Starting phenix.real_space_refine on Fri Mar 14 03:43:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vqa_43436/03_2025/8vqa_43436.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vqa_43436/03_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_43436/03_2025/8vqa_43436.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vqa_43436/03_2025/8vqa_43436.map" model { file = "/net/cci-nas-00/data/ceres_data/8vqa_43436/03_2025/8vqa_43436.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vqa_43436/03_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 6.43, per 1000 atoms: 0.68 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: 2.82 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: 0.97 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: 2.74 Time building geometry restraints manager: 3.22 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: 3.840 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 25.380 Find NCS groups from input model: 0.400 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: 0.010 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.070 ------------------------------------------------------------------------------- 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 : 0.880 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: 0.3495 time to fit residues: 61.7260 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 : 0.897 ------------------------------------------------------------------------------- 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 9687 Z= 0.216 Angle : 0.598 6.975 13236 Z= 0.322 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 *********************** 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 : 0.942 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: 0.2949 time to fit residues: 32.3880 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 : 1.030 ------------------------------------------------------------------------------- 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: 0.0870 chunk 52 optimal weight: 0.3980 chunk 48 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 overall best weight: 0.3958 ------------------------------------------------------------------------------- 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 = 0.4000 r_free = 0.4000 target = 0.177052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.146348 restraints weight = 9992.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.150288 restraints weight = 6776.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.152606 restraints weight = 5221.547| |-----------------------------------------------------------------------------| r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9687 Z= 0.184 Angle : 0.525 5.920 13236 Z= 0.274 Chirality : 0.044 0.256 1641 Planarity : 0.005 0.050 1695 Dihedral : 4.208 40.848 1986 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.16 % Allowed : 6.82 % Favored : 92.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.24), residues: 1266 helix: 2.58 (0.21), residues: 582 sheet: 0.11 (0.37), residues: 165 loop : -1.20 (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 A1064 PHE 0.010 0.001 PHE C1121 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 104 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 95 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 815 ARG cc_start: 0.6529 (mtt90) cc_final: 0.5426 (mtt180) REVERT: A 917 TYR cc_start: 0.8070 (m-10) cc_final: 0.7869 (m-10) REVERT: B 752 LEU cc_start: 0.8630 (mt) cc_final: 0.8369 (mt) REVERT: B 895 GLN cc_start: 0.6863 (OUTLIER) cc_final: 0.6156 (mt0) REVERT: C 752 LEU cc_start: 0.8563 (mt) cc_final: 0.8265 (mt) REVERT: C 815 ARG cc_start: 0.6896 (mtt90) cc_final: 0.5782 (mtt180) outliers start: 9 outliers final: 3 residues processed: 103 average time/residue: 0.3792 time to fit residues: 50.0134 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 : 1.028 ------------------------------------------------------------------------------- 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: 1.9990 chunk 77 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 86 optimal weight: 0.6980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 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 = 0.4027 r_free = 0.4027 target = 0.178228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.150495 restraints weight = 10202.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.153156 restraints weight = 7616.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.155058 restraints weight = 6282.937| |-----------------------------------------------------------------------------| r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.3237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 9687 Z= 0.351 Angle : 0.639 8.671 13236 Z= 0.332 Chirality : 0.048 0.274 1641 Planarity : 0.005 0.054 1695 Dihedral : 4.577 35.075 1986 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.54 % Allowed : 8.62 % Favored : 89.83 % 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: 0.45 (0.23), residues: 1266 helix: 1.97 (0.21), residues: 597 sheet: -0.12 (0.33), residues: 195 loop : -1.79 (0.25), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.002 TRP C 886 HIS 0.006 0.002 HIS A1064 PHE 0.014 0.002 PHE C 802 TYR 0.021 0.002 TYR A1067 ARG 0.004 0.000 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 96 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 1.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 815 ARG cc_start: 0.6712 (OUTLIER) cc_final: 0.5713 (mtt180) REVERT: A 917 TYR cc_start: 0.8289 (m-10) cc_final: 0.8018 (m-10) REVERT: A 1031 GLU cc_start: 0.7687 (mt-10) cc_final: 0.7467 (mt-10) REVERT: B 752 LEU cc_start: 0.8958 (mt) cc_final: 0.8654 (mt) REVERT: B 815 ARG cc_start: 0.6806 (OUTLIER) cc_final: 0.5724 (mtt180) REVERT: C 752 LEU cc_start: 0.8901 (mt) cc_final: 0.8550 (mt) outliers start: 12 outliers final: 9 residues processed: 95 average time/residue: 0.3298 time to fit residues: 42.0611 Evaluate side-chains 85 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 1.119 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 101 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 115 optimal weight: 0.9980 chunk 102 optimal weight: 0.3980 chunk 116 optimal weight: 0.7980 chunk 76 optimal weight: 0.5980 chunk 90 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 121 optimal weight: 0.5980 chunk 51 optimal weight: 0.6980 chunk 98 optimal weight: 4.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1101 HIS C1106 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.181296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.154842 restraints weight = 10206.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.157409 restraints weight = 7877.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.158845 restraints weight = 6637.906| |-----------------------------------------------------------------------------| r_work (final): 0.3834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.3410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9687 Z= 0.217 Angle : 0.526 5.573 13236 Z= 0.270 Chirality : 0.044 0.279 1641 Planarity : 0.005 0.049 1695 Dihedral : 4.240 33.339 1986 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % 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: -0.26 (0.37), residues: 165 loop : -1.55 (0.25), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP C 886 HIS 0.003 0.001 HIS C1088 PHE 0.014 0.001 PHE C1121 TYR 0.020 0.001 TYR C1067 ARG 0.002 0.000 ARG C 995 *********************** 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 : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 756 TYR cc_start: 0.8234 (m-80) cc_final: 0.8023 (m-80) REVERT: A 917 TYR cc_start: 0.8104 (m-10) cc_final: 0.7837 (m-10) REVERT: A 1011 MET cc_start: 0.6611 (mmt) cc_final: 0.6264 (mmt) REVERT: A 1031 GLU cc_start: 0.7650 (mt-10) cc_final: 0.7443 (mt-10) REVERT: B 752 LEU cc_start: 0.8851 (mt) cc_final: 0.8531 (mt) REVERT: B 1011 MET cc_start: 0.6343 (mmt) cc_final: 0.6012 (mmt) REVERT: C 752 LEU cc_start: 0.8822 (mt) cc_final: 0.8498 (mt) REVERT: C 815 ARG cc_start: 0.6805 (mtt90) cc_final: 0.5908 (mtt180) REVERT: C 1014 ARG cc_start: 0.5923 (OUTLIER) cc_final: 0.5154 (mtm180) outliers start: 10 outliers final: 5 residues processed: 92 average time/residue: 0.2510 time to fit residues: 31.9324 Evaluate side-chains 84 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 78 time to evaluate : 0.962 ------------------------------------------------------------------------------- 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 1074 ASN Chi-restraints excluded: chain C residue 1014 ARG Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 80 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 chunk 90 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 125 optimal weight: 0.3980 chunk 38 optimal weight: 0.9980 chunk 121 optimal weight: 0.9990 chunk 105 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1106 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.178189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.151101 restraints weight = 10237.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.153763 restraints weight = 7622.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.155646 restraints weight = 6300.238| |-----------------------------------------------------------------------------| r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.3760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 9687 Z= 0.288 Angle : 0.571 6.071 13236 Z= 0.296 Chirality : 0.045 0.271 1641 Planarity : 0.005 0.046 1695 Dihedral : 4.323 29.676 1986 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.45 % Allowed : 9.40 % 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: 0.45 (0.23), residues: 1266 helix: 2.03 (0.21), residues: 594 sheet: -0.37 (0.39), residues: 165 loop : -1.65 (0.24), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 886 HIS 0.005 0.002 HIS A1064 PHE 0.015 0.002 PHE B1121 TYR 0.021 0.002 TYR A 789 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 100 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 81 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 756 TYR cc_start: 0.8328 (m-80) cc_final: 0.7992 (m-80) REVERT: A 815 ARG cc_start: 0.6531 (OUTLIER) cc_final: 0.5604 (mtt180) REVERT: A 917 TYR cc_start: 0.8150 (m-10) cc_final: 0.7886 (m-10) REVERT: A 934 ILE cc_start: 0.8318 (tp) cc_final: 0.8030 (tp) REVERT: A 1031 GLU cc_start: 0.7753 (mt-10) cc_final: 0.7521 (mt-10) REVERT: A 1091 ARG cc_start: 0.8545 (tpp-160) cc_final: 0.8315 (tpp80) REVERT: B 815 ARG cc_start: 0.6814 (OUTLIER) cc_final: 0.5678 (mtt180) REVERT: C 752 LEU cc_start: 0.8875 (mt) cc_final: 0.8561 (mt) REVERT: C 1014 ARG cc_start: 0.6001 (OUTLIER) cc_final: 0.5227 (mtm180) outliers start: 19 outliers final: 9 residues processed: 98 average time/residue: 0.2468 time to fit residues: 33.3640 Evaluate side-chains 91 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 729 VAL 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 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 ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/iotbx/cli_parser.py", line 980, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 51.9149 > 50: distance: 41 - 82: 28.697 distance: 44 - 79: 12.892 distance: 65 - 66: 4.139 distance: 66 - 67: 4.313 distance: 66 - 69: 4.528 distance: 67 - 68: 12.402 distance: 67 - 74: 16.381 distance: 69 - 70: 4.255 distance: 72 - 73: 3.132 distance: 74 - 75: 10.715 distance: 75 - 76: 11.125 distance: 75 - 78: 7.219 distance: 76 - 77: 7.566 distance: 76 - 79: 13.850 distance: 79 - 80: 21.967 distance: 80 - 81: 37.833 distance: 80 - 83: 13.578 distance: 81 - 82: 32.617 distance: 81 - 89: 9.710 distance: 83 - 84: 7.870 distance: 84 - 85: 12.940 distance: 84 - 86: 5.792 distance: 85 - 87: 9.342 distance: 86 - 88: 10.351 distance: 87 - 88: 6.467 distance: 89 - 90: 18.019 distance: 89 - 196: 14.042 distance: 90 - 91: 7.883 distance: 90 - 93: 20.784 distance: 91 - 92: 17.668 distance: 91 - 100: 27.534 distance: 92 - 193: 11.148 distance: 93 - 94: 8.441 distance: 94 - 95: 14.502 distance: 94 - 96: 12.325 distance: 95 - 97: 7.139 distance: 96 - 98: 14.590 distance: 97 - 99: 14.056 distance: 98 - 99: 17.906 distance: 100 - 101: 22.785 distance: 100 - 106: 14.150 distance: 101 - 102: 17.413 distance: 101 - 104: 13.957 distance: 102 - 103: 16.877 distance: 102 - 107: 19.652 distance: 104 - 105: 11.698 distance: 105 - 106: 9.609 distance: 107 - 108: 23.275 distance: 108 - 109: 29.866 distance: 108 - 111: 15.717 distance: 109 - 110: 14.424 distance: 109 - 118: 41.642 distance: 111 - 112: 6.055 distance: 112 - 113: 4.886 distance: 113 - 114: 3.907 distance: 115 - 117: 3.796 distance: 118 - 119: 24.846 distance: 119 - 120: 28.676 distance: 119 - 122: 21.581 distance: 120 - 121: 34.851 distance: 120 - 123: 23.798 distance: 123 - 124: 29.721 distance: 124 - 125: 28.353 distance: 125 - 126: 23.677 distance: 125 - 127: 22.613 distance: 127 - 128: 6.562 distance: 127 - 167: 10.870 distance: 128 - 129: 12.598 distance: 128 - 131: 7.598 distance: 129 - 130: 12.084 distance: 129 - 134: 8.287 distance: 130 - 164: 18.767 distance: 131 - 132: 6.710 distance: 131 - 133: 16.000 distance: 134 - 135: 15.027 distance: 135 - 136: 12.027 distance: 135 - 138: 11.016 distance: 136 - 137: 15.865 distance: 136 - 145: 16.548 distance: 138 - 139: 10.570 distance: 139 - 141: 7.630 distance: 140 - 142: 6.053 distance: 141 - 143: 10.195 distance: 142 - 144: 11.452 distance: 143 - 144: 11.795