Starting phenix.real_space_refine on Thu Jan 16 13:23:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vqa_43436/01_2025/8vqa_43436.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vqa_43436/01_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_43436/01_2025/8vqa_43436.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vqa_43436/01_2025/8vqa_43436.map" model { file = "/net/cci-nas-00/data/ceres_data/8vqa_43436/01_2025/8vqa_43436.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vqa_43436/01_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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: 6.51, 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: 2.60 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: 0.96 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: 2.76 Time building geometry restraints manager: 2.95 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: 5.000 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 24.080 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.120 ------------------------------------------------------------------------------- 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 9687 Z= 0.712 Angle : 1.337 17.624 13236 Z= 0.886 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 *********************** 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 : 0.937 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: 0.3747 time to fit residues: 66.1257 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 : 1.177 ------------------------------------------------------------------------------- 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 = 0.4034 r_free = 0.4034 target = 0.179995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.148982 restraints weight = 9866.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.152987 restraints weight = 6668.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.155692 restraints weight = 5131.214| |-----------------------------------------------------------------------------| r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 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 9687 Z= 0.216 Angle : 0.598 6.972 13236 Z= 0.322 Chirality : 0.044 0.234 1641 Planarity : 0.005 0.046 1695 Dihedral : 4.740 44.150 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 *********************** 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 : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 720 ILE cc_start: 0.8104 (mm) cc_final: 0.7676 (mm) REVERT: B 752 LEU cc_start: 0.8716 (mt) cc_final: 0.8441 (mt) REVERT: C 752 LEU cc_start: 0.8627 (mt) cc_final: 0.8125 (mp) outliers start: 4 outliers final: 3 residues processed: 83 average time/residue: 0.3004 time to fit residues: 32.9041 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 : 1.219 ------------------------------------------------------------------------------- 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: 0.0060 chunk 9 optimal weight: 1.9990 chunk 38 optimal weight: 0.0870 chunk 60 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 56 optimal weight: 0.0370 chunk 52 optimal weight: 0.1980 chunk 48 optimal weight: 0.4980 chunk 16 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 overall best weight: 0.1652 ------------------------------------------------------------------------------- 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 = 0.4062 r_free = 0.4062 target = 0.183668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.152766 restraints weight = 10014.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.156730 restraints weight = 6932.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.159253 restraints weight = 5395.973| |-----------------------------------------------------------------------------| r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9687 Z= 0.144 Angle : 0.500 6.197 13236 Z= 0.261 Chirality : 0.043 0.256 1641 Planarity : 0.005 0.049 1695 Dihedral : 4.113 41.096 1986 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.03 % Allowed : 7.34 % Favored : 91.63 % 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: 1.21 (0.24), residues: 1266 helix: 2.59 (0.21), residues: 588 sheet: 0.11 (0.37), residues: 165 loop : -1.17 (0.26), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 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 *********************** 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 100 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 92 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 789 TYR cc_start: 0.5596 (t80) cc_final: 0.5330 (t80) REVERT: A 815 ARG cc_start: 0.6461 (mtt90) cc_final: 0.5380 (mtt180) REVERT: A 917 TYR cc_start: 0.7961 (m-10) cc_final: 0.7704 (m-10) REVERT: B 752 LEU cc_start: 0.8435 (mt) cc_final: 0.8125 (mt) REVERT: C 752 LEU cc_start: 0.8512 (mt) cc_final: 0.8196 (mt) REVERT: C 789 TYR cc_start: 0.5650 (t80) cc_final: 0.5436 (t80) outliers start: 8 outliers final: 4 residues processed: 99 average time/residue: 0.3105 time to fit residues: 40.3549 Evaluate side-chains 80 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 76 time to evaluate : 1.058 ------------------------------------------------------------------------------- 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 731 MET 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: 0.7980 chunk 22 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 86 optimal weight: 0.5980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 779 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.175971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.147985 restraints weight = 10251.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.150707 restraints weight = 7707.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.152167 restraints weight = 6397.257| |-----------------------------------------------------------------------------| r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.3329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.092 9687 Z= 0.461 Angle : 0.715 8.611 13236 Z= 0.371 Chirality : 0.050 0.273 1641 Planarity : 0.005 0.055 1695 Dihedral : 4.813 34.697 1986 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.42 % Allowed : 7.85 % Favored : 90.73 % 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: 0.26 (0.23), residues: 1266 helix: 1.97 (0.21), residues: 576 sheet: -0.20 (0.33), residues: 195 loop : -1.94 (0.24), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP C 886 HIS 0.008 0.003 HIS A1064 PHE 0.019 0.003 PHE A 802 TYR 0.022 0.003 TYR A1067 ARG 0.004 0.001 ARG A1019 *********************** 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 105 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 1.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 815 ARG cc_start: 0.6790 (OUTLIER) cc_final: 0.5824 (mtt180) REVERT: A 823 PHE cc_start: 0.7625 (t80) cc_final: 0.7134 (t80) REVERT: A 917 TYR cc_start: 0.8382 (m-10) cc_final: 0.8151 (m-10) REVERT: A 1011 MET cc_start: 0.6791 (mmt) cc_final: 0.6398 (mmt) REVERT: A 1031 GLU cc_start: 0.7740 (mt-10) cc_final: 0.7497 (mt-10) REVERT: A 1115 ILE cc_start: 0.7938 (mt) cc_final: 0.7703 (mt) REVERT: B 752 LEU cc_start: 0.8963 (mt) cc_final: 0.8693 (mt) REVERT: B 815 ARG cc_start: 0.6825 (OUTLIER) cc_final: 0.5735 (mtt180) REVERT: B 1014 ARG cc_start: 0.6447 (ttm170) cc_final: 0.6075 (ttm170) REVERT: C 752 LEU cc_start: 0.8944 (mt) cc_final: 0.8611 (mt) REVERT: C 1011 MET cc_start: 0.6640 (mmt) cc_final: 0.6244 (mmt) outliers start: 11 outliers final: 9 residues processed: 105 average time/residue: 0.3320 time to fit residues: 44.5845 Evaluate side-chains 88 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 772 VAL 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 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 101 optimal weight: 0.8980 chunk 20 optimal weight: 0.3980 chunk 115 optimal weight: 0.5980 chunk 102 optimal weight: 0.6980 chunk 116 optimal weight: 0.5980 chunk 76 optimal weight: 0.2980 chunk 90 optimal weight: 0.7980 chunk 52 optimal weight: 0.9980 chunk 121 optimal weight: 1.9990 chunk 51 optimal weight: 0.0570 chunk 98 optimal weight: 4.9990 overall best weight: 0.3898 ------------------------------------------------------------------------------- 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** 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 = 0.4061 r_free = 0.4061 target = 0.181558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.154250 restraints weight = 10070.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.157266 restraints weight = 7239.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.159100 restraints weight = 5819.615| |-----------------------------------------------------------------------------| r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 9687 Z= 0.185 Angle : 0.513 5.071 13236 Z= 0.264 Chirality : 0.044 0.285 1641 Planarity : 0.005 0.049 1695 Dihedral : 4.179 33.665 1986 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.29 % Allowed : 9.65 % Favored : 89.06 % 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: 2.20 (0.21), residues: 597 sheet: -0.33 (0.37), residues: 165 loop : -1.51 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 886 HIS 0.003 0.001 HIS C1088 PHE 0.024 0.001 PHE C 823 TYR 0.020 0.001 TYR C1067 ARG 0.002 0.000 ARG A1019 *********************** 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 92 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 82 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 756 TYR cc_start: 0.8221 (m-80) cc_final: 0.8003 (m-80) REVERT: A 1011 MET cc_start: 0.6578 (mmt) cc_final: 0.6183 (mmt) REVERT: B 752 LEU cc_start: 0.8902 (mt) cc_final: 0.8583 (mt) REVERT: B 1115 ILE cc_start: 0.7838 (mt) cc_final: 0.7508 (mt) REVERT: C 752 LEU cc_start: 0.8761 (mt) cc_final: 0.8396 (mt) REVERT: C 1014 ARG cc_start: 0.5794 (OUTLIER) cc_final: 0.5014 (mtm180) outliers start: 10 outliers final: 6 residues processed: 91 average time/residue: 0.2464 time to fit residues: 31.3559 Evaluate side-chains 83 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 76 time to evaluate : 0.955 ------------------------------------------------------------------------------- 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 780 GLU Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 1014 ARG Chi-restraints excluded: chain C residue 1074 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 80 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 90 optimal weight: 0.0670 chunk 49 optimal weight: 1.9990 chunk 125 optimal weight: 0.9990 chunk 38 optimal weight: 0.0270 chunk 121 optimal weight: 0.9980 chunk 105 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 overall best weight: 0.5976 ------------------------------------------------------------------------------- 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** 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 = 0.4057 r_free = 0.4057 target = 0.181219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.153866 restraints weight = 10149.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.156668 restraints weight = 7480.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.158678 restraints weight = 6138.713| |-----------------------------------------------------------------------------| r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.3652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 9687 Z= 0.241 Angle : 0.536 6.301 13236 Z= 0.278 Chirality : 0.044 0.272 1641 Planarity : 0.005 0.047 1695 Dihedral : 4.132 31.068 1986 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.80 % Allowed : 9.91 % 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: 0.67 (0.23), residues: 1266 helix: 2.21 (0.21), residues: 597 sheet: -0.35 (0.39), residues: 165 loop : -1.52 (0.25), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP C 886 HIS 0.004 0.001 HIS B1064 PHE 0.023 0.001 PHE C 823 TYR 0.020 0.002 TYR A1067 ARG 0.002 0.000 ARG A1019 *********************** 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 93 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 756 TYR cc_start: 0.8290 (m-80) cc_final: 0.7962 (m-80) REVERT: A 917 TYR cc_start: 0.8073 (m-10) cc_final: 0.7747 (m-10) REVERT: A 934 ILE cc_start: 0.8298 (tp) cc_final: 0.7979 (tp) REVERT: B 752 LEU cc_start: 0.8937 (mt) cc_final: 0.8648 (mt) REVERT: C 752 LEU cc_start: 0.8787 (mt) cc_final: 0.8485 (mt) REVERT: C 1014 ARG cc_start: 0.5810 (OUTLIER) cc_final: 0.5044 (mtm180) outliers start: 14 outliers final: 8 residues processed: 92 average time/residue: 0.2109 time to fit residues: 28.1095 Evaluate side-chains 86 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 1.085 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 101 optimal weight: 0.9980 chunk 19 optimal weight: 0.0980 chunk 68 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 chunk 123 optimal weight: 1.9990 chunk 103 optimal weight: 0.0040 chunk 46 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 44 optimal weight: 0.6980 chunk 71 optimal weight: 0.5980 chunk 99 optimal weight: 10.0000 overall best weight: 0.4592 ------------------------------------------------------------------------------- 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 = 0.4060 r_free = 0.4060 target = 0.181260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.154284 restraints weight = 10118.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.157268 restraints weight = 7347.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.158955 restraints weight = 5941.257| |-----------------------------------------------------------------------------| r_work (final): 0.3859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.3846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 9687 Z= 0.195 Angle : 0.504 5.089 13236 Z= 0.260 Chirality : 0.043 0.267 1641 Planarity : 0.004 0.043 1695 Dihedral : 3.937 29.787 1986 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.67 % Allowed : 9.91 % 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: 0.75 (0.24), residues: 1266 helix: 2.30 (0.21), residues: 594 sheet: -0.45 (0.39), residues: 165 loop : -1.44 (0.25), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 886 HIS 0.003 0.001 HIS C1101 PHE 0.021 0.001 PHE C 823 TYR 0.020 0.001 TYR A1067 ARG 0.006 0.000 ARG A1091 *********************** 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 94 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 815 ARG cc_start: 0.6608 (OUTLIER) cc_final: 0.5724 (mtt180) REVERT: A 934 ILE cc_start: 0.8163 (tp) cc_final: 0.7917 (tp) REVERT: A 1091 ARG cc_start: 0.8382 (tpp80) cc_final: 0.8130 (ttm-80) REVERT: B 815 ARG cc_start: 0.6932 (OUTLIER) cc_final: 0.5790 (mtt180) REVERT: C 752 LEU cc_start: 0.8775 (mt) cc_final: 0.8471 (mt) REVERT: C 1014 ARG cc_start: 0.5802 (OUTLIER) cc_final: 0.5063 (mtm180) outliers start: 13 outliers final: 9 residues processed: 93 average time/residue: 0.2436 time to fit residues: 31.3310 Evaluate side-chains 93 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 0.891 ------------------------------------------------------------------------------- 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 882 ILE Chi-restraints excluded: chain C residue 934 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: 0.9980 chunk 16 optimal weight: 0.9990 chunk 106 optimal weight: 0.3980 chunk 46 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 19 optimal weight: 0.0060 chunk 67 optimal weight: 0.6980 chunk 102 optimal weight: 2.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- 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 = 0.4034 r_free = 0.4034 target = 0.178634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.151473 restraints weight = 10274.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.154506 restraints weight = 7401.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.156420 restraints weight = 5944.048| |-----------------------------------------------------------------------------| r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.3985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 9687 Z= 0.228 Angle : 0.517 5.328 13236 Z= 0.266 Chirality : 0.043 0.259 1641 Planarity : 0.004 0.042 1695 Dihedral : 3.942 27.155 1986 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.67 % Allowed : 9.78 % 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 (0.24), residues: 1266 helix: 2.27 (0.21), residues: 597 sheet: -0.30 (0.35), residues: 195 loop : -1.64 (0.25), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP C 886 HIS 0.004 0.001 HIS B1064 PHE 0.019 0.001 PHE C 823 TYR 0.020 0.002 TYR A1067 ARG 0.005 0.000 ARG A1091 *********************** 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 97 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 1.162 Fit side-chains revert: symmetry clash REVERT: A 815 ARG cc_start: 0.6751 (OUTLIER) cc_final: 0.5794 (mtt180) REVERT: A 934 ILE cc_start: 0.8180 (tp) cc_final: 0.7931 (tp) REVERT: A 1011 MET cc_start: 0.6352 (mmt) cc_final: 0.5883 (mmt) REVERT: A 1091 ARG cc_start: 0.8418 (tpp80) cc_final: 0.8216 (ttm-80) REVERT: B 752 LEU cc_start: 0.8908 (mt) cc_final: 0.8552 (mp) REVERT: B 815 ARG cc_start: 0.6866 (OUTLIER) cc_final: 0.5747 (mtt180) REVERT: C 752 LEU cc_start: 0.8823 (mt) cc_final: 0.8500 (mt) outliers start: 13 outliers final: 8 residues processed: 95 average time/residue: 0.2428 time to fit residues: 32.8269 Evaluate side-chains 90 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 time to evaluate : 1.312 ------------------------------------------------------------------------------- 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 C residue 882 ILE Chi-restraints excluded: chain C residue 934 ILE 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 100 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 118 optimal weight: 0.9980 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: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.4021 r_free = 0.4021 target = 0.177082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.149952 restraints weight = 10216.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.152966 restraints weight = 7401.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.154850 restraints weight = 5962.083| |-----------------------------------------------------------------------------| r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.4086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9687 Z= 0.268 Angle : 0.535 5.506 13236 Z= 0.275 Chirality : 0.044 0.262 1641 Planarity : 0.005 0.054 1695 Dihedral : 3.939 26.199 1982 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.03 % Allowed : 10.94 % 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: 0.60 (0.23), residues: 1266 helix: 2.26 (0.21), residues: 594 sheet: -0.41 (0.34), residues: 195 loop : -1.75 (0.25), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 886 HIS 0.004 0.001 HIS A1064 PHE 0.019 0.002 PHE C 823 TYR 0.021 0.002 TYR A1067 ARG 0.005 0.000 ARG A1091 *********************** 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 94 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 86 time to evaluate : 1.037 Fit side-chains revert: symmetry clash REVERT: A 815 ARG cc_start: 0.6712 (OUTLIER) cc_final: 0.5741 (mtt180) REVERT: A 934 ILE cc_start: 0.8221 (tp) cc_final: 0.7982 (tp) REVERT: A 1011 MET cc_start: 0.6352 (mmt) cc_final: 0.5922 (mmt) REVERT: B 815 ARG cc_start: 0.6813 (OUTLIER) cc_final: 0.5750 (mtt180) REVERT: B 992 GLN cc_start: 0.7376 (mm-40) cc_final: 0.7120 (mm-40) REVERT: C 752 LEU cc_start: 0.8834 (mt) cc_final: 0.8523 (mt) outliers start: 8 outliers final: 5 residues processed: 91 average time/residue: 0.1984 time to fit residues: 26.8395 Evaluate side-chains 91 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 84 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 815 ARG 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 1104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 128 optimal weight: 0.1980 chunk 47 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 58 optimal weight: 0.0870 chunk 95 optimal weight: 1.9990 chunk 18 optimal weight: 0.0370 chunk 48 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 70 optimal weight: 0.9990 overall best weight: 0.3838 ------------------------------------------------------------------------------- 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 = 0.3939 r_free = 0.3939 target = 0.171527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.141547 restraints weight = 10541.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.145263 restraints weight = 7063.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.147643 restraints weight = 5413.091| |-----------------------------------------------------------------------------| r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.4168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9687 Z= 0.183 Angle : 0.501 5.253 13236 Z= 0.257 Chirality : 0.043 0.262 1641 Planarity : 0.005 0.057 1695 Dihedral : 3.684 24.106 1980 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.77 % Allowed : 10.94 % 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: 0.73 (0.24), residues: 1266 helix: 2.33 (0.21), residues: 597 sheet: -0.35 (0.35), residues: 195 loop : -1.65 (0.26), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 886 HIS 0.003 0.001 HIS B1088 PHE 0.018 0.001 PHE C 823 TYR 0.020 0.001 TYR A1067 ARG 0.005 0.000 ARG A1091 ********************** 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 87 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 81 time to evaluate : 1.032 Fit side-chains revert: symmetry clash REVERT: A 815 ARG cc_start: 0.6851 (OUTLIER) cc_final: 0.5768 (mtt180) REVERT: A 934 ILE cc_start: 0.8035 (tp) cc_final: 0.7750 (tp) REVERT: A 1111 GLU cc_start: 0.7146 (mm-30) cc_final: 0.6827 (mt-10) REVERT: B 815 ARG cc_start: 0.6918 (OUTLIER) cc_final: 0.5682 (mtt180) REVERT: B 992 GLN cc_start: 0.7486 (mm-40) cc_final: 0.7223 (mm-40) REVERT: C 752 LEU cc_start: 0.8663 (mt) cc_final: 0.8338 (mt) outliers start: 6 outliers final: 4 residues processed: 86 average time/residue: 0.2143 time to fit residues: 26.8601 Evaluate side-chains 83 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 77 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 815 ARG 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 1104 VAL 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: 0.0870 chunk 67 optimal weight: 0.0770 chunk 81 optimal weight: 0.9980 chunk 128 optimal weight: 0.6980 chunk 95 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 124 optimal weight: 0.9980 chunk 71 optimal weight: 0.5980 overall best weight: 0.4716 ------------------------------------------------------------------------------- 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 = 0.3939 r_free = 0.3939 target = 0.171345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.141638 restraints weight = 10451.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.145235 restraints weight = 7106.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.147541 restraints weight = 5494.211| |-----------------------------------------------------------------------------| r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.4253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9687 Z= 0.197 Angle : 0.503 5.181 13236 Z= 0.256 Chirality : 0.043 0.256 1641 Planarity : 0.004 0.053 1695 Dihedral : 3.642 22.936 1980 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.16 % Allowed : 10.55 % 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: 0.74 (0.24), residues: 1266 helix: 2.35 (0.21), residues: 597 sheet: -0.32 (0.35), residues: 195 loop : -1.67 (0.26), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 886 HIS 0.003 0.001 HIS A1064 PHE 0.018 0.001 PHE C 823 TYR 0.020 0.001 TYR C1067 ARG 0.005 0.000 ARG A1091 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2644.07 seconds wall clock time: 48 minutes 38.10 seconds (2918.10 seconds total)