Starting phenix.real_space_refine on Fri Jul 3 15:33:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6nn6_0458/07_2026/6nn6_0458.cif Found real_map, /net/cci-nas-00/data/ceres_data/6nn6_0458/07_2026/6nn6_0458.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6nn6_0458/07_2026/6nn6_0458.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6nn6_0458/07_2026/6nn6_0458.map" model { file = "/net/cci-nas-00/data/ceres_data/6nn6_0458/07_2026/6nn6_0458.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6nn6_0458/07_2026/6nn6_0458.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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: 5 Type Number sf(0) Gaussians P 288 5.49 5 S 27 5.16 5 C 8631 2.51 5 N 2781 2.21 5 O 3398 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15125 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "C" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 804 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "D" Number of atoms: 723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 723 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "G" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 809 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "H" Number of atoms: 723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 723 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2952 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2987 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "K" Number of atoms: 2671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2671 Classifications: {'peptide': 328} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 309} Chain: "L" Number of atoms: 593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 593 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N LEU L 73 " occ=0.45 ... (6 atoms not shown) pdb=" CD2 LEU L 73 " occ=0.45 residue: pdb=" N ARG L 74 " occ=0.45 ... (9 atoms not shown) pdb=" NH2 ARG L 74 " occ=0.45 Time building chain proxies: 3.30, per 1000 atoms: 0.22 Number of scatterers: 15125 At special positions: 0 Unit cell: (124.2, 117.72, 116.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 27 16.00 P 288 15.00 O 3398 8.00 N 2781 7.00 C 8631 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 1.19 Conformation dependent library (CDL) restraints added in 532.1 milliseconds 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2164 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 10 sheets defined 56.5% alpha, 5.4% beta 115 base pairs and 212 stacking pairs defined. Time for finding SS restraints: 2.14 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 removed outlier: 3.599A pdb=" N ARG A 49 " --> pdb=" O THR A 45 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG A 52 " --> pdb=" O LEU A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 75 removed outlier: 4.035A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLN A 68 " --> pdb=" O LYS A 64 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLU A 73 " --> pdb=" O ARG A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 78 No H-bonds generated for 'chain 'A' and resid 76 through 78' Processing helix chain 'A' and resid 87 through 114 removed outlier: 3.625A pdb=" N LEU A 100 " --> pdb=" O SER A 96 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ALA A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N CYS A 110 " --> pdb=" O ASP A 106 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE A 112 " --> pdb=" O ASN A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.809A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LEU A 126 " --> pdb=" O LYS A 122 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG A 129 " --> pdb=" O GLN A 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 removed outlier: 3.775A pdb=" N ILE B 34 " --> pdb=" O THR B 30 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG B 39 " --> pdb=" O ARG B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.579A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLY B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LYS B 59 " --> pdb=" O ARG B 55 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASN B 64 " --> pdb=" O VAL B 60 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL B 65 " --> pdb=" O PHE B 61 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 removed outlier: 4.084A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL B 87 " --> pdb=" O ALA B 83 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N TYR B 88 " --> pdb=" O MET B 84 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ARG B 92 " --> pdb=" O TYR B 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 37 removed outlier: 4.024A pdb=" N ARG C 35 " --> pdb=" O HIS C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 72 removed outlier: 3.506A pdb=" N GLU C 56 " --> pdb=" O ALA C 52 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU C 63 " --> pdb=" O THR C 59 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLU C 64 " --> pdb=" O ALA C 60 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN C 68 " --> pdb=" O GLU C 64 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA C 69 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG C 71 " --> pdb=" O GLY C 67 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ASP C 72 " --> pdb=" O ASN C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 88 removed outlier: 3.551A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN C 84 " --> pdb=" O PRO C 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 49 removed outlier: 3.583A pdb=" N VAL D 48 " --> pdb=" O VAL D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 84 removed outlier: 3.715A pdb=" N ILE D 61 " --> pdb=" O LYS D 57 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N MET D 62 " --> pdb=" O ALA D 58 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL D 66 " --> pdb=" O MET D 62 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLU D 71 " --> pdb=" O ASN D 67 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N SER D 78 " --> pdb=" O ALA D 74 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA D 81 " --> pdb=" O ALA D 77 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N HIS D 82 " --> pdb=" O SER D 78 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TYR D 83 " --> pdb=" O ARG D 79 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 4.360A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN D 95 " --> pdb=" O SER D 91 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG D 99 " --> pdb=" O GLN D 95 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU D 100 " --> pdb=" O THR D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 124 removed outlier: 3.603A pdb=" N ALA D 107 " --> pdb=" O PRO D 103 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N HIS D 109 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER D 112 " --> pdb=" O LYS D 108 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS D 116 " --> pdb=" O SER D 112 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ALA D 117 " --> pdb=" O GLU D 113 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA D 124 " --> pdb=" O CYS D 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 55 removed outlier: 4.125A pdb=" N ARG E 52 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 75 removed outlier: 3.808A pdb=" N GLU E 73 " --> pdb=" O ARG E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 78 No H-bonds generated for 'chain 'E' and resid 76 through 78' Processing helix chain 'E' and resid 86 through 114 removed outlier: 3.684A pdb=" N MET E 90 " --> pdb=" O SER E 86 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N LEU E 92 " --> pdb=" O ALA E 88 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA E 98 " --> pdb=" O GLU E 94 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA E 102 " --> pdb=" O ALA E 98 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU E 105 " --> pdb=" O VAL E 101 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU E 109 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N CYS E 110 " --> pdb=" O ASP E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 131 removed outlier: 4.002A pdb=" N ARG E 129 " --> pdb=" O GLN E 125 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG E 131 " --> pdb=" O ALA E 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 42 removed outlier: 3.568A pdb=" N ARG F 40 " --> pdb=" O ARG F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 76 removed outlier: 3.902A pdb=" N GLU F 63 " --> pdb=" O LYS F 59 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ARG F 67 " --> pdb=" O GLU F 63 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 4.094A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 removed outlier: 3.659A pdb=" N ALA G 21 " --> pdb=" O ARG G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 34 removed outlier: 3.573A pdb=" N HIS G 31 " --> pdb=" O VAL G 27 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 71 removed outlier: 3.841A pdb=" N VAL G 54 " --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG G 71 " --> pdb=" O GLY G 67 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 removed outlier: 3.773A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN G 84 " --> pdb=" O PRO G 80 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN G 89 " --> pdb=" O LEU G 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 97 removed outlier: 3.688A pdb=" N LYS G 95 " --> pdb=" O GLU G 91 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU G 96 " --> pdb=" O GLU G 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 47 removed outlier: 3.765A pdb=" N VAL H 41 " --> pdb=" O TYR H 37 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N TYR H 42 " --> pdb=" O ALA H 38 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS H 43 " --> pdb=" O ILE H 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 58 through 74 removed outlier: 3.874A pdb=" N MET H 62 " --> pdb=" O ALA H 58 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER H 64 " --> pdb=" O SER H 60 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL H 66 " --> pdb=" O MET H 62 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASN H 67 " --> pdb=" O ASN H 63 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ASP H 68 " --> pdb=" O SER H 64 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU H 71 " --> pdb=" O ASN H 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 76 through 83 removed outlier: 3.810A pdb=" N HIS H 82 " --> pdb=" O SER H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 92 through 102 removed outlier: 4.040A pdb=" N LEU H 100 " --> pdb=" O THR H 96 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU H 101 " --> pdb=" O ALA H 97 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 124 removed outlier: 3.564A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N HIS H 109 " --> pdb=" O GLU H 105 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N SER H 112 " --> pdb=" O LYS H 108 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA H 117 " --> pdb=" O GLU H 113 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA H 124 " --> pdb=" O CYS H 120 " (cutoff:3.500A) Processing helix chain 'K' and resid 32 through 45 removed outlier: 3.628A pdb=" N ILE K 37 " --> pdb=" O ALA K 33 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ILE K 38 " --> pdb=" O ALA K 34 " (cutoff:3.500A) Processing helix chain 'K' and resid 48 through 57 removed outlier: 3.641A pdb=" N LEU K 53 " --> pdb=" O PRO K 49 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA K 54 " --> pdb=" O ASP K 50 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASN K 57 " --> pdb=" O LEU K 53 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 90 removed outlier: 3.576A pdb=" N LEU K 74 " --> pdb=" O SER K 70 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA K 81 " --> pdb=" O LYS K 77 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASP K 83 " --> pdb=" O ASN K 79 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER K 84 " --> pdb=" O ARG K 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 103 through 118 removed outlier: 3.680A pdb=" N HIS K 109 " --> pdb=" O GLY K 105 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU K 111 " --> pdb=" O LEU K 107 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLN K 112 " --> pdb=" O ARG K 108 " (cutoff:3.500A) Processing helix chain 'K' and resid 122 through 127 removed outlier: 3.637A pdb=" N ASN K 127 " --> pdb=" O LYS K 124 " (cutoff:3.500A) Processing helix chain 'K' and resid 140 through 151 removed outlier: 3.890A pdb=" N VAL K 144 " --> pdb=" O SER K 140 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA K 145 " --> pdb=" O PHE K 141 " (cutoff:3.500A) Processing helix chain 'K' and resid 167 through 175 Processing helix chain 'K' and resid 189 through 209 removed outlier: 4.300A pdb=" N THR K 197 " --> pdb=" O LYS K 193 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE K 202 " --> pdb=" O MET K 198 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS K 207 " --> pdb=" O ARG K 203 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N TYR K 209 " --> pdb=" O TRP K 205 " (cutoff:3.500A) Processing helix chain 'K' and resid 227 through 233 removed outlier: 3.880A pdb=" N ARG K 231 " --> pdb=" O GLU K 227 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA K 233 " --> pdb=" O ARG K 229 " (cutoff:3.500A) Processing helix chain 'K' and resid 246 through 257 Processing helix chain 'K' and resid 286 through 289 removed outlier: 3.686A pdb=" N THR K 289 " --> pdb=" O ASP K 286 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 286 through 289' Processing helix chain 'K' and resid 319 through 331 removed outlier: 4.259A pdb=" N GLU K 323 " --> pdb=" O ARG K 319 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN K 324 " --> pdb=" O THR K 320 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LYS K 330 " --> pdb=" O PHE K 326 " (cutoff:3.500A) Processing helix chain 'L' and resid 22 through 34 Processing helix chain 'L' and resid 37 through 39 No H-bonds generated for 'chain 'L' and resid 37 through 39' Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.943A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.498A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.173A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA5, first strand: chain 'C' and resid 101 through 102 removed outlier: 7.116A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.837A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'K' and resid 6 through 9 removed outlier: 3.603A pdb=" N LEU K 9 " --> pdb=" O ALA K 18 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA K 18 " --> pdb=" O LEU K 9 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'K' and resid 218 through 220 removed outlier: 5.792A pdb=" N GLY K 184 " --> pdb=" O GLU K 219 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N VAL K 185 " --> pdb=" O PHE K 159 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ASP K 161 " --> pdb=" O VAL K 185 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE K 266 " --> pdb=" O HIS K 315 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 12 through 16 removed outlier: 3.642A pdb=" N VAL L 5 " --> pdb=" O ILE L 13 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU L 15 " --> pdb=" O ILE L 3 " (cutoff:3.500A) removed outlier: 9.416A pdb=" N LEU L 67 " --> pdb=" O GLN L 2 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N PHE L 4 " --> pdb=" O LEU L 67 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N LEU L 69 " --> pdb=" O PHE L 4 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N LYS L 6 " --> pdb=" O LEU L 69 " (cutoff:3.500A) removed outlier: 9.196A pdb=" N LEU L 71 " --> pdb=" O LYS L 6 " (cutoff:3.500A) 366 hydrogen bonds defined for protein. 1086 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 271 hydrogen bonds 486 hydrogen bond angles 0 basepair planarities 115 basepair parallelities 212 stacking parallelities Total time for adding SS restraints: 2.95 Time building geometry restraints manager: 1.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2821 1.33 - 1.45: 5116 1.45 - 1.57: 7443 1.57 - 1.69: 576 1.69 - 1.82: 47 Bond restraints: 16003 Sorted by residual: bond pdb=" C3' DG I -30 " pdb=" C2' DG I -30 " ideal model delta sigma weight residual 1.516 1.551 -0.035 8.00e-03 1.56e+04 1.90e+01 bond pdb=" C3' DA I -54 " pdb=" O3' DA I -54 " ideal model delta sigma weight residual 1.435 1.381 0.054 1.30e-02 5.92e+03 1.76e+01 bond pdb=" C3' DC I -63 " pdb=" C2' DC I -63 " ideal model delta sigma weight residual 1.516 1.547 -0.031 8.00e-03 1.56e+04 1.54e+01 bond pdb=" C LEU A 65 " pdb=" N PRO A 66 " ideal model delta sigma weight residual 1.336 1.381 -0.046 1.23e-02 6.61e+03 1.37e+01 bond pdb=" C3' DC J 37 " pdb=" C2' DC J 37 " ideal model delta sigma weight residual 1.516 1.546 -0.030 8.00e-03 1.56e+04 1.37e+01 ... (remaining 15998 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 20107 1.66 - 3.31: 2447 3.31 - 4.97: 265 4.97 - 6.62: 34 6.62 - 8.28: 24 Bond angle restraints: 22877 Sorted by residual: angle pdb=" O4' DT J -59 " pdb=" C4' DT J -59 " pdb=" C3' DT J -59 " ideal model delta sigma weight residual 106.00 102.43 3.57 6.00e-01 2.78e+00 3.53e+01 angle pdb=" O4' DC J 52 " pdb=" C4' DC J 52 " pdb=" C3' DC J 52 " ideal model delta sigma weight residual 106.00 102.83 3.17 6.00e-01 2.78e+00 2.80e+01 angle pdb=" O4' DC I -63 " pdb=" C1' DC I -63 " pdb=" N1 DC I -63 " ideal model delta sigma weight residual 108.00 111.51 -3.51 7.00e-01 2.04e+00 2.52e+01 angle pdb=" C4' DC I -63 " pdb=" O4' DC I -63 " pdb=" C1' DC I -63 " ideal model delta sigma weight residual 110.10 105.32 4.78 1.00e+00 1.00e+00 2.29e+01 angle pdb=" O4' DA J -1 " pdb=" C4' DA J -1 " pdb=" C3' DA J -1 " ideal model delta sigma weight residual 106.00 103.15 2.85 6.00e-01 2.78e+00 2.25e+01 ... (remaining 22872 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.46: 7467 35.46 - 70.91: 1377 70.91 - 106.37: 42 106.37 - 141.82: 5 141.82 - 177.28: 1 Dihedral angle restraints: 8892 sinusoidal: 5543 harmonic: 3349 Sorted by residual: dihedral pdb=" CA LEU D 100 " pdb=" C LEU D 100 " pdb=" N LEU D 101 " pdb=" CA LEU D 101 " ideal model delta harmonic sigma weight residual -180.00 -150.22 -29.78 0 5.00e+00 4.00e-02 3.55e+01 dihedral pdb=" CA ILE F 29 " pdb=" C ILE F 29 " pdb=" N THR F 30 " pdb=" CA THR F 30 " ideal model delta harmonic sigma weight residual 180.00 -156.34 -23.66 0 5.00e+00 4.00e-02 2.24e+01 dihedral pdb=" CA SER H 60 " pdb=" C SER H 60 " pdb=" N ILE H 61 " pdb=" CA ILE H 61 " ideal model delta harmonic sigma weight residual 180.00 158.30 21.70 0 5.00e+00 4.00e-02 1.88e+01 ... (remaining 8889 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1651 0.052 - 0.103: 739 0.103 - 0.155: 180 0.155 - 0.207: 17 0.207 - 0.259: 2 Chirality restraints: 2589 Sorted by residual: chirality pdb=" CB ILE K 279 " pdb=" CA ILE K 279 " pdb=" CG1 ILE K 279 " pdb=" CG2 ILE K 279 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" C3' DC I -29 " pdb=" C4' DC I -29 " pdb=" O3' DC I -29 " pdb=" C2' DC I -29 " both_signs ideal model delta sigma weight residual False -2.73 -2.52 -0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA LEU A 65 " pdb=" N LEU A 65 " pdb=" C LEU A 65 " pdb=" CB LEU A 65 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 2586 not shown) Planarity restraints: 1901 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR H 40 " -0.022 2.00e-02 2.50e+03 2.12e-02 8.96e+00 pdb=" CG TYR H 40 " 0.049 2.00e-02 2.50e+03 pdb=" CD1 TYR H 40 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR H 40 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR H 40 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR H 40 " -0.018 2.00e-02 2.50e+03 pdb=" CZ TYR H 40 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR H 40 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER K 132 " 0.040 5.00e-02 4.00e+02 6.09e-02 5.94e+00 pdb=" N PRO K 133 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO K 133 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO K 133 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE G 79 " 0.040 5.00e-02 4.00e+02 5.98e-02 5.72e+00 pdb=" N PRO G 80 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO G 80 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO G 80 " 0.033 5.00e-02 4.00e+02 ... (remaining 1898 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.70: 978 2.70 - 3.25: 13268 3.25 - 3.80: 27575 3.80 - 4.35: 34217 4.35 - 4.90: 49936 Nonbonded interactions: 125974 Sorted by model distance: nonbonded pdb=" O ILE E 62 " pdb=" O ARG E 63 " model vdw 2.144 3.040 nonbonded pdb=" OE2 GLU C 56 " pdb=" NH2 ARG K 282 " model vdw 2.267 3.120 nonbonded pdb=" OH TYR K 136 " pdb=" OE2 GLU K 138 " model vdw 2.273 3.040 nonbonded pdb=" O LYS C 15 " pdb=" O THR C 16 " model vdw 2.274 3.040 nonbonded pdb=" O2 DC I 56 " pdb=" N2 DG J -56 " model vdw 2.284 3.120 ... (remaining 125969 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' and resid 39 through 134) selection = (chain 'E' and resid 39 through 134) } ncs_group { reference = (chain 'B' and resid 25 through 101) selection = (chain 'F' and resid 25 through 101) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 15 through 118) } ncs_group { reference = chain 'D' selection = chain 'H' } 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=0.45 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: 3.150 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: 0.230 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 16.070 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 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 : 0.010 0.100 16003 Z= 0.742 Angle : 1.106 8.280 22877 Z= 0.827 Chirality : 0.057 0.259 2589 Planarity : 0.007 0.061 1901 Dihedral : 25.945 177.280 6728 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.81 % Favored : 96.01 % Rotamer: Outliers : 0.81 % Allowed : 1.73 % Favored : 97.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.04 (0.18), residues: 1129 helix: -4.32 (0.09), residues: 622 sheet: -1.07 (0.58), residues: 74 loop : -1.83 (0.25), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 128 TYR 0.049 0.004 TYR H 40 PHE 0.022 0.003 PHE B 100 TRP 0.023 0.003 TRP K 228 HIS 0.020 0.003 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.01019 / 0.74 (16003) covalent geometry : angle 1.10632 / 0.83 (22877) hydrogen bonds : bond 0.34078 / 22.46 ( 637) hydrogen bonds : angle 10.56686 / 7.09 ( 1572) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 364 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 THR cc_start: 0.9345 (m) cc_final: 0.8720 (p) REVERT: B 53 GLU cc_start: 0.8396 (tp30) cc_final: 0.8048 (tp30) REVERT: C 91 GLU cc_start: 0.8262 (tm-30) cc_final: 0.8035 (tp30) REVERT: C 94 ASN cc_start: 0.8724 (t0) cc_final: 0.8483 (t0) REVERT: C 95 LYS cc_start: 0.8955 (ttmt) cc_final: 0.8673 (mttm) REVERT: D 42 TYR cc_start: 0.7942 (t80) cc_final: 0.7541 (t80) REVERT: D 87 SER cc_start: 0.8668 (m) cc_final: 0.8441 (t) REVERT: E 122 LYS cc_start: 0.9370 (ptpt) cc_final: 0.9085 (ptpp) REVERT: F 59 LYS cc_start: 0.8846 (tttp) cc_final: 0.8639 (tttm) REVERT: G 61 GLU cc_start: 0.8581 (tp30) cc_final: 0.8157 (tp30) REVERT: G 74 LYS cc_start: 0.8904 (mppt) cc_final: 0.8395 (mmtp) REVERT: G 112 GLN cc_start: 0.8827 (mm-40) cc_final: 0.8429 (mm-40) REVERT: H 32 THR cc_start: 0.7817 (p) cc_final: 0.7519 (p) REVERT: H 43 LYS cc_start: 0.9214 (mttt) cc_final: 0.8842 (mttp) REVERT: H 76 GLU cc_start: 0.8449 (tp30) cc_final: 0.8115 (tp30) REVERT: H 87 SER cc_start: 0.8994 (m) cc_final: 0.8635 (p) REVERT: K 71 MET cc_start: 0.5125 (mmm) cc_final: 0.4323 (mmm) REVERT: K 149 ASP cc_start: 0.6601 (m-30) cc_final: 0.6289 (m-30) REVERT: K 189 ASP cc_start: 0.7951 (m-30) cc_final: 0.7277 (p0) REVERT: K 198 MET cc_start: 0.2109 (mmm) cc_final: 0.1409 (mmm) REVERT: K 205 TRP cc_start: 0.5089 (m100) cc_final: 0.4829 (m100) REVERT: K 206 MET cc_start: 0.6165 (mmm) cc_final: 0.5609 (ppp) REVERT: K 252 GLN cc_start: 0.7306 (mt0) cc_final: 0.6991 (mp10) REVERT: K 291 MET cc_start: 0.8538 (ptp) cc_final: 0.8209 (ptp) REVERT: L 51 GLU cc_start: 0.7849 (tt0) cc_final: 0.7308 (mp0) outliers start: 8 outliers final: 3 residues processed: 368 average time/residue: 0.1901 time to fit residues: 92.0275 Evaluate side-chains 249 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 246 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 79 ARG Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain K residue 282 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 98 optimal weight: 20.0000 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 9.9990 chunk 55 optimal weight: 0.7980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN A 108 ASN A 125 GLN C 110 ASN D 67 ASN E 68 GLN E 76 GLN G 84 GLN G 104 GLN H 67 ASN K 109 HIS K 113 GLN K 259 ASN K 315 HIS L 40 GLN ** L 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 60 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.127962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.092055 restraints weight = 43736.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.091744 restraints weight = 30632.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.091919 restraints weight = 26688.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.092003 restraints weight = 23478.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.092086 restraints weight = 21493.840| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3312 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3312 r_free = 0.3312 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3311 r_free = 0.3311 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (10 function evaluations) r_final: 0.3311 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 16003 Z= 0.233 Angle : 0.845 10.523 22877 Z= 0.474 Chirality : 0.055 0.309 2589 Planarity : 0.006 0.045 1901 Dihedral : 31.051 172.824 4451 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 3.66 % Allowed : 10.26 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.20 (0.21), residues: 1129 helix: -2.49 (0.16), residues: 642 sheet: -0.86 (0.58), residues: 77 loop : -1.39 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 20 TYR 0.018 0.002 TYR E 99 PHE 0.026 0.002 PHE L 45 TRP 0.009 0.001 TRP K 208 HIS 0.009 0.002 HIS K 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.23 (16003) covalent geometry : angle 0.84526 / 0.47 (22877) hydrogen bonds : bond 0.11236 / 7.06 ( 637) hydrogen bonds : angle 4.84093 / 3.31 ( 1572) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 279 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 ASN cc_start: 0.8867 (OUTLIER) cc_final: 0.8576 (t0) REVERT: A 118 THR cc_start: 0.9475 (m) cc_final: 0.8944 (p) REVERT: A 120 MET cc_start: 0.8403 (OUTLIER) cc_final: 0.7974 (mtt) REVERT: B 24 ASP cc_start: 0.5994 (t0) cc_final: 0.5683 (t0) REVERT: B 64 ASN cc_start: 0.9277 (m-40) cc_final: 0.9004 (m-40) REVERT: C 95 LYS cc_start: 0.8951 (ttmt) cc_final: 0.8739 (mttm) REVERT: C 115 LEU cc_start: 0.8790 (mt) cc_final: 0.8512 (mt) REVERT: D 42 TYR cc_start: 0.7876 (t80) cc_final: 0.7612 (t80) REVERT: D 79 ARG cc_start: 0.8384 (OUTLIER) cc_final: 0.7950 (mtp85) REVERT: D 86 ARG cc_start: 0.8139 (OUTLIER) cc_final: 0.7398 (mtm-85) REVERT: D 87 SER cc_start: 0.8764 (m) cc_final: 0.8352 (t) REVERT: E 63 ARG cc_start: 0.8233 (OUTLIER) cc_final: 0.7659 (mmp-170) REVERT: E 122 LYS cc_start: 0.9300 (ptpt) cc_final: 0.9050 (ptpp) REVERT: F 80 THR cc_start: 0.9289 (m) cc_final: 0.8884 (p) REVERT: F 91 LYS cc_start: 0.9214 (ttmt) cc_final: 0.8953 (ttpp) REVERT: G 38 ASN cc_start: 0.8316 (m-40) cc_final: 0.7956 (m110) REVERT: G 74 LYS cc_start: 0.8990 (mppt) cc_final: 0.8716 (mtmm) REVERT: H 62 MET cc_start: 0.9193 (mmm) cc_final: 0.8921 (mmp) REVERT: K 55 MET cc_start: -0.1590 (mmp) cc_final: -0.1966 (mmt) REVERT: K 108 ARG cc_start: 0.7223 (ttm110) cc_final: 0.6928 (tpt170) REVERT: K 198 MET cc_start: 0.1890 (mmm) cc_final: 0.0729 (mmm) REVERT: K 206 MET cc_start: 0.6064 (mmm) cc_final: 0.5520 (ppp) REVERT: K 212 LYS cc_start: 0.2581 (tptt) cc_final: 0.1806 (tptm) REVERT: K 282 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.7849 (ttm-80) REVERT: L 51 GLU cc_start: 0.7624 (tt0) cc_final: 0.7129 (mp0) outliers start: 36 outliers final: 20 residues processed: 301 average time/residue: 0.1440 time to fit residues: 60.2587 Evaluate side-chains 274 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 248 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 79 ARG Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 86 ARG Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 84 GLN Chi-restraints excluded: chain H residue 108 LYS Chi-restraints excluded: chain K residue 275 LEU Chi-restraints excluded: chain K residue 282 ARG Chi-restraints excluded: chain K residue 318 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 116 optimal weight: 10.0000 chunk 81 optimal weight: 10.0000 chunk 113 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 chunk 105 optimal weight: 4.9990 chunk 85 optimal weight: 30.0000 chunk 74 optimal weight: 9.9990 chunk 64 optimal weight: 0.0030 chunk 119 optimal weight: 2.9990 overall best weight: 0.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN E 68 GLN G 84 GLN H 63 ASN H 67 ASN L 40 GLN ** L 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.129346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.093875 restraints weight = 43654.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.093260 restraints weight = 35533.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.093456 restraints weight = 31667.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.093547 restraints weight = 26908.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.093595 restraints weight = 24642.117| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3340 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3340 r_free = 0.3340 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3340 r_free = 0.3340 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3340 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16003 Z= 0.173 Angle : 0.714 8.037 22877 Z= 0.415 Chirality : 0.049 0.247 2589 Planarity : 0.004 0.035 1901 Dihedral : 30.844 177.760 4451 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.05 % Allowed : 14.13 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.16 (0.23), residues: 1129 helix: -1.49 (0.18), residues: 642 sheet: -1.14 (0.58), residues: 78 loop : -1.06 (0.29), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 229 TYR 0.022 0.002 TYR D 40 PHE 0.019 0.001 PHE K 159 TRP 0.014 0.002 TRP K 228 HIS 0.006 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.17 (16003) covalent geometry : angle 0.71446 / 0.41 (22877) hydrogen bonds : bond 0.09647 / 6.10 ( 637) hydrogen bonds : angle 4.17251 / 2.87 ( 1572) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 267 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8498 (OUTLIER) cc_final: 0.8031 (mtt) REVERT: B 43 VAL cc_start: 0.8848 (t) cc_final: 0.8531 (m) REVERT: C 91 GLU cc_start: 0.8343 (tp30) cc_final: 0.7663 (tp30) REVERT: D 42 TYR cc_start: 0.7925 (t80) cc_final: 0.7695 (t80) REVERT: D 59 MET cc_start: 0.8763 (tpt) cc_final: 0.8317 (tpp) REVERT: D 86 ARG cc_start: 0.8234 (OUTLIER) cc_final: 0.7498 (mtm-85) REVERT: D 87 SER cc_start: 0.8861 (m) cc_final: 0.8421 (t) REVERT: E 122 LYS cc_start: 0.9307 (ptpt) cc_final: 0.9068 (ptpp) REVERT: F 80 THR cc_start: 0.9381 (m) cc_final: 0.9001 (p) REVERT: F 88 TYR cc_start: 0.8605 (m-10) cc_final: 0.7566 (m-10) REVERT: F 91 LYS cc_start: 0.9220 (ttmt) cc_final: 0.8980 (ttpp) REVERT: G 74 LYS cc_start: 0.9083 (mppt) cc_final: 0.8730 (mtmm) REVERT: G 112 GLN cc_start: 0.8899 (mm-40) cc_final: 0.8537 (mm-40) REVERT: H 62 MET cc_start: 0.9223 (mmm) cc_final: 0.8888 (mmp) REVERT: H 87 SER cc_start: 0.9335 (m) cc_final: 0.9062 (p) REVERT: K 55 MET cc_start: -0.1318 (mmp) cc_final: -0.1670 (mmt) REVERT: K 71 MET cc_start: 0.5227 (mmm) cc_final: 0.4318 (mmm) REVERT: K 108 ARG cc_start: 0.7220 (ttm110) cc_final: 0.6755 (tpt170) REVERT: K 147 MET cc_start: 0.7140 (tmm) cc_final: 0.5794 (mtt) REVERT: K 206 MET cc_start: 0.6148 (mmm) cc_final: 0.5598 (ppp) REVERT: K 282 ARG cc_start: 0.8109 (OUTLIER) cc_final: 0.7871 (ttm-80) REVERT: K 286 ASP cc_start: 0.8529 (t70) cc_final: 0.8221 (t70) outliers start: 30 outliers final: 18 residues processed: 279 average time/residue: 0.1364 time to fit residues: 53.5675 Evaluate side-chains 270 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 249 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 86 ARG Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 108 LYS Chi-restraints excluded: chain K residue 275 LEU Chi-restraints excluded: chain K residue 282 ARG Chi-restraints excluded: chain K residue 318 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 30 optimal weight: 0.3980 chunk 102 optimal weight: 0.7980 chunk 99 optimal weight: 0.0070 chunk 134 optimal weight: 6.9990 chunk 101 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 71 optimal weight: 20.0000 chunk 24 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 overall best weight: 1.0402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN E 68 GLN E 93 GLN H 67 ASN ** K 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 40 GLN ** L 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.129295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.093449 restraints weight = 44093.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.093241 restraints weight = 33620.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.093297 restraints weight = 28413.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.093388 restraints weight = 25305.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.093372 restraints weight = 23611.773| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3325 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3325 r_free = 0.3325 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3325 r_free = 0.3325 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.91 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3325 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.3618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 16003 Z= 0.172 Angle : 0.684 7.375 22877 Z= 0.393 Chirality : 0.048 0.236 2589 Planarity : 0.004 0.037 1901 Dihedral : 30.728 178.722 4443 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 3.15 % Allowed : 15.24 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.24), residues: 1129 helix: -0.74 (0.20), residues: 637 sheet: -1.15 (0.57), residues: 78 loop : -0.85 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 265 TYR 0.025 0.002 TYR H 40 PHE 0.015 0.001 PHE K 159 TRP 0.026 0.002 TRP K 228 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.17 (16003) covalent geometry : angle 0.68449 / 0.39 (22877) hydrogen bonds : bond 0.08829 / 5.58 ( 637) hydrogen bonds : angle 3.87595 / 2.68 ( 1572) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 251 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 ASN cc_start: 0.9107 (t0) cc_final: 0.8183 (t0) REVERT: A 120 MET cc_start: 0.8224 (OUTLIER) cc_final: 0.7715 (mtt) REVERT: C 91 GLU cc_start: 0.8146 (tp30) cc_final: 0.7619 (tp30) REVERT: D 86 ARG cc_start: 0.8241 (OUTLIER) cc_final: 0.7596 (mtm-85) REVERT: D 87 SER cc_start: 0.8790 (m) cc_final: 0.8397 (t) REVERT: E 68 GLN cc_start: 0.8717 (tt0) cc_final: 0.8257 (tm-30) REVERT: E 122 LYS cc_start: 0.9255 (ptpt) cc_final: 0.8986 (ptpp) REVERT: G 59 THR cc_start: 0.9447 (p) cc_final: 0.9192 (m) REVERT: G 75 LYS cc_start: 0.8218 (mttm) cc_final: 0.7888 (mtpp) REVERT: G 99 ARG cc_start: 0.7968 (mmm-85) cc_final: 0.7652 (mmm160) REVERT: K 71 MET cc_start: 0.5679 (mmm) cc_final: 0.4750 (mmm) REVERT: K 108 ARG cc_start: 0.7253 (ttm110) cc_final: 0.6747 (tpt170) REVERT: K 147 MET cc_start: 0.7203 (tmm) cc_final: 0.5766 (mtt) REVERT: K 198 MET cc_start: 0.2947 (mmm) cc_final: 0.1721 (mmm) REVERT: K 205 TRP cc_start: 0.4761 (m100) cc_final: 0.4306 (m100) REVERT: K 206 MET cc_start: 0.6078 (mmm) cc_final: 0.5603 (tmm) REVERT: K 212 LYS cc_start: 0.2983 (tptt) cc_final: 0.1977 (tptm) REVERT: K 252 GLN cc_start: 0.6597 (mt0) cc_final: 0.6366 (mt0) outliers start: 31 outliers final: 23 residues processed: 264 average time/residue: 0.1418 time to fit residues: 52.7042 Evaluate side-chains 262 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 237 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 86 ARG Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 108 LYS Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain K residue 267 VAL Chi-restraints excluded: chain K residue 275 LEU Chi-restraints excluded: chain K residue 318 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 43 optimal weight: 0.0870 chunk 123 optimal weight: 4.9990 chunk 137 optimal weight: 6.9990 chunk 113 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 127 optimal weight: 8.9990 chunk 24 optimal weight: 1.9990 chunk 130 optimal weight: 5.9990 chunk 126 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 overall best weight: 1.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 ASN D 67 ASN E 113 HIS K 168 GLN ** K 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.129435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.094117 restraints weight = 43533.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.093399 restraints weight = 36804.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.093633 restraints weight = 32652.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.093715 restraints weight = 27588.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.093792 restraints weight = 25459.974| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3340 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3340 r_free = 0.3340 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.91 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3340 r_free = 0.3340 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.91 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3340 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.3876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16003 Z= 0.164 Angle : 0.659 6.910 22877 Z= 0.379 Chirality : 0.047 0.343 2589 Planarity : 0.004 0.034 1901 Dihedral : 30.615 178.915 4439 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.46 % Allowed : 16.26 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.24), residues: 1129 helix: -0.38 (0.20), residues: 640 sheet: -1.06 (0.58), residues: 78 loop : -0.75 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 72 TYR 0.034 0.002 TYR H 83 PHE 0.011 0.001 PHE K 159 TRP 0.030 0.002 TRP K 228 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.16 (16003) covalent geometry : angle 0.65925 / 0.38 (22877) hydrogen bonds : bond 0.08589 / 5.42 ( 637) hydrogen bonds : angle 3.74337 / 2.60 ( 1572) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 243 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8307 (OUTLIER) cc_final: 0.7788 (mtt) REVERT: C 91 GLU cc_start: 0.8283 (tp30) cc_final: 0.7758 (tp30) REVERT: D 86 ARG cc_start: 0.8379 (OUTLIER) cc_final: 0.7729 (mtm-85) REVERT: D 87 SER cc_start: 0.8996 (m) cc_final: 0.8580 (t) REVERT: E 90 MET cc_start: 0.8343 (mmp) cc_final: 0.8089 (mmt) REVERT: E 94 GLU cc_start: 0.7742 (mm-30) cc_final: 0.7386 (mm-30) REVERT: E 122 LYS cc_start: 0.9330 (ptpt) cc_final: 0.9067 (ptpp) REVERT: F 84 MET cc_start: 0.7276 (mmm) cc_final: 0.7055 (mmm) REVERT: G 75 LYS cc_start: 0.8253 (mttm) cc_final: 0.7911 (mtpp) REVERT: H 87 SER cc_start: 0.9370 (m) cc_final: 0.9122 (p) REVERT: H 93 GLU cc_start: 0.8759 (mp0) cc_final: 0.8163 (mp0) REVERT: K 71 MET cc_start: 0.5673 (mmm) cc_final: 0.4733 (mmm) REVERT: K 108 ARG cc_start: 0.7267 (ttm110) cc_final: 0.6762 (tpt170) REVERT: K 147 MET cc_start: 0.6932 (tmm) cc_final: 0.5795 (mtt) REVERT: K 198 MET cc_start: 0.3398 (mmm) cc_final: 0.2165 (mmm) REVERT: K 203 ARG cc_start: 0.7050 (ttp-110) cc_final: 0.6772 (ptp90) REVERT: K 206 MET cc_start: 0.6107 (mmm) cc_final: 0.5608 (tmm) REVERT: K 212 LYS cc_start: 0.2708 (tptt) cc_final: 0.1623 (tptm) REVERT: K 252 GLN cc_start: 0.6505 (mt0) cc_final: 0.6233 (mt0) outliers start: 34 outliers final: 23 residues processed: 258 average time/residue: 0.1436 time to fit residues: 51.4142 Evaluate side-chains 254 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 229 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 86 ARG Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain K residue 144 VAL Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain K residue 267 VAL Chi-restraints excluded: chain K residue 318 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 105 optimal weight: 0.3980 chunk 82 optimal weight: 9.9990 chunk 137 optimal weight: 7.9990 chunk 129 optimal weight: 4.9990 chunk 75 optimal weight: 10.0000 chunk 99 optimal weight: 2.9990 chunk 106 optimal weight: 6.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 9.9990 chunk 136 optimal weight: 10.0000 chunk 74 optimal weight: 9.9990 overall best weight: 4.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 ASN B 75 HIS C 84 GLN D 84 ASN E 68 GLN ** L 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.124204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.089254 restraints weight = 44081.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.088283 restraints weight = 36485.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.088614 restraints weight = 36034.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.088644 restraints weight = 30181.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.088669 restraints weight = 28106.726| |-----------------------------------------------------------------------------| r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3246 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3246 r_free = 0.3246 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.91 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3246 r_free = 0.3246 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3246 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.3890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.080 16003 Z= 0.463 Angle : 0.955 13.501 22877 Z= 0.506 Chirality : 0.058 0.261 2589 Planarity : 0.007 0.055 1901 Dihedral : 30.992 179.722 4439 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 16.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 5.59 % Allowed : 15.75 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.64 (0.24), residues: 1129 helix: -0.87 (0.19), residues: 643 sheet: -1.53 (0.57), residues: 75 loop : -1.07 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 72 TYR 0.051 0.003 TYR H 83 PHE 0.028 0.003 PHE B 100 TRP 0.017 0.002 TRP K 228 HIS 0.014 0.003 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.01015 / 0.46 (16003) covalent geometry : angle 0.95452 / 0.51 (22877) hydrogen bonds : bond 0.11060 / 7.25 ( 637) hydrogen bonds : angle 4.86128 / 3.39 ( 1572) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 217 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.7675 (mt-10) cc_final: 0.7427 (mt-10) REVERT: C 91 GLU cc_start: 0.8396 (tp30) cc_final: 0.8047 (tp30) REVERT: D 86 ARG cc_start: 0.8579 (OUTLIER) cc_final: 0.7828 (mtm-85) REVERT: D 87 SER cc_start: 0.8838 (m) cc_final: 0.8520 (t) REVERT: E 94 GLU cc_start: 0.7881 (mm-30) cc_final: 0.7513 (mm-30) REVERT: E 122 LYS cc_start: 0.9176 (ptpt) cc_final: 0.8837 (ptpp) REVERT: E 131 ARG cc_start: 0.8898 (OUTLIER) cc_final: 0.8457 (mtt180) REVERT: G 16 THR cc_start: 0.8870 (OUTLIER) cc_final: 0.8622 (p) REVERT: G 39 TYR cc_start: 0.8933 (m-80) cc_final: 0.8716 (m-80) REVERT: G 112 GLN cc_start: 0.8998 (mm-40) cc_final: 0.8683 (mm-40) REVERT: K 71 MET cc_start: 0.5233 (mmm) cc_final: 0.4287 (mmm) REVERT: K 108 ARG cc_start: 0.7414 (ttm110) cc_final: 0.7029 (tpt170) REVERT: K 147 MET cc_start: 0.6800 (tmm) cc_final: 0.5788 (mtt) REVERT: K 197 THR cc_start: 0.3851 (OUTLIER) cc_final: 0.3614 (p) outliers start: 55 outliers final: 41 residues processed: 248 average time/residue: 0.1496 time to fit residues: 51.1108 Evaluate side-chains 253 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 208 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 86 ARG Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 108 LYS Chi-restraints excluded: chain K residue 144 VAL Chi-restraints excluded: chain K residue 197 THR Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain K residue 267 VAL Chi-restraints excluded: chain K residue 318 ASP Chi-restraints excluded: chain K residue 329 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.9131 > 50: distance: 51 - 73: 33.290 distance: 61 - 65: 34.636 distance: 65 - 66: 41.031 distance: 66 - 69: 38.934 distance: 67 - 73: 39.868 distance: 70 - 71: 40.220 distance: 70 - 72: 40.325 distance: 75 - 76: 70.010 distance: 75 - 81: 39.406 distance: 78 - 79: 39.403 distance: 81 - 87: 40.700 distance: 82 - 85: 40.341 distance: 83 - 88: 56.873 distance: 84 - 109: 45.147 distance: 89 - 90: 40.947 distance: 90 - 91: 40.423 distance: 90 - 92: 39.103 distance: 92 - 93: 40.781 distance: 93 - 94: 56.505 distance: 94 - 101: 40.136 distance: 97 - 98: 39.221 distance: 98 - 100: 56.477 distance: 101 - 102: 56.981 distance: 102 - 103: 39.669 distance: 103 - 109: 21.363 distance: 104 - 133: 38.489 distance: 105 - 106: 40.399 distance: 106 - 107: 40.726 distance: 106 - 108: 40.353 distance: 109 - 110: 12.378 distance: 110 - 111: 11.041 distance: 110 - 113: 27.664 distance: 111 - 112: 40.557 distance: 111 - 114: 36.802 distance: 112 - 138: 35.547 distance: 114 - 115: 3.652 distance: 115 - 116: 39.070 distance: 118 - 119: 39.245 distance: 120 - 121: 40.853 distance: 125 - 126: 40.066 distance: 125 - 133: 40.225 distance: 126 - 151: 33.433 distance: 127 - 128: 44.050 distance: 128 - 129: 16.833 distance: 128 - 130: 17.765 distance: 134 - 135: 69.683 distance: 134 - 137: 39.296 distance: 135 - 136: 38.947 distance: 135 - 138: 34.798 distance: 136 - 159: 34.115