.004 0.001 HIS B1064 PHE 0.014 0.001 PHE C1121 TYR 0.021 0.002 TYR A1067 ARG 0.002 0.000 ARG A1019 Details of bonding type rmsd link_NAG-ASN : bond 0.00323 ( 18) link_NAG-ASN : angle 2.14585 ( 54) link_BETA1-4 : bond 0.00334 ( 12) link_BETA1-4 : angle 0.99155 ( 36) hydrogen bonds : bond 0.04637 ( 525) hydrogen bonds : angle 4.54554 ( 1665) SS BOND : bond 0.00379 ( 21) SS BOND : angle 2.27178 ( 42) covalent geometry : bond 0.00366 ( 9687) covalent geometry : angle 0.52687 (13236) *********************** 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 95 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 2.923 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 815 ARG cc_start: 0.6661 (OUTLIER) cc_final: 0.5746 (mtt180) REVERT: A 934 ILE cc_start: 0.8237 (tp) cc_final: 0.7986 (tp) REVERT: A 1091 ARG cc_start: 0.8555 (tpp-160) cc_final: 0.8266 (ttm-80) REVERT: B 752 LEU cc_start: 0.8887 (mt) cc_final: 0.8630 (mt) REVERT: B 815 ARG cc_start: 0.6799 (OUTLIER) cc_final: 0.5708 (mtt180) REVERT: C 752 LEU cc_start: 0.8847 (mt) cc_final: 0.8539 (mt) REVERT: C 1014 ARG cc_start: 0.5886 (OUTLIER) cc_final: 0.5047 (mtm180) outliers start: 11 outliers final: 6 residues processed: 94 average time/residue: 0.3527 time to fit residues: 47.2852 Evaluate side-chains 91 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 82 time to evaluate : 1.744 ------------------------------------------------------------------------------- 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 C residue 772 VAL Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 1014 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 100 optimal weight: 0.0030 chunk 12 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 118 optimal weight: 0.0870 chunk 0 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 123 optimal weight: 0.4980 chunk 111 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.6970 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1101 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.177632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.150832 restraints weight = 10261.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.153784 restraints weight = 7428.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.155671 restraints weight = 5997.829| |-----------------------------------------------------------------------------| r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.4076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 9738 Z= 0.156 Angle : 0.558 9.151 13368 Z= 0.281 Chirality : 0.044 0.263 1641 Planarity : 0.004 0.042 1695 Dihedral : 3.917 26.325 1982 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.03 % Allowed : 10.81 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.23), residues: 1266 helix: 2.22 (0.21), residues: 597 sheet: -0.38 (0.34), residues: 195 loop : -1.75 (0.25), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 886 HIS 0.004 0.001 HIS A1064 PHE 0.015 0.001 PHE C1121 TYR 0.021 0.002 TYR A1067 ARG 0.002 0.000 ARG A1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00411 ( 18) link_NAG-ASN : angle 2.08802 ( 54) link_BETA1-4 : bond 0.00354 ( 12) link_BETA1-4 : angle 0.96604 ( 36) hydrogen bonds : bond 0.04621 ( 525) hydrogen bonds : angle 4.55662 ( 1665) SS BOND : bond 0.00377 ( 21) SS BOND : angle 2.21375 ( 42) covalent geometry : bond 0.00382 ( 9687) covalent geometry : angle 0.52802 (13236) *********************** 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 91 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 83 time to evaluate : 1.519 Fit side-chains revert: symmetry clash REVERT: A 815 ARG cc_start: 0.6581 (OUTLIER) cc_final: 0.5657 (mtt180) REVERT: A 934 ILE cc_start: 0.8219 (tp) cc_final: 0.7983 (tp) REVERT: A 1091 ARG cc_start: 0.8562 (tpp-160) cc_final: 0.8272 (ttm-80) REVERT: B 752 LEU cc_start: 0.8865 (mt) cc_final: 0.8614 (mt) REVERT: B 815 ARG cc_start: 0.6809 (OUTLIER) cc_final: 0.5732 (mtt180) REVERT: C 752 LEU cc_start: 0.8843 (mt) cc_final: 0.8550 (mt) REVERT: C 1014 ARG cc_start: 0.5873 (OUTLIER) cc_final: 0.5053 (mtm180) outliers start: 8 outliers final: 5 residues processed: 90 average time/residue: 0.2806 time to fit residues: 36.5217 Evaluate side-chains 90 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 815 ARG 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 882 ILE Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 1014 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 128 optimal weight: 0.0870 chunk 47 optimal weight: 0.9990 chunk 63 optimal weight: 0.6980 chunk 58 optimal weight: 0.0000 chunk 95 optimal weight: 0.9990 chunk 18 optimal weight: 0.3980 chunk 48 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 overall best weight: 0.4362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1101 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.170761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.141106 restraints weight = 10565.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.144777 restraints weight = 7148.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.146877 restraints weight = 5495.147| |-----------------------------------------------------------------------------| r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.4141 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= 0.125 Angle : 0.529 7.437 13368 Z= 0.265 Chirality : 0.043 0.262 1641 Planarity : 0.004 0.042 1695 Dihedral : 3.689 24.643 1980 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.16 % Allowed : 10.30 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.23), residues: 1266 helix: 2.31 (0.21), residues: 597 sheet: -0.32 (0.35), residues: 195 loop : -1.68 (0.25), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 886 HIS 0.003 0.001 HIS B1064 PHE 0.014 0.001 PHE C1121 TYR 0.020 0.001 TYR A1067 ARG 0.002 0.000 ARG A1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00351 ( 18) link_NAG-ASN : angle 1.98086 ( 54) link_BETA1-4 : bond 0.00367 ( 12) link_BETA1-4 : angle 0.93260 ( 36) hydrogen bonds : bond 0.04329 ( 525) hydrogen bonds : angle 4.45094 ( 1665) SS BOND : bond 0.00376 ( 21) SS BOND : angle 1.90096 ( 42) covalent geometry : bond 0.00294 ( 9687) covalent geometry : angle 0.50226 (13236) ********************** 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 92 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 83 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 815 ARG cc_start: 0.6653 (OUTLIER) cc_final: 0.5590 (mtt180) REVERT: A 934 ILE cc_start: 0.8073 (tp) cc_final: 0.7778 (tp) REVERT: A 1091 ARG cc_start: 0.8606 (tpp-160) cc_final: 0.8329 (ttm-80) REVERT: A 1111 GLU cc_start: 0.7190 (mm-30) cc_final: 0.6838 (mt-10) REVERT: B 752 LEU cc_start: 0.8639 (mt) cc_final: 0.8387 (mt) REVERT: B 815 ARG cc_start: 0.6918 (OUTLIER) cc_final: 0.5690 (mtt180) REVERT: C 752 LEU cc_start: 0.8685 (mt) cc_final: 0.8379 (mt) REVERT: C 1014 ARG cc_start: 0.5793 (OUTLIER) cc_final: 0.4974 (mtm180) outliers start: 9 outliers final: 5 residues processed: 91 average time/residue: 0.2334 time to fit residues: 29.5798 Evaluate side-chains 89 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 815 ARG Chi-restraints excluded: chain A residue 882 ILE 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 C residue 882 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1014 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 23 optimal weight: 1.9990 chunk 125 optimal weight: 0.9980 chunk 67 optimal weight: 0.0970 chunk 81 optimal weight: 1.9990 chunk 128 optimal weight: 0.5980 chunk 95 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 124 optimal weight: 0.4980 chunk 71 optimal weight: 0.5980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 777 ASN C1101 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.169769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.140432 restraints weight = 10433.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.144038 restraints weight = 7073.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.146424 restraints weight = 5444.070| |-----------------------------------------------------------------------------| r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.4218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9738 Z= 0.136 Angle : 0.530 6.528 13368 Z= 0.266 Chirality : 0.043 0.258 1641 Planarity : 0.004 0.050 1695 Dihedral : 3.690 23.366 1980 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.16 % Allowed : 10.68 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.24), residues: 1266 helix: 2.32 (0.21), residues: 597 sheet: -0.30 (0.35), residues: 195 loop : -1.72 (0.25), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 886 HIS 0.004 0.001 HIS B1064 PHE 0.015 0.001 PHE C1121 TYR 0.020 0.002 TYR A1067 ARG 0.002 0.000 ARG A1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00357 ( 18) link_NAG-ASN : angle 1.93375 ( 54) link_BETA1-4 : bond 0.00353 ( 12) link_BETA1-4 : angle 0.95102 ( 36) hydrogen bonds : bond 0.04337 ( 525) hydrogen bonds : angle 4.47522 ( 1665) SS BOND : bond 0.00344 ( 21) SS BOND : angle 1.78829 ( 42) covalent geometry : bond 0.00330 ( 9687) covalent geometry : angle 0.50566 (13236) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2906.24 seconds wall clock time: 52 minutes 16.09 seconds (3136.09 seconds total)