Starting phenix.real_space_refine on Thu Mar 5 14:59:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9sjn_54948/03_2026/9sjn_54948.cif Found real_map, /net/cci-nas-00/data/ceres_data/9sjn_54948/03_2026/9sjn_54948.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9sjn_54948/03_2026/9sjn_54948.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9sjn_54948/03_2026/9sjn_54948.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9sjn_54948/03_2026/9sjn_54948.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9sjn_54948/03_2026/9sjn_54948.map" } resolution = 3.03 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= 0.002 sd= 0.029 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 59 5.49 5 S 116 5.16 5 C 14311 2.51 5 N 3817 2.21 5 O 4476 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 114 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22779 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2684 Classifications: {'peptide': 336} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 17, 'TRANS': 318} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 1986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1986 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 8, 'TRANS': 243} Chain: "I" Number of atoms: 1438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1438 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 6, 'TRANS': 171} Chain: "D" Number of atoms: 2521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2521 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 13, 'TRANS': 296} Chain breaks: 1 Chain: "E" Number of atoms: 2603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2603 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 15, 'TRANS': 304} Chain: "F" Number of atoms: 2610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2610 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 15, 'TRANS': 305} Chain: "C" Number of atoms: 2630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2630 Classifications: {'peptide': 323} Link IDs: {'CIS': 1, 'PTRANS': 15, 'TRANS': 306} Chain: "G" Number of atoms: 2610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2610 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 15, 'TRANS': 305} Chain: "H" Number of atoms: 2409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2409 Classifications: {'peptide': 295} Link IDs: {'PTRANS': 11, 'TRANS': 283} Chain breaks: 1 Chain: "J" Number of atoms: 1288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 1288 Classifications: {'RNA': 60} Modifications used: {'5*END': 1, 'rna2p_pur': 18, 'rna2p_pyr': 10, 'rna3p_pur': 19, 'rna3p_pyr': 13} Link IDs: {'rna2p': 28, 'rna3p': 31} Time building chain proxies: 4.40, per 1000 atoms: 0.19 Number of scatterers: 22779 At special positions: 0 Unit cell: (131.95, 146.45, 150.8, 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 116 16.00 P 59 15.00 O 4476 8.00 N 3817 7.00 C 14311 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: 1.53 Conformation dependent library (CDL) restraints added in 762.1 milliseconds 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5054 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 35 sheets defined 34.8% alpha, 8.4% beta 6 base pairs and 25 stacking pairs defined. Time for finding SS restraints: 2.73 Creating SS restraints... Processing helix chain 'A' and resid 5 through 10 Processing helix chain 'A' and resid 15 through 30 Processing helix chain 'A' and resid 42 through 44 No H-bonds generated for 'chain 'A' and resid 42 through 44' Processing helix chain 'A' and resid 83 through 86 Processing helix chain 'A' and resid 87 through 95 Processing helix chain 'A' and resid 104 through 109 removed outlier: 3.867A pdb=" N GLN A 108 " --> pdb=" O MET A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 122 Processing helix chain 'A' and resid 125 through 134 Processing helix chain 'A' and resid 166 through 179 removed outlier: 4.099A pdb=" N ARG A 179 " --> pdb=" O ASP A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 199 removed outlier: 3.656A pdb=" N GLY A 199 " --> pdb=" O ALA A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 206 Processing helix chain 'A' and resid 217 through 221 Processing helix chain 'A' and resid 223 through 229 Processing helix chain 'A' and resid 252 through 254 No H-bonds generated for 'chain 'A' and resid 252 through 254' Processing helix chain 'A' and resid 255 through 264 removed outlier: 4.231A pdb=" N ILE A 259 " --> pdb=" O LEU A 255 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE A 260 " --> pdb=" O LEU A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 292 removed outlier: 3.645A pdb=" N TYR A 292 " --> pdb=" O PHE A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 312 Processing helix chain 'A' and resid 324 through 339 Processing helix chain 'B' and resid 28 through 46 removed outlier: 3.609A pdb=" N PHE B 32 " --> pdb=" O ALA B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 130 removed outlier: 4.058A pdb=" N GLU B 130 " --> pdb=" O LYS B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 170 removed outlier: 3.674A pdb=" N LEU B 167 " --> pdb=" O ARG B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 186 Processing helix chain 'B' and resid 235 through 240 removed outlier: 3.863A pdb=" N LEU B 240 " --> pdb=" O ASN B 237 " (cutoff:3.500A) Processing helix chain 'I' and resid 15 through 24 removed outlier: 3.566A pdb=" N ILE I 24 " --> pdb=" O ILE I 20 " (cutoff:3.500A) Processing helix chain 'I' and resid 24 through 35 Processing helix chain 'I' and resid 64 through 70 Processing helix chain 'I' and resid 72 through 77 removed outlier: 3.655A pdb=" N HIS I 76 " --> pdb=" O CYS I 72 " (cutoff:3.500A) Processing helix chain 'I' and resid 107 through 118 Processing helix chain 'I' and resid 124 through 138 removed outlier: 3.608A pdb=" N GLU I 128 " --> pdb=" O GLY I 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 104 No H-bonds generated for 'chain 'D' and resid 102 through 104' Processing helix chain 'D' and resid 111 through 129 Processing helix chain 'D' and resid 131 through 144 Processing helix chain 'D' and resid 175 through 177 No H-bonds generated for 'chain 'D' and resid 175 through 177' Processing helix chain 'D' and resid 186 through 201 Processing helix chain 'D' and resid 250 through 259 Processing helix chain 'D' and resid 267 through 272 Processing helix chain 'D' and resid 296 through 306 Processing helix chain 'D' and resid 312 through 326 Processing helix chain 'E' and resid 63 through 70 removed outlier: 3.949A pdb=" N LYS E 69 " --> pdb=" O ASP E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 104 No H-bonds generated for 'chain 'E' and resid 102 through 104' Processing helix chain 'E' and resid 111 through 129 Processing helix chain 'E' and resid 131 through 144 Processing helix chain 'E' and resid 175 through 177 No H-bonds generated for 'chain 'E' and resid 175 through 177' Processing helix chain 'E' and resid 186 through 201 Processing helix chain 'E' and resid 250 through 259 Processing helix chain 'E' and resid 267 through 272 Processing helix chain 'E' and resid 296 through 306 Processing helix chain 'E' and resid 312 through 326 Processing helix chain 'F' and resid 36 through 40 Processing helix chain 'F' and resid 63 through 71 removed outlier: 4.736A pdb=" N LYS F 69 " --> pdb=" O ASP F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 106 removed outlier: 3.885A pdb=" N MET F 106 " --> pdb=" O LYS F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 129 Processing helix chain 'F' and resid 131 through 144 Processing helix chain 'F' and resid 186 through 202 Processing helix chain 'F' and resid 250 through 259 removed outlier: 3.553A pdb=" N ILE F 254 " --> pdb=" O HIS F 250 " (cutoff:3.500A) Processing helix chain 'F' and resid 267 through 272 removed outlier: 3.544A pdb=" N TYR F 271 " --> pdb=" O ASP F 267 " (cutoff:3.500A) Processing helix chain 'F' and resid 296 through 306 Processing helix chain 'F' and resid 312 through 326 Processing helix chain 'C' and resid 63 through 71 removed outlier: 5.064A pdb=" N LYS C 69 " --> pdb=" O ASP C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 106 removed outlier: 3.626A pdb=" N MET C 106 " --> pdb=" O LYS C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 129 Processing helix chain 'C' and resid 131 through 144 Processing helix chain 'C' and resid 145 through 153 removed outlier: 6.313A pdb=" N ARG C 150 " --> pdb=" O PHE C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 202 Processing helix chain 'C' and resid 242 through 246 Processing helix chain 'C' and resid 250 through 259 Processing helix chain 'C' and resid 267 through 272 Processing helix chain 'C' and resid 296 through 306 Processing helix chain 'C' and resid 312 through 326 Processing helix chain 'G' and resid 36 through 40 removed outlier: 3.665A pdb=" N ARG G 40 " --> pdb=" O PHE G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 70 removed outlier: 3.855A pdb=" N GLU G 68 " --> pdb=" O PRO G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 104 No H-bonds generated for 'chain 'G' and resid 102 through 104' Processing helix chain 'G' and resid 111 through 129 Processing helix chain 'G' and resid 131 through 144 Processing helix chain 'G' and resid 186 through 202 Processing helix chain 'G' and resid 250 through 259 removed outlier: 3.508A pdb=" N ILE G 254 " --> pdb=" O HIS G 250 " (cutoff:3.500A) Processing helix chain 'G' and resid 267 through 272 Processing helix chain 'G' and resid 296 through 305 Processing helix chain 'G' and resid 312 through 326 Processing helix chain 'H' and resid 36 through 40 Processing helix chain 'H' and resid 102 through 104 No H-bonds generated for 'chain 'H' and resid 102 through 104' Processing helix chain 'H' and resid 111 through 129 Processing helix chain 'H' and resid 131 through 144 Processing helix chain 'H' and resid 145 through 153 removed outlier: 6.162A pdb=" N ARG H 150 " --> pdb=" O PHE H 147 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS H 153 " --> pdb=" O ARG H 150 " (cutoff:3.500A) Processing helix chain 'H' and resid 186 through 202 Processing helix chain 'H' and resid 250 through 259 Processing helix chain 'H' and resid 267 through 272 Processing helix chain 'H' and resid 292 through 295 Processing helix chain 'H' and resid 296 through 306 Processing helix chain 'H' and resid 312 through 326 Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 37 Processing sheet with id=AA2, first strand: chain 'A' and resid 39 through 40 Processing sheet with id=AA3, first strand: chain 'A' and resid 148 through 152 removed outlier: 4.288A pdb=" N LYS A 148 " --> pdb=" O ILE A 163 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 159 through 163 current: chain 'B' and resid 101 through 112 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 101 through 112 current: chain 'B' and resid 137 through 141 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 137 through 141 current: chain 'B' and resid 214 through 229 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 214 through 229 current: chain 'B' and resid 249 through 253 Processing sheet with id=AA4, first strand: chain 'A' and resid 184 through 186 Processing sheet with id=AA5, first strand: chain 'A' and resid 302 through 305 Processing sheet with id=AA6, first strand: chain 'B' and resid 66 through 68 Processing sheet with id=AA7, first strand: chain 'I' and resid 39 through 42 removed outlier: 3.707A pdb=" N THR I 91 " --> pdb=" O SER I 3 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 47 through 48 Processing sheet with id=AA9, first strand: chain 'I' and resid 142 through 143 Processing sheet with id=AB1, first strand: chain 'D' and resid 106 through 109 Processing sheet with id=AB2, first strand: chain 'D' and resid 25 through 27 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 25 through 27 current: chain 'D' and resid 45 through 46 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 45 through 46 current: chain 'D' and resid 172 through 173 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 172 through 173 current: chain 'D' and resid 246 through 249 No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'D' and resid 50 through 51 removed outlier: 4.219A pdb=" N CYS D 82 " --> pdb=" O VAL D 223 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 54 through 57 Processing sheet with id=AB5, first strand: chain 'E' and resid 106 through 109 Processing sheet with id=AB6, first strand: chain 'E' and resid 25 through 27 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 25 through 27 current: chain 'E' and resid 45 through 46 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 45 through 46 current: chain 'E' and resid 172 through 173 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 172 through 173 current: chain 'E' and resid 246 through 249 No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'E' and resid 50 through 57 removed outlier: 4.159A pdb=" N CYS E 82 " --> pdb=" O VAL E 223 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 227 through 228 removed outlier: 4.549A pdb=" N LYS E 239 " --> pdb=" O GLU E 228 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 282 through 283 removed outlier: 3.981A pdb=" N ALA E 283 " --> pdb=" O ILE E 288 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ILE E 288 " --> pdb=" O ALA E 283 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'F' and resid 25 through 27 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 25 through 27 current: chain 'F' and resid 45 through 46 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 45 through 46 current: chain 'F' and resid 167 through 168 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 167 through 168 current: chain 'F' and resid 246 through 249 No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'F' and resid 54 through 57 removed outlier: 3.579A pdb=" N GLN F 77 " --> pdb=" O VAL F 54 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 82 through 83 removed outlier: 4.462A pdb=" N CYS F 82 " --> pdb=" O VAL F 223 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 227 through 228 removed outlier: 4.578A pdb=" N LYS F 239 " --> pdb=" O GLU F 228 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 260 through 262 Processing sheet with id=AC6, first strand: chain 'C' and resid 25 through 27 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 25 through 27 current: chain 'C' and resid 45 through 46 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 45 through 46 current: chain 'C' and resid 172 through 173 No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'C' and resid 50 through 56 removed outlier: 4.233A pdb=" N CYS C 82 " --> pdb=" O VAL C 223 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 106 through 109 Processing sheet with id=AC9, first strand: chain 'G' and resid 25 through 27 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 25 through 27 current: chain 'G' and resid 45 through 46 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 45 through 46 current: chain 'G' and resid 167 through 168 No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'G' and resid 50 through 55 removed outlier: 4.135A pdb=" N CYS G 82 " --> pdb=" O VAL G 223 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 227 through 228 removed outlier: 4.283A pdb=" N LYS G 239 " --> pdb=" O GLU G 228 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 242 through 243 Processing sheet with id=AD4, first strand: chain 'G' and resid 260 through 262 Processing sheet with id=AD5, first strand: chain 'G' and resid 282 through 283 removed outlier: 3.917A pdb=" N ALA G 283 " --> pdb=" O ILE G 288 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ILE G 288 " --> pdb=" O ALA G 283 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'H' and resid 106 through 108 removed outlier: 7.037A pdb=" N SER H 20 " --> pdb=" O TYR H 107 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 25 through 27 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 25 through 27 current: chain 'H' and resid 45 through 46 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 45 through 46 current: chain 'H' and resid 167 through 168 No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'H' and resid 260 through 262 656 hydrogen bonds defined for protein. 1821 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 17 hydrogen bonds 30 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 25 stacking parallelities Total time for adding SS restraints: 3.68 Time building geometry restraints manager: 2.12 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: 6658 1.33 - 1.46: 4442 1.46 - 1.58: 11999 1.58 - 1.70: 118 1.70 - 1.82: 185 Bond restraints: 23402 Sorted by residual: bond pdb=" CA ALA G 22 " pdb=" CB ALA G 22 " ideal model delta sigma weight residual 1.532 1.478 0.053 1.59e-02 3.96e+03 1.13e+01 bond pdb=" CA LYS I 85 " pdb=" CB LYS I 85 " ideal model delta sigma weight residual 1.527 1.563 -0.036 1.27e-02 6.20e+03 8.03e+00 bond pdb=" C ILE A 14 " pdb=" N PRO A 15 " ideal model delta sigma weight residual 1.332 1.367 -0.035 1.30e-02 5.92e+03 7.31e+00 bond pdb=" CA TYR G 265 " pdb=" C TYR G 265 " ideal model delta sigma weight residual 1.522 1.488 0.033 1.29e-02 6.01e+03 6.73e+00 bond pdb=" CA TYR E 265 " pdb=" C TYR E 265 " ideal model delta sigma weight residual 1.528 1.498 0.030 1.18e-02 7.18e+03 6.45e+00 ... (remaining 23397 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 31360 2.36 - 4.71: 474 4.71 - 7.07: 33 7.07 - 9.43: 19 9.43 - 11.78: 4 Bond angle restraints: 31890 Sorted by residual: angle pdb=" O3' A J 39 " pdb=" C3' A J 39 " pdb=" C2' A J 39 " ideal model delta sigma weight residual 109.50 121.28 -11.78 1.50e+00 4.44e-01 6.17e+01 angle pdb=" N ILE A 259 " pdb=" CA ILE A 259 " pdb=" C ILE A 259 " ideal model delta sigma weight residual 110.53 105.58 4.95 9.40e-01 1.13e+00 2.78e+01 angle pdb=" CA PHE G 21 " pdb=" CB PHE G 21 " pdb=" CG PHE G 21 " ideal model delta sigma weight residual 113.80 118.83 -5.03 1.00e+00 1.00e+00 2.53e+01 angle pdb=" CA TYR E 265 " pdb=" CB TYR E 265 " pdb=" CG TYR E 265 " ideal model delta sigma weight residual 113.90 122.63 -8.73 1.80e+00 3.09e-01 2.35e+01 angle pdb=" C TRP H 149 " pdb=" CA TRP H 149 " pdb=" CB TRP H 149 " ideal model delta sigma weight residual 116.63 111.24 5.39 1.16e+00 7.43e-01 2.16e+01 ... (remaining 31885 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.38: 13278 31.38 - 62.76: 875 62.76 - 94.14: 105 94.14 - 125.53: 5 125.53 - 156.91: 1 Dihedral angle restraints: 14264 sinusoidal: 6437 harmonic: 7827 Sorted by residual: dihedral pdb=" C4' G J 59 " pdb=" C3' G J 59 " pdb=" C2' G J 59 " pdb=" C1' G J 59 " ideal model delta sinusoidal sigma weight residual -35.00 35.73 -70.73 1 8.00e+00 1.56e-02 1.00e+02 dihedral pdb=" C5' G J 59 " pdb=" C4' G J 59 " pdb=" C3' G J 59 " pdb=" O3' G J 59 " ideal model delta sinusoidal sigma weight residual 147.00 76.92 70.08 1 8.00e+00 1.56e-02 9.89e+01 dihedral pdb=" O4' G J 59 " pdb=" C4' G J 59 " pdb=" C3' G J 59 " pdb=" C2' G J 59 " ideal model delta sinusoidal sigma weight residual 24.00 -37.04 61.04 1 8.00e+00 1.56e-02 7.74e+01 ... (remaining 14261 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.113: 3456 0.113 - 0.226: 73 0.226 - 0.338: 1 0.338 - 0.451: 1 0.451 - 0.564: 2 Chirality restraints: 3533 Sorted by residual: chirality pdb=" P A J 40 " pdb=" OP1 A J 40 " pdb=" OP2 A J 40 " pdb=" O5' A J 40 " both_signs ideal model delta sigma weight residual True 2.41 -2.97 -0.56 2.00e-01 2.50e+01 7.96e+00 chirality pdb=" P A J 39 " pdb=" OP1 A J 39 " pdb=" OP2 A J 39 " pdb=" O5' A J 39 " both_signs ideal model delta sigma weight residual True 2.41 -2.94 -0.53 2.00e-01 2.50e+01 7.00e+00 chirality pdb=" C3' G J 59 " pdb=" C4' G J 59 " pdb=" O3' G J 59 " pdb=" C2' G J 59 " both_signs ideal model delta sigma weight residual False -2.74 -2.37 -0.38 2.00e-01 2.50e+01 3.55e+00 ... (remaining 3530 not shown) Planarity restraints: 3870 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 92 " -0.023 2.00e-02 2.50e+03 2.47e-02 1.07e+01 pdb=" CG PHE A 92 " 0.057 2.00e-02 2.50e+03 pdb=" CD1 PHE A 92 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 PHE A 92 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE A 92 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 92 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 92 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP E 264 " 0.012 2.00e-02 2.50e+03 2.46e-02 6.04e+00 pdb=" C TRP E 264 " -0.042 2.00e-02 2.50e+03 pdb=" O TRP E 264 " 0.016 2.00e-02 2.50e+03 pdb=" N TYR E 265 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP F 166 " -0.012 2.00e-02 2.50e+03 2.34e-02 5.48e+00 pdb=" C ASP F 166 " 0.040 2.00e-02 2.50e+03 pdb=" O ASP F 166 " -0.015 2.00e-02 2.50e+03 pdb=" N LYS F 167 " -0.014 2.00e-02 2.50e+03 ... (remaining 3867 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2010 2.74 - 3.28: 23882 3.28 - 3.82: 41266 3.82 - 4.36: 51354 4.36 - 4.90: 82848 Nonbonded interactions: 201360 Sorted by model distance: nonbonded pdb=" OG1 THR A 81 " pdb=" O ASP A 83 " model vdw 2.196 3.040 nonbonded pdb=" O PRO A 298 " pdb=" NE2 GLN I 136 " model vdw 2.198 3.120 nonbonded pdb=" O LEU G 55 " pdb=" O2' A J 37 " model vdw 2.201 3.040 nonbonded pdb=" OH TYR F 265 " pdb=" O PHE F 273 " model vdw 2.213 3.040 nonbonded pdb=" OH TYR C 169 " pdb=" OE1 GLN C 195 " model vdw 2.213 3.040 ... (remaining 201355 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 'C' and (resid 12 through 52 or resid 79 through 331)) selection = (chain 'D' and (resid 12 through 52 or resid 79 through 331)) selection = (chain 'E' and (resid 12 through 52 or resid 79 through 331)) selection = (chain 'F' and (resid 12 through 52 or resid 79 through 331)) selection = (chain 'G' and (resid 12 through 52 or resid 79 through 331)) selection = (chain 'H' and resid 12 through 331) } 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 individual isotropic 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: 4.520 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: 0.430 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 20.150 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 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 : 0.004 0.055 23402 Z= 0.199 Angle : 0.726 11.783 31890 Z= 0.425 Chirality : 0.045 0.564 3533 Planarity : 0.005 0.057 3870 Dihedral : 19.331 156.906 9210 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 15.80 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.64 % Favored : 93.28 % Rotamer: Outliers : 0.42 % Allowed : 28.34 % Favored : 71.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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: -0.73 (0.16), residues: 2634 helix: 0.97 (0.19), residues: 749 sheet: -0.36 (0.25), residues: 445 loop : -1.34 (0.16), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 101 TYR 0.027 0.001 TYR E 265 PHE 0.057 0.002 PHE A 92 TRP 0.022 0.001 TRP H 33 HIS 0.013 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00399 (23402) covalent geometry : angle 0.72611 (31890) hydrogen bonds : bond 0.15012 ( 673) hydrogen bonds : angle 6.67859 ( 1851) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 591 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 581 time to evaluate : 0.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.5469 (mtt) cc_final: 0.5221 (mtt) REVERT: A 118 MET cc_start: 0.1180 (tpt) cc_final: 0.0887 (tpt) REVERT: A 171 TYR cc_start: 0.6205 (t80) cc_final: 0.5760 (t80) REVERT: A 180 SER cc_start: 0.6997 (t) cc_final: 0.6748 (m) REVERT: A 311 GLN cc_start: 0.7501 (mm-40) cc_final: 0.7120 (mm-40) REVERT: B 219 GLU cc_start: 0.7772 (pt0) cc_final: 0.7558 (pt0) REVERT: I 115 MET cc_start: 0.0148 (mmm) cc_final: -0.0059 (mmm) REVERT: D 23 ARG cc_start: 0.7760 (ptp90) cc_final: 0.7447 (ptt-90) REVERT: D 89 ASP cc_start: 0.8187 (p0) cc_final: 0.7656 (p0) REVERT: D 227 GLN cc_start: 0.8363 (tt0) cc_final: 0.8084 (tt0) REVERT: D 228 GLU cc_start: 0.7411 (mm-30) cc_final: 0.7147 (mm-30) REVERT: D 262 ASP cc_start: 0.8061 (t0) cc_final: 0.7670 (t0) REVERT: D 320 MET cc_start: 0.7907 (mmp) cc_final: 0.7452 (mmp) REVERT: E 45 LEU cc_start: 0.8143 (mt) cc_final: 0.7909 (mt) REVERT: E 123 ASP cc_start: 0.7556 (m-30) cc_final: 0.7351 (m-30) REVERT: E 244 GLU cc_start: 0.7847 (mt-10) cc_final: 0.7606 (mt-10) REVERT: E 275 ILE cc_start: 0.8077 (pt) cc_final: 0.7715 (pt) REVERT: F 51 ASP cc_start: 0.7294 (m-30) cc_final: 0.7068 (m-30) REVERT: F 72 MET cc_start: -0.0237 (ptp) cc_final: -0.0554 (ptp) REVERT: F 119 TYR cc_start: 0.7929 (m-10) cc_final: 0.7497 (m-10) REVERT: F 123 ASP cc_start: 0.8209 (m-30) cc_final: 0.7942 (m-30) REVERT: F 125 TYR cc_start: 0.8325 (t80) cc_final: 0.8093 (t80) REVERT: F 224 TYR cc_start: 0.8077 (m-80) cc_final: 0.7560 (m-80) REVERT: F 278 GLU cc_start: 0.6739 (mt-10) cc_final: 0.6412 (mt-10) REVERT: F 303 ARG cc_start: 0.7905 (mtp180) cc_final: 0.7647 (mtp180) REVERT: C 72 MET cc_start: -0.1089 (ttm) cc_final: -0.1540 (ttm) REVERT: C 103 LYS cc_start: 0.8245 (mtmm) cc_final: 0.7512 (mtpt) REVERT: C 104 GLU cc_start: 0.6865 (mp0) cc_final: 0.6524 (mp0) REVERT: C 121 LYS cc_start: 0.7493 (mmtt) cc_final: 0.7006 (mmtt) REVERT: C 173 ASN cc_start: 0.8219 (t0) cc_final: 0.7780 (t0) REVERT: C 228 GLU cc_start: 0.7749 (mm-30) cc_final: 0.7509 (mt-10) REVERT: C 262 ASP cc_start: 0.8482 (t0) cc_final: 0.8190 (t0) REVERT: C 304 MET cc_start: 0.7826 (ttm) cc_final: 0.7542 (ttm) REVERT: G 21 PHE cc_start: 0.7911 (m-80) cc_final: 0.7673 (m-10) REVERT: G 41 HIS cc_start: 0.7415 (m-70) cc_final: 0.7170 (m170) REVERT: G 165 GLU cc_start: 0.7122 (mm-30) cc_final: 0.6866 (mm-30) REVERT: G 188 THR cc_start: 0.8159 (p) cc_final: 0.7804 (t) REVERT: G 198 ASP cc_start: 0.7025 (m-30) cc_final: 0.6633 (m-30) REVERT: G 288 ILE cc_start: 0.5257 (OUTLIER) cc_final: 0.5048 (mt) REVERT: G 300 LEU cc_start: 0.8044 (mm) cc_final: 0.7836 (mt) REVERT: H 121 LYS cc_start: 0.7448 (mmtp) cc_final: 0.7141 (mmtm) REVERT: H 132 LEU cc_start: 0.7609 (tp) cc_final: 0.7181 (pp) REVERT: H 149 TRP cc_start: 0.6903 (m100) cc_final: 0.6082 (m100) REVERT: H 167 LYS cc_start: 0.7174 (tttm) cc_final: 0.6964 (tttm) REVERT: H 186 ASN cc_start: 0.6562 (m-40) cc_final: 0.6239 (m-40) REVERT: H 206 TYR cc_start: 0.7918 (p90) cc_final: 0.7627 (p90) REVERT: H 208 ASN cc_start: 0.7997 (m-40) cc_final: 0.7555 (m-40) REVERT: H 241 PHE cc_start: 0.6699 (t80) cc_final: 0.5872 (t80) outliers start: 10 outliers final: 2 residues processed: 589 average time/residue: 0.1702 time to fit residues: 151.2442 Evaluate side-chains 507 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 504 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain G residue 267 ASP Chi-restraints excluded: chain G residue 288 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 0.0870 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.0060 chunk 155 optimal weight: 0.0970 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 0.9980 chunk 111 optimal weight: 0.1980 overall best weight: 0.2172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 47 ASN ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 149 GLN A 328 HIS B 21 ASN B 98 ASN ** D 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 178 ASN D 279 ASN E 173 ASN E 279 ASN F 41 HIS F 190 ASN F 256 ASN C 26 ASN ** C 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 GLN G 279 ASN H 141 ASN H 252 GLN H 256 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.181016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.142177 restraints weight = 34532.248| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 2.31 r_work: 0.3705 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3552 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23402 Z= 0.122 Angle : 0.580 13.622 31890 Z= 0.304 Chirality : 0.041 0.282 3533 Planarity : 0.005 0.047 3870 Dihedral : 14.845 151.197 3810 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.50 % Favored : 94.46 % Rotamer: Outliers : 2.83 % Allowed : 26.57 % Favored : 70.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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: -0.64 (0.16), residues: 2634 helix: 1.04 (0.19), residues: 750 sheet: -0.27 (0.25), residues: 440 loop : -1.31 (0.16), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 15 TYR 0.016 0.001 TYR H 125 PHE 0.044 0.001 PHE A 92 TRP 0.010 0.001 TRP E 149 HIS 0.012 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00265 (23402) covalent geometry : angle 0.57955 (31890) hydrogen bonds : bond 0.04096 ( 673) hydrogen bonds : angle 5.60660 ( 1851) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 603 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 536 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.5508 (mtt) cc_final: 0.5260 (mtt) REVERT: A 171 TYR cc_start: 0.6624 (t80) cc_final: 0.6148 (t80) REVERT: A 180 SER cc_start: 0.7333 (t) cc_final: 0.7087 (m) REVERT: A 233 LEU cc_start: 0.7042 (OUTLIER) cc_final: 0.6742 (mm) REVERT: A 282 GLU cc_start: 0.6994 (pm20) cc_final: 0.6534 (pm20) REVERT: A 311 GLN cc_start: 0.7641 (mm-40) cc_final: 0.7256 (mm-40) REVERT: B 126 LYS cc_start: 0.8406 (ttmm) cc_final: 0.8133 (ttmm) REVERT: B 138 ILE cc_start: 0.8384 (mp) cc_final: 0.8105 (mp) REVERT: B 175 MET cc_start: 0.6480 (mmm) cc_final: 0.6068 (mmm) REVERT: B 185 GLN cc_start: 0.6993 (OUTLIER) cc_final: 0.6518 (pm20) REVERT: B 219 GLU cc_start: 0.8404 (pt0) cc_final: 0.8121 (pt0) REVERT: B 240 LEU cc_start: 0.8244 (mp) cc_final: 0.7965 (mp) REVERT: B 246 GLU cc_start: 0.5922 (OUTLIER) cc_final: 0.5698 (mm-30) REVERT: D 89 ASP cc_start: 0.8607 (p0) cc_final: 0.7850 (p0) REVERT: D 91 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8238 (tp) REVERT: D 262 ASP cc_start: 0.8364 (t0) cc_final: 0.8076 (t0) REVERT: D 320 MET cc_start: 0.8108 (mmp) cc_final: 0.7716 (mmp) REVERT: E 45 LEU cc_start: 0.8471 (mt) cc_final: 0.8209 (mt) REVERT: E 128 GLU cc_start: 0.7508 (tm-30) cc_final: 0.7210 (tm-30) REVERT: E 190 ASN cc_start: 0.8190 (m-40) cc_final: 0.7668 (m110) REVERT: E 244 GLU cc_start: 0.8253 (mt-10) cc_final: 0.7889 (mt-10) REVERT: E 249 MET cc_start: 0.8634 (mtp) cc_final: 0.8430 (ttm) REVERT: E 303 ARG cc_start: 0.8342 (mtp180) cc_final: 0.7967 (mtp85) REVERT: F 103 LYS cc_start: 0.8655 (mtmm) cc_final: 0.8276 (mtmm) REVERT: F 125 TYR cc_start: 0.8497 (t80) cc_final: 0.8071 (t80) REVERT: F 177 PHE cc_start: 0.8542 (m-80) cc_final: 0.8226 (m-80) REVERT: F 265 TYR cc_start: 0.8268 (p90) cc_final: 0.7861 (p90) REVERT: F 278 GLU cc_start: 0.7765 (mt-10) cc_final: 0.7500 (mt-10) REVERT: F 298 TYR cc_start: 0.8408 (m-80) cc_final: 0.8078 (m-80) REVERT: C 103 LYS cc_start: 0.8447 (mtmm) cc_final: 0.7766 (mtpt) REVERT: C 104 GLU cc_start: 0.7511 (mp0) cc_final: 0.7136 (mp0) REVERT: C 121 LYS cc_start: 0.7902 (mmtt) cc_final: 0.7451 (mmtt) REVERT: C 179 LEU cc_start: 0.8521 (mt) cc_final: 0.8301 (mt) REVERT: C 241 PHE cc_start: 0.8673 (t80) cc_final: 0.8309 (t80) REVERT: C 304 MET cc_start: 0.8044 (OUTLIER) cc_final: 0.7791 (ttp) REVERT: G 115 ARG cc_start: 0.8004 (ttm170) cc_final: 0.7389 (ttm170) REVERT: G 159 GLU cc_start: 0.8030 (tt0) cc_final: 0.7619 (tt0) REVERT: G 188 THR cc_start: 0.8283 (p) cc_final: 0.7882 (t) REVERT: G 198 ASP cc_start: 0.7846 (m-30) cc_final: 0.7526 (m-30) REVERT: G 214 PHE cc_start: 0.8454 (m-80) cc_final: 0.8222 (m-80) REVERT: G 300 LEU cc_start: 0.8494 (mm) cc_final: 0.8278 (mt) REVERT: H 39 LYS cc_start: 0.8196 (OUTLIER) cc_final: 0.7708 (pttp) REVERT: H 113 ASN cc_start: 0.7359 (p0) cc_final: 0.7072 (p0) REVERT: H 121 LYS cc_start: 0.7900 (mmtp) cc_final: 0.7609 (mmtm) REVERT: H 149 TRP cc_start: 0.6975 (m100) cc_final: 0.6300 (m100) REVERT: H 186 ASN cc_start: 0.7202 (m-40) cc_final: 0.6885 (m-40) REVERT: H 208 ASN cc_start: 0.8030 (m-40) cc_final: 0.7570 (m-40) REVERT: H 210 TYR cc_start: 0.7605 (m-80) cc_final: 0.7349 (m-80) REVERT: H 241 PHE cc_start: 0.6968 (t80) cc_final: 0.6496 (t80) REVERT: H 243 PHE cc_start: 0.7987 (t80) cc_final: 0.7785 (t80) REVERT: H 253 LYS cc_start: 0.8353 (tptt) cc_final: 0.8113 (tppt) REVERT: H 299 LYS cc_start: 0.7890 (mtpt) cc_final: 0.7381 (mtmt) REVERT: H 303 ARG cc_start: 0.8147 (ttp-170) cc_final: 0.7853 (ttm170) outliers start: 67 outliers final: 32 residues processed: 582 average time/residue: 0.1632 time to fit residues: 144.8510 Evaluate side-chains 553 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 515 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 328 HIS Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 185 GLN Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain I residue 7 ILE Chi-restraints excluded: chain I residue 144 ILE Chi-restraints excluded: chain I residue 169 PHE Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain E residue 39 LYS Chi-restraints excluded: chain E residue 103 LYS Chi-restraints excluded: chain E residue 251 SER Chi-restraints excluded: chain E residue 311 LEU Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 304 MET Chi-restraints excluded: chain G residue 113 ASN Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 223 VAL Chi-restraints excluded: chain H residue 39 LYS Chi-restraints excluded: chain H residue 93 ILE Chi-restraints excluded: chain H residue 164 ILE Chi-restraints excluded: chain H residue 222 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 171 optimal weight: 3.9990 chunk 144 optimal weight: 7.9990 chunk 41 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 147 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 168 optimal weight: 0.8980 chunk 3 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 237 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 328 HIS B 21 ASN B 98 ASN ** B 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 140 ASN F 151 ASN ** C 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 GLN C 252 GLN G 308 ASN ** H 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 317 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.174330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.134774 restraints weight = 34018.212| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 2.31 r_work: 0.3585 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3427 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 23402 Z= 0.287 Angle : 0.644 7.439 31890 Z= 0.340 Chirality : 0.045 0.302 3533 Planarity : 0.005 0.081 3870 Dihedral : 14.740 159.081 3805 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.96 % Favored : 94.00 % Rotamer: Outliers : 5.16 % Allowed : 25.30 % Favored : 69.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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: -0.95 (0.16), residues: 2634 helix: 0.68 (0.18), residues: 754 sheet: -0.44 (0.24), residues: 479 loop : -1.45 (0.16), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG H 146 TYR 0.031 0.002 TYR H 125 PHE 0.029 0.002 PHE A 92 TRP 0.018 0.002 TRP C 33 HIS 0.014 0.002 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00667 (23402) covalent geometry : angle 0.64384 (31890) hydrogen bonds : bond 0.04693 ( 673) hydrogen bonds : angle 5.65465 ( 1851) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 680 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 558 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ILE cc_start: 0.5307 (tp) cc_final: 0.4953 (mt) REVERT: A 92 PHE cc_start: 0.7482 (OUTLIER) cc_final: 0.7154 (t80) REVERT: A 104 MET cc_start: 0.5879 (OUTLIER) cc_final: 0.5446 (mtt) REVERT: A 169 LEU cc_start: 0.6605 (tp) cc_final: 0.6350 (tp) REVERT: A 171 TYR cc_start: 0.6673 (t80) cc_final: 0.6190 (t80) REVERT: A 180 SER cc_start: 0.7424 (t) cc_final: 0.7193 (m) REVERT: A 233 LEU cc_start: 0.7261 (OUTLIER) cc_final: 0.6915 (mm) REVERT: A 265 ARG cc_start: 0.6967 (mtm110) cc_final: 0.6658 (ttm110) REVERT: A 282 GLU cc_start: 0.6995 (pm20) cc_final: 0.6528 (pm20) REVERT: A 311 GLN cc_start: 0.7852 (mm-40) cc_final: 0.7449 (mm-40) REVERT: B 126 LYS cc_start: 0.8510 (ttmm) cc_final: 0.8131 (ttmm) REVERT: B 148 ILE cc_start: 0.7382 (OUTLIER) cc_final: 0.7175 (tp) REVERT: B 185 GLN cc_start: 0.7081 (OUTLIER) cc_final: 0.6455 (pm20) REVERT: B 213 LYS cc_start: 0.7768 (mmtm) cc_final: 0.7527 (mmtm) REVERT: B 240 LEU cc_start: 0.8520 (mp) cc_final: 0.8237 (mp) REVERT: I 90 ILE cc_start: 0.4432 (OUTLIER) cc_final: 0.3993 (mp) REVERT: I 115 MET cc_start: -0.0095 (mmm) cc_final: -0.0331 (mmm) REVERT: D 89 ASP cc_start: 0.8749 (p0) cc_final: 0.8268 (p0) REVERT: D 104 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7452 (mt-10) REVERT: D 227 GLN cc_start: 0.8707 (tt0) cc_final: 0.8349 (tt0) REVERT: D 262 ASP cc_start: 0.8488 (t0) cc_final: 0.8048 (t0) REVERT: E 28 THR cc_start: 0.8648 (p) cc_final: 0.8397 (p) REVERT: E 195 GLN cc_start: 0.8345 (mt0) cc_final: 0.8032 (mt0) REVERT: F 103 LYS cc_start: 0.8782 (mtmm) cc_final: 0.8443 (mtmm) REVERT: F 125 TYR cc_start: 0.8547 (t80) cc_final: 0.8189 (t80) REVERT: F 136 LYS cc_start: 0.8242 (mttp) cc_final: 0.7960 (mttt) REVERT: F 265 TYR cc_start: 0.8388 (p90) cc_final: 0.7941 (p90) REVERT: F 303 ARG cc_start: 0.8461 (mtp-110) cc_final: 0.8106 (mtp180) REVERT: C 72 MET cc_start: -0.0178 (ttm) cc_final: -0.0870 (ttm) REVERT: C 121 LYS cc_start: 0.7991 (mmtt) cc_final: 0.7447 (mmtt) REVERT: C 173 ASN cc_start: 0.8481 (t0) cc_final: 0.8230 (t0) REVERT: C 195 GLN cc_start: 0.8455 (mt0) cc_final: 0.8229 (mt0) REVERT: C 304 MET cc_start: 0.8162 (OUTLIER) cc_final: 0.7879 (ttp) REVERT: G 104 GLU cc_start: 0.8011 (mp0) cc_final: 0.7357 (mp0) REVERT: G 159 GLU cc_start: 0.7952 (tt0) cc_final: 0.7510 (tt0) REVERT: G 188 THR cc_start: 0.8389 (p) cc_final: 0.7937 (t) REVERT: G 198 ASP cc_start: 0.7917 (m-30) cc_final: 0.7586 (m-30) REVERT: G 214 PHE cc_start: 0.8549 (m-80) cc_final: 0.8260 (m-80) REVERT: G 231 PHE cc_start: 0.6498 (OUTLIER) cc_final: 0.6155 (m-80) REVERT: G 244 GLU cc_start: 0.8231 (mt-10) cc_final: 0.7970 (mt-10) REVERT: G 278 GLU cc_start: 0.7363 (OUTLIER) cc_final: 0.6994 (mp0) REVERT: G 300 LEU cc_start: 0.8502 (mm) cc_final: 0.8180 (mt) REVERT: H 113 ASN cc_start: 0.7568 (p0) cc_final: 0.7304 (p0) REVERT: H 121 LYS cc_start: 0.8048 (mmtp) cc_final: 0.7836 (mmtm) REVERT: H 149 TRP cc_start: 0.7305 (m100) cc_final: 0.6682 (m100) REVERT: H 167 LYS cc_start: 0.8047 (tttm) cc_final: 0.7822 (tttm) REVERT: H 186 ASN cc_start: 0.7156 (m-40) cc_final: 0.6742 (m-40) REVERT: H 208 ASN cc_start: 0.8102 (m-40) cc_final: 0.7664 (m-40) REVERT: H 241 PHE cc_start: 0.7209 (t80) cc_final: 0.6609 (t80) REVERT: H 243 PHE cc_start: 0.8000 (t80) cc_final: 0.7717 (t80) REVERT: H 253 LYS cc_start: 0.8312 (tptt) cc_final: 0.8079 (tppt) REVERT: H 299 LYS cc_start: 0.8029 (mtpt) cc_final: 0.7454 (mtmt) REVERT: H 303 ARG cc_start: 0.8278 (ttp-170) cc_final: 0.7957 (ttm170) REVERT: H 320 MET cc_start: 0.7809 (mmm) cc_final: 0.7494 (mmt) outliers start: 122 outliers final: 65 residues processed: 641 average time/residue: 0.1695 time to fit residues: 164.4623 Evaluate side-chains 621 residues out of total 2365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 547 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 92 PHE Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 159 HIS Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 185 GLN Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain I residue 7 ILE Chi-restraints excluded: chain I residue 41 ILE Chi-restraints excluded: chain I residue 89 GLU Chi-restraints excluded: chain I residue 90 ILE Chi-restraints excluded: chain I residue 144 ILE Chi-restraints excluded: chain I residue 162 THR Chi-restraints excluded: chain D residue 26 ASN Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 311 LEU Chi-restraints excluded: chain F residue 105 SER Chi-restraints excluded: chain F residue 267 ASP Chi-restraints excluded: chain F residue 322 ILE Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 108 SER Chi-restraints excluded: chain C residue 136 LYS Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 252 GLN Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain C residue 304 MET Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 109 CYS Chi-restraints excluded: chain G residue 217 ILE Chi-restraints excluded: chain G residue 221 MET Chi-restraints excluded: chain G residue 223 VAL Chi-restraints excluded: chain G residue 231 PHE Chi-restraints excluded: chain G residue 267 ASP Chi-restraints excluded: chain G residue 275 ILE Chi-restraints excluded: chain G residue 278 GLU Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 93 ILE Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 171 SER Chi-restraints excluded: chain H residue 176 SER Chi-restraints excluded: chain H residue 222 GLU Chi-restraints excluded: chain H residue 249 MET Chi-restraints excluded: chain H residue 275 ILE Chi-restraints excluded: chain H residue 311 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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-5986/lib/python3.9/site-packages/iotbx/cli_parser.py", line 995, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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-5986/lib/python3.9/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-5986/lib/python3.9/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-5986/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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-5986/lib/python3.9/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-5986/lib/python3.9/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-5986/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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-5986/lib/python3.9/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-5986/lib/python3.9/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-5986/lib/python3.9/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-5986/lib/python3.9/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-5986/lib/python3.9/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-5986/lib/python3.9/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-5986/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1590, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1493, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1374, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 68.2295 > 50: distance: 72 - 80: 33.422 distance: 80 - 81: 48.016 distance: 81 - 82: 14.006 distance: 81 - 84: 44.364 distance: 84 - 85: 41.088 distance: 90 - 91: 7.487 distance: 91 - 92: 8.746 distance: 91 - 94: 50.589 distance: 92 - 93: 3.224 distance: 92 - 97: 40.715 distance: 94 - 95: 40.760 distance: 97 - 98: 13.891 distance: 98 - 99: 40.610 distance: 98 - 101: 34.901 distance: 99 - 100: 39.966 distance: 99 - 108: 28.143 distance: 101 - 102: 22.155 distance: 102 - 103: 28.282 distance: 102 - 104: 35.981 distance: 103 - 105: 10.832 distance: 104 - 106: 35.222 distance: 105 - 107: 27.478 distance: 106 - 107: 6.446 distance: 108 - 109: 29.095 distance: 109 - 110: 20.898 distance: 109 - 112: 10.966 distance: 110 - 111: 14.277 distance: 110 - 117: 48.871 distance: 112 - 113: 41.596 distance: 114 - 115: 6.363 distance: 115 - 116: 34.186 distance: 117 - 118: 26.870 distance: 118 - 119: 59.022 distance: 118 - 121: 14.070 distance: 119 - 120: 27.633 distance: 119 - 125: 46.148 distance: 121 - 122: 52.013 distance: 122 - 123: 3.585 distance: 122 - 124: 56.194 distance: 125 - 126: 46.338 distance: 125 - 131: 13.680 distance: 126 - 127: 47.260 distance: 126 - 129: 17.887 distance: 127 - 132: 27.974 distance: 129 - 130: 56.306 distance: 130 - 131: 16.276 distance: 132 - 133: 55.999 distance: 133 - 134: 29.307 distance: 133 - 136: 36.538 distance: 134 - 135: 10.045 distance: 134 - 140: 20.200 distance: 136 - 137: 12.171 distance: 137 - 138: 31.745 distance: 137 - 139: 39.424 distance: 140 - 141: 9.059 distance: 141 - 144: 29.286 distance: 142 - 148: 42.105 distance: 144 - 145: 34.731 distance: 145 - 146: 25.701 distance: 145 - 147: 6.632 distance: 148 - 149: 41.340 distance: 149 - 152: 39.775 distance: 150 - 151: 8.842 distance: 150 - 156: 22.976 distance: 152 - 153: 16.496 distance: 156 - 157: 17.034 distance: 156 - 187: 28.072 distance: 157 - 158: 29.612 distance: 157 - 160: 40.875 distance: 158 - 159: 25.611 distance: 158 - 163: 21.139 distance: 159 - 184: 13.734 distance: 160 - 161: 23.421 distance: 160 - 162: 5.164