Starting phenix.real_space_refine on Sun Aug 24 14:05:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6x6a_22074/08_2025/6x6a_22074.cif Found real_map, /net/cci-nas-00/data/ceres_data/6x6a_22074/08_2025/6x6a_22074.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6x6a_22074/08_2025/6x6a_22074.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6x6a_22074/08_2025/6x6a_22074.map" model { file = "/net/cci-nas-00/data/ceres_data/6x6a_22074/08_2025/6x6a_22074.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6x6a_22074/08_2025/6x6a_22074.cif" } resolution = 3.6 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 100 5.16 5 C 13051 2.51 5 N 3429 2.21 5 O 3660 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-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20240 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 846, 6816 Classifications: {'peptide': 846} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 54, 'TRANS': 791} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1068 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 10, 'TRANS': 123} Chain: "G" Number of atoms: 1107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1107 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 10, 'TRANS': 127} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 1136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1136 Classifications: {'peptide': 144} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 11, 'TRANS': 132} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "D" Number of atoms: 6816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 846, 6816 Classifications: {'peptide': 846} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 54, 'TRANS': 791} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "E" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1053 Classifications: {'peptide': 134} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 123} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'PHE:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "I" Number of atoms: 1103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1103 Classifications: {'peptide': 138} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 127} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 1141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1141 Classifications: {'peptide': 144} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 11, 'TRANS': 132} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.94, per 1000 atoms: 0.24 Number of scatterers: 20240 At special positions: 0 Unit cell: (129.525, 161.7, 114.675, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 100 16.00 O 3660 8.00 N 3429 7.00 C 13051 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: 1.50 Conformation dependent library (CDL) restraints added in 891.9 milliseconds Enol-peptide restraints added in 1.4 microseconds 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4696 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 39 sheets defined 18.7% alpha, 25.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid 30 through 49 removed outlier: 4.191A pdb=" N TYR A 44 " --> pdb=" O GLY A 40 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLY A 46 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N LEU A 47 " --> pdb=" O LYS A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 120 removed outlier: 3.540A pdb=" N VAL A 120 " --> pdb=" O HIS A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 133 Processing helix chain 'A' and resid 243 through 250 Processing helix chain 'A' and resid 341 through 346 Processing helix chain 'A' and resid 382 through 384 No H-bonds generated for 'chain 'A' and resid 382 through 384' Processing helix chain 'A' and resid 392 through 403 Processing helix chain 'A' and resid 446 through 450 Processing helix chain 'A' and resid 583 through 587 Processing helix chain 'A' and resid 661 through 671 removed outlier: 3.608A pdb=" N ASN A 665 " --> pdb=" O TYR A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 691 Processing helix chain 'A' and resid 692 through 694 No H-bonds generated for 'chain 'A' and resid 692 through 694' Processing helix chain 'A' and resid 700 through 716 Processing helix chain 'A' and resid 730 through 743 Processing helix chain 'A' and resid 758 through 762 Processing helix chain 'A' and resid 763 through 771 removed outlier: 4.295A pdb=" N ARG A 769 " --> pdb=" O GLY A 765 " (cutoff:3.500A) Processing helix chain 'A' and resid 777 through 785 Processing helix chain 'A' and resid 786 through 793 removed outlier: 3.825A pdb=" N VAL A 790 " --> pdb=" O ALA A 787 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N GLU A 791 " --> pdb=" O LEU A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 812 through 827 removed outlier: 4.297A pdb=" N THR A 816 " --> pdb=" O HIS A 812 " (cutoff:3.500A) Processing helix chain 'A' and resid 844 through 863 Processing helix chain 'B' and resid 1132 through 1137 removed outlier: 3.565A pdb=" N GLY B1137 " --> pdb=" O ASP B1133 " (cutoff:3.500A) Processing helix chain 'G' and resid 1256 through 1270 Processing helix chain 'C' and resid 1258 through 1270 removed outlier: 4.133A pdb=" N ALA C1262 " --> pdb=" O SER C1258 " (cutoff:3.500A) Processing helix chain 'C' and resid 1295 through 1300 removed outlier: 4.120A pdb=" N MET C1299 " --> pdb=" O SER C1295 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 49 removed outlier: 3.801A pdb=" N TYR D 44 " --> pdb=" O GLY D 40 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU D 47 " --> pdb=" O LYS D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 120 removed outlier: 3.544A pdb=" N VAL D 120 " --> pdb=" O HIS D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 133 Processing helix chain 'D' and resid 243 through 250 Processing helix chain 'D' and resid 294 through 298 Processing helix chain 'D' and resid 341 through 346 Processing helix chain 'D' and resid 382 through 384 No H-bonds generated for 'chain 'D' and resid 382 through 384' Processing helix chain 'D' and resid 392 through 403 Processing helix chain 'D' and resid 661 through 671 removed outlier: 3.622A pdb=" N ASN D 665 " --> pdb=" O TYR D 661 " (cutoff:3.500A) Processing helix chain 'D' and resid 686 through 691 Processing helix chain 'D' and resid 692 through 694 No H-bonds generated for 'chain 'D' and resid 692 through 694' Processing helix chain 'D' and resid 700 through 716 Processing helix chain 'D' and resid 730 through 743 Processing helix chain 'D' and resid 758 through 762 Processing helix chain 'D' and resid 763 through 771 removed outlier: 4.095A pdb=" N ARG D 769 " --> pdb=" O GLY D 765 " (cutoff:3.500A) Processing helix chain 'D' and resid 777 through 785 Processing helix chain 'D' and resid 786 through 793 removed outlier: 4.033A pdb=" N VAL D 790 " --> pdb=" O ALA D 787 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N GLU D 791 " --> pdb=" O LEU D 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 812 through 827 removed outlier: 4.393A pdb=" N THR D 816 " --> pdb=" O HIS D 812 " (cutoff:3.500A) Processing helix chain 'D' and resid 844 through 863 Processing helix chain 'E' and resid 1132 through 1137 Processing helix chain 'E' and resid 1141 through 1145 Processing helix chain 'I' and resid 1256 through 1270 Processing helix chain 'F' and resid 1228 through 1236 removed outlier: 3.788A pdb=" N SER F1233 " --> pdb=" O ILE F1229 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL F1234 " --> pdb=" O PRO F1230 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU F1236 " --> pdb=" O THR F1232 " (cutoff:3.500A) Processing helix chain 'F' and resid 1258 through 1270 Processing sheet with id=AA1, first strand: chain 'A' and resid 54 through 60 removed outlier: 5.954A pdb=" N ASP A 55 " --> pdb=" O LEU A 75 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N LEU A 75 " --> pdb=" O ASP A 55 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 100 through 103 removed outlier: 3.652A pdb=" N LEU A 100 " --> pdb=" O LEU B1194 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N VAL G1217 " --> pdb=" O ALA B1185 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N PHE B1187 " --> pdb=" O LEU G1215 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N LEU G1215 " --> pdb=" O PHE B1187 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 142 through 145 removed outlier: 4.135A pdb=" N ALA A 155 " --> pdb=" O SER A 158 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER A 158 " --> pdb=" O ALA A 155 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 189 through 193 removed outlier: 6.491A pdb=" N SER A 202 " --> pdb=" O PRO A 191 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N ILE A 193 " --> pdb=" O PHE A 200 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N PHE A 200 " --> pdb=" O ILE A 193 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 237 through 239 removed outlier: 3.679A pdb=" N SER A 263 " --> pdb=" O THR A 272 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 256 through 258 removed outlier: 9.093A pdb=" N LEU A 317 " --> pdb=" O LEU A 338 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N LEU A 338 " --> pdb=" O LEU A 317 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 287 through 291 Processing sheet with id=AA8, first strand: chain 'A' and resid 351 through 357 removed outlier: 5.470A pdb=" N ILE A 352 " --> pdb=" O LEU A 369 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LEU A 369 " --> pdb=" O ILE A 352 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG A 354 " --> pdb=" O MET A 367 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU A 376 " --> pdb=" O GLU A 414 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N GLU A 414 " --> pdb=" O LEU A 376 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LEU A 378 " --> pdb=" O VAL A 412 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 427 through 429 removed outlier: 3.527A pdb=" N HIS A 453 " --> pdb=" O ASN A 445 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 505 through 507 Processing sheet with id=AB2, first strand: chain 'A' and resid 547 through 552 removed outlier: 6.458A pdb=" N VAL A 572 " --> pdb=" O MET A 595 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N LYS A 576 " --> pdb=" O PHE A 591 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N PHE A 591 " --> pdb=" O LYS A 576 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N SER A 578 " --> pdb=" O PRO A 589 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 609 through 614 removed outlier: 4.457A pdb=" N ILE A 677 " --> pdb=" O PHE A 642 " (cutoff:3.500A) removed outlier: 10.207A pdb=" N HIS A 637 " --> pdb=" O LEU A 721 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ARG A 723 " --> pdb=" O HIS A 637 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N TRP A 729 " --> pdb=" O VAL A 643 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ALA A 750 " --> pdb=" O LEU A 801 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N LEU A 803 " --> pdb=" O ALA A 750 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ALA A 752 " --> pdb=" O LEU A 803 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N GLY A 805 " --> pdb=" O ALA A 752 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 1089 through 1092 removed outlier: 3.671A pdb=" N VAL B1091 " --> pdb=" O LEU B1097 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N LEU B1097 " --> pdb=" O VAL B1091 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL B1123 " --> pdb=" O PHE B1102 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 1116 through 1118 removed outlier: 3.837A pdb=" N VAL B1164 " --> pdb=" O LEU B1207 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG B1199 " --> pdb=" O VAL B1206 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 1230 through 1231 removed outlier: 3.550A pdb=" N LEU G1284 " --> pdb=" O VAL G1231 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 1238 through 1239 removed outlier: 3.531A pdb=" N VAL G1273 " --> pdb=" O HIS G1239 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 1247 through 1251 removed outlier: 3.512A pdb=" N TYR G1324 " --> pdb=" O GLU G1301 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU G1301 " --> pdb=" O TYR G1324 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 1306 through 1308 removed outlier: 4.176A pdb=" N VAL G1336 " --> pdb=" O TRP G1346 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N TRP G1346 " --> pdb=" O VAL G1336 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ASP G1338 " --> pdb=" O LEU G1344 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N LEU G1344 " --> pdb=" O ASP G1338 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 1238 through 1241 removed outlier: 6.069A pdb=" N VAL C1246 " --> pdb=" O VAL C1325 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 1306 through 1309 removed outlier: 3.851A pdb=" N LEU C1309 " --> pdb=" O CYS C1288 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N CYS C1288 " --> pdb=" O LEU C1309 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE C1332 " --> pdb=" O VAL C1350 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 54 through 60 removed outlier: 4.291A pdb=" N PHE D 56 " --> pdb=" O TYR D 73 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N TYR D 73 " --> pdb=" O PHE D 56 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N PHE D 58 " --> pdb=" O ARG D 71 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ARG D 71 " --> pdb=" O PHE D 58 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N GLN D 60 " --> pdb=" O SER D 69 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N SER D 69 " --> pdb=" O GLN D 60 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 100 through 103 removed outlier: 3.686A pdb=" N LEU D 100 " --> pdb=" O LEU E1194 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 142 through 145 Processing sheet with id=AC6, first strand: chain 'D' and resid 189 through 193 removed outlier: 6.463A pdb=" N SER D 202 " --> pdb=" O PRO D 191 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N ILE D 193 " --> pdb=" O PHE D 200 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N PHE D 200 " --> pdb=" O ILE D 193 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 237 through 239 Processing sheet with id=AC8, first strand: chain 'D' and resid 256 through 258 removed outlier: 9.030A pdb=" N LEU D 317 " --> pdb=" O LEU D 338 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N LEU D 338 " --> pdb=" O LEU D 317 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 287 through 291 Processing sheet with id=AD1, first strand: chain 'D' and resid 351 through 357 removed outlier: 6.686A pdb=" N MET D 367 " --> pdb=" O ALA D 353 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ALA D 355 " --> pdb=" O TRP D 365 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N TRP D 365 " --> pdb=" O ALA D 355 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LEU D 376 " --> pdb=" O GLU D 414 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N GLU D 414 " --> pdb=" O LEU D 376 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU D 378 " --> pdb=" O VAL D 412 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 427 through 429 Processing sheet with id=AD3, first strand: chain 'D' and resid 505 through 507 Processing sheet with id=AD4, first strand: chain 'D' and resid 547 through 552 removed outlier: 6.586A pdb=" N VAL D 572 " --> pdb=" O MET D 595 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N LYS D 576 " --> pdb=" O PHE D 591 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N PHE D 591 " --> pdb=" O LYS D 576 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N SER D 578 " --> pdb=" O PRO D 589 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 609 through 614 removed outlier: 4.309A pdb=" N TYR D 622 " --> pdb=" O ASP D 678 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ILE D 677 " --> pdb=" O PHE D 642 " (cutoff:3.500A) removed outlier: 9.567A pdb=" N HIS D 637 " --> pdb=" O LEU D 721 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N ARG D 723 " --> pdb=" O HIS D 637 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N VAL D 749 " --> pdb=" O SER D 722 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL D 724 " --> pdb=" O VAL D 749 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N ILE D 751 " --> pdb=" O VAL D 724 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ILE D 726 " --> pdb=" O ILE D 751 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N GLY D 753 " --> pdb=" O ILE D 726 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N GLY D 728 " --> pdb=" O GLY D 753 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ALA D 750 " --> pdb=" O LEU D 801 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N LEU D 803 " --> pdb=" O ALA D 750 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ALA D 752 " --> pdb=" O LEU D 803 " (cutoff:3.500A) removed outlier: 8.599A pdb=" N GLY D 805 " --> pdb=" O ALA D 752 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 1116 through 1118 removed outlier: 3.646A pdb=" N CYS E1116 " --> pdb=" O HIS E1165 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 1199 through 1200 removed outlier: 3.934A pdb=" N ARG E1199 " --> pdb=" O VAL E1206 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 1230 through 1231 removed outlier: 3.773A pdb=" N LEU I1284 " --> pdb=" O VAL I1231 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 1237 through 1238 Processing sheet with id=AE1, first strand: chain 'I' and resid 1290 through 1294 removed outlier: 7.476A pdb=" N VAL I1336 " --> pdb=" O VAL I1345 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 1273 through 1274 removed outlier: 3.997A pdb=" N THR F1247 " --> pdb=" O ARG F1240 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N VAL F1246 " --> pdb=" O VAL F1325 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'F' and resid 1290 through 1293 removed outlier: 6.616A pdb=" N ASP F1338 " --> pdb=" O LEU F1344 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N LEU F1344 " --> pdb=" O ASP F1338 " (cutoff:3.500A) 676 hydrogen bonds defined for protein. 1779 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.82 Time building geometry restraints manager: 2.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3347 1.32 - 1.44: 5827 1.44 - 1.57: 11501 1.57 - 1.69: 7 1.69 - 1.81: 156 Bond restraints: 20838 Sorted by residual: bond pdb=" C TYR A 731 " pdb=" O TYR A 731 " ideal model delta sigma weight residual 1.237 1.192 0.045 1.17e-02 7.31e+03 1.48e+01 bond pdb=" C GLY A 728 " pdb=" O GLY A 728 " ideal model delta sigma weight residual 1.233 1.196 0.037 9.80e-03 1.04e+04 1.40e+01 bond pdb=" C ARG A 371 " pdb=" O ARG A 371 " ideal model delta sigma weight residual 1.244 1.211 0.033 9.80e-03 1.04e+04 1.11e+01 bond pdb=" N ASN E1140 " pdb=" CA ASN E1140 " ideal model delta sigma weight residual 1.461 1.490 -0.029 9.20e-03 1.18e+04 9.60e+00 bond pdb=" C SER A 730 " pdb=" O SER A 730 " ideal model delta sigma weight residual 1.235 1.197 0.039 1.26e-02 6.30e+03 9.48e+00 ... (remaining 20833 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.68: 26818 2.68 - 5.35: 1254 5.35 - 8.03: 180 8.03 - 10.71: 41 10.71 - 13.38: 5 Bond angle restraints: 28298 Sorted by residual: angle pdb=" N ASN E1140 " pdb=" CA ASN E1140 " pdb=" C ASN E1140 " ideal model delta sigma weight residual 112.75 124.46 -11.71 1.36e+00 5.41e-01 7.42e+01 angle pdb=" N LYS I1220 " pdb=" CA LYS I1220 " pdb=" C LYS I1220 " ideal model delta sigma weight residual 111.28 120.22 -8.94 1.09e+00 8.42e-01 6.73e+01 angle pdb=" N TRP D 729 " pdb=" CA TRP D 729 " pdb=" C TRP D 729 " ideal model delta sigma weight residual 111.96 123.41 -11.45 1.41e+00 5.03e-01 6.59e+01 angle pdb=" CA TRP D 729 " pdb=" C TRP D 729 " pdb=" N SER D 730 " ideal model delta sigma weight residual 117.34 126.21 -8.87 1.22e+00 6.72e-01 5.28e+01 angle pdb=" N ILE I1302 " pdb=" CA ILE I1302 " pdb=" C ILE I1302 " ideal model delta sigma weight residual 107.75 117.75 -10.00 1.42e+00 4.96e-01 4.96e+01 ... (remaining 28293 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 11053 17.76 - 35.52: 1061 35.52 - 53.28: 169 53.28 - 71.03: 47 71.03 - 88.79: 12 Dihedral angle restraints: 12342 sinusoidal: 5024 harmonic: 7318 Sorted by residual: dihedral pdb=" CA TYR D 770 " pdb=" C TYR D 770 " pdb=" N MET D 771 " pdb=" CA MET D 771 " ideal model delta harmonic sigma weight residual 180.00 150.54 29.46 0 5.00e+00 4.00e-02 3.47e+01 dihedral pdb=" CA LEU C1300 " pdb=" C LEU C1300 " pdb=" N GLU C1301 " pdb=" CA GLU C1301 " ideal model delta harmonic sigma weight residual -180.00 -151.67 -28.33 0 5.00e+00 4.00e-02 3.21e+01 dihedral pdb=" CA SER I1233 " pdb=" C SER I1233 " pdb=" N VAL I1234 " pdb=" CA VAL I1234 " ideal model delta harmonic sigma weight residual -180.00 -152.73 -27.27 0 5.00e+00 4.00e-02 2.97e+01 ... (remaining 12339 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 2410 0.093 - 0.185: 506 0.185 - 0.278: 77 0.278 - 0.370: 16 0.370 - 0.463: 4 Chirality restraints: 3013 Sorted by residual: chirality pdb=" CB ILE C1302 " pdb=" CA ILE C1302 " pdb=" CG1 ILE C1302 " pdb=" CG2 ILE C1302 " both_signs ideal model delta sigma weight residual False 2.64 2.18 0.46 2.00e-01 2.50e+01 5.35e+00 chirality pdb=" CA ASN E1140 " pdb=" N ASN E1140 " pdb=" C ASN E1140 " pdb=" CB ASN E1140 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.21e+00 chirality pdb=" CB ILE D 426 " pdb=" CA ILE D 426 " pdb=" CG1 ILE D 426 " pdb=" CG2 ILE D 426 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.40 2.00e-01 2.50e+01 3.96e+00 ... (remaining 3010 not shown) Planarity restraints: 3657 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL I1292 " 0.020 2.00e-02 2.50e+03 4.06e-02 1.64e+01 pdb=" C VAL I1292 " -0.070 2.00e-02 2.50e+03 pdb=" O VAL I1292 " 0.026 2.00e-02 2.50e+03 pdb=" N SER I1293 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 393 " 0.019 2.00e-02 2.50e+03 3.77e-02 1.42e+01 pdb=" C GLU A 393 " -0.065 2.00e-02 2.50e+03 pdb=" O GLU A 393 " 0.024 2.00e-02 2.50e+03 pdb=" N GLU A 394 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU D 393 " -0.018 2.00e-02 2.50e+03 3.56e-02 1.27e+01 pdb=" C GLU D 393 " 0.062 2.00e-02 2.50e+03 pdb=" O GLU D 393 " -0.023 2.00e-02 2.50e+03 pdb=" N GLU D 394 " -0.021 2.00e-02 2.50e+03 ... (remaining 3654 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 2520 2.74 - 3.28: 19071 3.28 - 3.82: 35094 3.82 - 4.36: 41632 4.36 - 4.90: 71084 Nonbonded interactions: 169401 Sorted by model distance: nonbonded pdb=" OH TYR A 644 " pdb=" O SER C1213 " model vdw 2.206 3.040 nonbonded pdb=" OH TYR D 73 " pdb=" OD2 ASP D 164 " model vdw 2.210 3.040 nonbonded pdb=" CG TYR G1238 " pdb=" OE2 GLU G1267 " model vdw 2.213 3.260 nonbonded pdb=" O LYS A 348 " pdb=" OD1 ASP A 370 " model vdw 2.225 3.040 nonbonded pdb=" OG SER D 230 " pdb=" OD1 ASN D 231 " model vdw 2.254 3.040 ... (remaining 169396 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = (chain 'B' and ((resid 1079 through 1080 and (name N or name CA or name C or nam \ e O or name CB )) or resid 1081 through 1212)) selection = chain 'E' } ncs_group { reference = (chain 'C' and ((resid 1213 and (name CA or name C or name O or name CB or name \ OG )) or resid 1214 through 1276 or (resid 1277 and (name N or name CA or name C \ or name O or name CB )) or resid 1278 through 1350)) selection = (chain 'F' and ((resid 1213 and (name CA or name C or name O or name CB or name \ OG )) or resid 1214 through 1225 or (resid 1226 and (name N or name CA or name C \ or name O or name CB )) or resid 1227 or (resid 1228 through 1229 and (name N o \ r name CA or name C or name O or name CB )) or resid 1230 through 1350)) selection = (chain 'G' and (resid 1213 through 1219 or (resid 1220 and (name N or name CA or \ name C or name O or name CB )) or resid 1221 through 1225 or (resid 1226 and (n \ ame N or name CA or name C or name O or name CB )) or resid 1227 or (resid 1228 \ through 1229 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 230 through 1276 or (resid 1277 and (name N or name CA or name C or name O or na \ me CB )) or resid 1278 through 1350)) selection = (chain 'I' and (resid 1213 through 1219 or (resid 1220 and (name N or name CA or \ name C or name O or name CB )) or resid 1221 through 1225 or (resid 1226 and (n \ ame N or name CA or name C or name O or name CB )) or resid 1227 or (resid 1228 \ through 1229 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 230 through 1350)) } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 20.880 Find NCS groups from input model: 0.320 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: 0.000 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 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 0.112 20838 Z= 0.444 Angle : 1.291 13.382 28298 Z= 0.727 Chirality : 0.078 0.463 3013 Planarity : 0.009 0.085 3657 Dihedral : 14.434 88.793 7646 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.50 % Favored : 92.38 % Rotamer: Outliers : 0.45 % Allowed : 1.27 % Favored : 98.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -2.80 (0.15), residues: 2508 helix: -1.59 (0.23), residues: 378 sheet: -2.25 (0.17), residues: 724 loop : -1.66 (0.15), residues: 1406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG G1333 TYR 0.056 0.004 TYR A 781 PHE 0.056 0.004 PHE D 711 TRP 0.039 0.004 TRP A 375 HIS 0.024 0.003 HIS A 111 Details of bonding type rmsd covalent geometry : bond 0.01009 (20838) covalent geometry : angle 1.29059 (28298) hydrogen bonds : bond 0.14437 ( 668) hydrogen bonds : angle 8.57491 ( 1779) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5016 Ramachandran restraints generated. 2508 Oldfield, 0 Emsley, 2508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 267 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ASP cc_start: 0.8060 (t0) cc_final: 0.7526 (t70) REVERT: A 738 MET cc_start: 0.8501 (mmm) cc_final: 0.8223 (mmm) REVERT: B 1099 ARG cc_start: 0.7178 (mtp-110) cc_final: 0.6868 (mtp180) REVERT: B 1119 MET cc_start: 0.6018 (ptp) cc_final: 0.5776 (pmm) REVERT: B 1178 ASP cc_start: 0.7384 (t0) cc_final: 0.7111 (t70) REVERT: B 1203 HIS cc_start: 0.6519 (m-70) cc_final: 0.6314 (m170) REVERT: G 1263 ILE cc_start: 0.7810 (pt) cc_final: 0.7471 (pt) REVERT: G 1330 SER cc_start: 0.7451 (t) cc_final: 0.7018 (m) REVERT: C 1260 ARG cc_start: 0.7587 (mtp180) cc_final: 0.7124 (ttt-90) REVERT: C 1286 MET cc_start: 0.3543 (ptt) cc_final: 0.3216 (ptm) REVERT: D 251 ASP cc_start: 0.8025 (m-30) cc_final: 0.7723 (t0) REVERT: D 684 GLN cc_start: 0.7870 (mp10) cc_final: 0.7034 (mp10) REVERT: E 1096 ASN cc_start: 0.7374 (t0) cc_final: 0.7122 (t0) REVERT: E 1119 MET cc_start: 0.5535 (tpp) cc_final: 0.5066 (mpp) REVERT: I 1227 ARG cc_start: 0.6008 (tpp-160) cc_final: 0.5740 (tpp-160) REVERT: I 1338 ASP cc_start: 0.6554 (t0) cc_final: 0.6299 (t0) REVERT: F 1289 ARG cc_start: 0.7427 (mtt180) cc_final: 0.7157 (mtm-85) outliers start: 10 outliers final: 5 residues processed: 276 average time/residue: 0.1780 time to fit residues: 73.2899 Evaluate side-chains 207 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 202 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain C residue 1217 VAL Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain I residue 1320 PHE Chi-restraints excluded: chain I residue 1332 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/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-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 57.5271 > 50: distance: 11 - 109: 16.661 distance: 20 - 100: 5.729 distance: 23 - 97: 8.325 distance: 59 - 65: 3.260 distance: 65 - 66: 19.481 distance: 65 - 71: 15.778 distance: 66 - 67: 10.100 distance: 66 - 69: 18.529 distance: 67 - 68: 21.714 distance: 67 - 72: 29.502 distance: 69 - 70: 7.049 distance: 70 - 71: 14.857 distance: 72 - 73: 22.960 distance: 73 - 74: 24.944 distance: 74 - 75: 17.055 distance: 74 - 76: 21.928 distance: 76 - 77: 29.581 distance: 77 - 78: 5.956 distance: 77 - 80: 20.176 distance: 78 - 79: 16.513 distance: 78 - 81: 10.249 distance: 81 - 82: 17.202 distance: 82 - 83: 7.684 distance: 82 - 85: 11.763 distance: 83 - 84: 10.845 distance: 83 - 88: 26.480 distance: 85 - 86: 14.469 distance: 85 - 87: 16.983 distance: 88 - 89: 8.354 distance: 89 - 90: 9.847 distance: 89 - 92: 7.820 distance: 90 - 91: 15.373 distance: 90 - 97: 19.114 distance: 92 - 93: 10.006 distance: 93 - 94: 9.750 distance: 94 - 95: 4.796 distance: 94 - 96: 5.368 distance: 97 - 98: 4.554 distance: 98 - 99: 5.074 distance: 98 - 101: 9.861 distance: 99 - 100: 3.753 distance: 99 - 102: 16.228 distance: 102 - 103: 11.592 distance: 103 - 104: 7.730 distance: 103 - 106: 5.815 distance: 104 - 105: 13.179 distance: 104 - 109: 6.740 distance: 106 - 107: 20.951 distance: 106 - 108: 15.942 distance: 109 - 110: 15.620 distance: 110 - 111: 7.472 distance: 110 - 113: 11.679 distance: 111 - 112: 10.030 distance: 111 - 119: 18.694 distance: 113 - 114: 6.440 distance: 114 - 115: 18.777 distance: 114 - 116: 13.266 distance: 115 - 117: 9.929 distance: 116 - 118: 14.056 distance: 117 - 118: 8.142 distance: 119 - 120: 14.324 distance: 120 - 121: 21.545 distance: 120 - 123: 11.454 distance: 121 - 122: 19.439 distance: 121 - 127: 11.943 distance: 123 - 124: 9.197 distance: 124 - 125: 18.984 distance: 124 - 126: 19.832 distance: 127 - 128: 17.269 distance: 127 - 133: 34.519 distance: 128 - 129: 16.941 distance: 128 - 131: 20.944 distance: 129 - 130: 30.860 distance: 129 - 134: 11.003 distance: 131 - 132: 40.450 distance: 132 - 133: 28.427