Starting phenix.real_space_refine on Sat Aug 23 14:15:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9erj_19916/08_2025/9erj_19916.cif Found real_map, /net/cci-nas-00/data/ceres_data/9erj_19916/08_2025/9erj_19916.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9erj_19916/08_2025/9erj_19916.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9erj_19916/08_2025/9erj_19916.map" model { file = "/net/cci-nas-00/data/ceres_data/9erj_19916/08_2025/9erj_19916.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9erj_19916/08_2025/9erj_19916.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.008 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: 7 Type Number sf(0) Gaussians Fe 42 7.16 5 P 3 5.49 5 S 158 5.16 5 Na 3 4.78 5 C 8074 2.51 5 N 2063 2.21 5 O 2320 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s 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: 12663 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1433 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 6, 'TRANS': 184} Chain: "B" Number of atoms: 2394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2394 Classifications: {'peptide': 333} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 315} Chain: "C" Number of atoms: 3287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3287 Classifications: {'peptide': 443} Link IDs: {'PTRANS': 29, 'TRANS': 413} Chain: "D" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2374 Classifications: {'peptide': 318} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 302} Chain: "E" Number of atoms: 1439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1439 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 9, 'TRANS': 186} Chain: "G" Number of atoms: 1531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1531 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 5, 'TRANS': 201} Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 5 Unusual residues: {' NA': 1, 'FES': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 64 Unusual residues: {'SF4': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "C" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 47 Unusual residues: {'FMN': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 57 Unusual residues: {'FMN': 1, 'RBF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'FMN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 199 SG CYS A 25 49.579 62.007 57.442 1.00 51.33 S ATOM 10283 SG CYS E 108 47.804 64.011 54.912 1.00 67.51 S ATOM 857 SG CYS A 113 47.539 59.507 51.450 1.00 60.62 S ATOM 9687 SG CYS E 25 49.832 58.092 54.030 1.00 31.32 S ATOM 2824 SG CYS B 200 59.149 82.820 111.924 1.00 31.17 S ATOM 2373 SG CYS B 138 58.503 76.443 112.910 1.00 25.64 S ATOM 2927 SG CYS B 213 64.145 78.959 112.991 1.00 28.88 S ATOM 2142 SG CYS B 106 60.816 78.688 107.256 1.00 31.76 S ATOM 2447 SG CYS B 148 57.923 74.831 96.280 1.00 21.64 S ATOM 2406 SG CYS B 142 60.301 74.545 102.403 1.00 18.61 S ATOM 2288 SG CYS B 125 56.867 69.843 100.181 1.00 15.63 S ATOM 2688 SG CYS B 182 53.960 75.684 100.916 1.00 23.62 S ATOM 1945 SG CYS B 75 46.354 81.869 72.256 1.00257.80 S ATOM 1840 SG CYS B 58 43.388 79.828 66.558 1.00255.78 S ATOM 1811 SG CYS B 53 45.034 76.484 72.484 1.00244.03 S ATOM 2474 SG CYS B 152 57.377 77.406 87.945 1.00 32.73 S ATOM 2642 SG CYS B 175 51.907 81.009 87.695 1.00 50.15 S ATOM 2623 SG CYS B 172 56.885 84.077 89.484 1.00 44.81 S ATOM 2661 SG CYS B 178 54.431 79.587 93.134 1.00 32.67 S ATOM 3219 SG CYS B 252 60.585 97.569 109.464 1.00 49.60 S ATOM 3013 SG CYS B 227 55.683 101.431 110.144 1.00 62.53 S ATOM 3166 SG CYS B 246 57.407 99.041 104.104 1.00 58.90 S ATOM 2986 SG CYS B 223 57.697 94.125 114.653 1.00 53.53 S ATOM 3249 SG CYS B 256 63.293 90.934 114.306 1.00 49.37 S ATOM 2952 SG CYS B 217 57.747 87.679 115.331 1.00 36.90 S ATOM 2971 SG CYS B 220 60.226 91.909 119.782 1.00 54.16 S ATOM 3650 SG CYS B 310 64.905 112.813 106.264 1.00152.67 S ATOM 3686 SG CYS B 316 61.639 115.064 100.727 1.00159.03 S ATOM 3488 SG CYS B 289 60.522 117.538 106.104 1.00213.89 S ATOM 3668 SG CYS B 313 59.264 110.964 104.659 1.00121.36 S ATOM 3720 SG CYS B 320 58.839 120.131 97.502 1.00212.49 S ATOM 3442 SG CYS B 282 60.138 126.397 98.147 1.00253.84 S ATOM 3423 SG CYS B 279 62.683 125.151 96.048 1.00242.96 S ATOM 3442 SG CYS B 282 60.138 126.397 98.147 1.00253.84 S ATOM 3460 SG CYS B 285 62.457 122.635 101.870 1.00260.55 S ATOM 6915 SG CYS C 418 52.734 46.612 96.042 1.00 8.44 S ATOM 6565 SG CYS C 372 51.049 41.879 92.522 1.00 19.37 S ATOM 6541 SG CYS C 369 52.111 47.790 89.772 1.00 9.31 S ATOM 6584 SG CYS C 375 46.811 46.055 93.570 1.00 7.43 S ATOM 6883 SG CYS C 414 45.532 49.415 99.633 1.00 6.25 S ATOM 6867 SG CYS C 411 41.279 47.687 103.841 1.00 14.73 S ATOM 6608 SG CYS C 379 39.582 47.485 97.763 1.00 17.72 S ATOM 6844 SG CYS C 408 40.508 53.299 100.703 1.00 21.84 S Time building chain proxies: 2.54, per 1000 atoms: 0.20 Number of scatterers: 12663 At special positions: 0 Unit cell: (88.92, 142.12, 158.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 42 26.01 S 158 16.00 P 3 15.00 Na 3 11.00 O 2320 8.00 N 2063 7.00 C 8074 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.93 Conformation dependent library (CDL) restraints added in 504.1 milliseconds Enol-peptide restraints added in 953.7 nanoseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES A 202 " pdb="FE2 FES A 202 " - pdb=" SG CYS E 25 " pdb="FE1 FES A 202 " - pdb=" SG CYS E 108 " pdb="FE1 FES A 202 " - pdb=" SG CYS A 25 " pdb="FE2 FES A 202 " - pdb=" SG CYS A 113 " pdb=" SF4 B 401 " pdb="FE2 SF4 B 401 " - pdb=" SG CYS B 138 " pdb="FE4 SF4 B 401 " - pdb=" SG CYS B 106 " pdb="FE1 SF4 B 401 " - pdb=" SG CYS B 200 " pdb="FE3 SF4 B 401 " - pdb=" SG CYS B 213 " pdb=" SF4 B 402 " pdb="FE2 SF4 B 402 " - pdb=" SG CYS B 142 " pdb="FE4 SF4 B 402 " - pdb=" SG CYS B 182 " pdb="FE1 SF4 B 402 " - pdb=" SG CYS B 148 " pdb="FE3 SF4 B 402 " - pdb=" SG CYS B 125 " pdb=" SF4 B 403 " pdb="FE1 SF4 B 403 " - pdb=" SG CYS B 75 " pdb="FE4 SF4 B 403 " - pdb=" SG CYS B 53 " pdb="FE3 SF4 B 403 " - pdb=" SG CYS B 58 " pdb=" SF4 B 404 " pdb="FE2 SF4 B 404 " - pdb=" SG CYS B 175 " pdb="FE3 SF4 B 404 " - pdb=" SG CYS B 172 " pdb="FE1 SF4 B 404 " - pdb=" SG CYS B 152 " pdb="FE4 SF4 B 404 " - pdb=" SG CYS B 178 " pdb=" SF4 B 405 " pdb="FE4 SF4 B 405 " - pdb=" SG CYS B 246 " pdb="FE1 SF4 B 405 " - pdb=" SG CYS B 252 " pdb="FE3 SF4 B 405 " - pdb=" SG CYS B 227 " pdb=" SF4 B 406 " pdb="FE4 SF4 B 406 " - pdb=" SG CYS B 220 " pdb="FE1 SF4 B 406 " - pdb=" SG CYS B 223 " pdb="FE3 SF4 B 406 " - pdb=" SG CYS B 217 " pdb="FE2 SF4 B 406 " - pdb=" SG CYS B 256 " pdb=" SF4 B 407 " pdb="FE4 SF4 B 407 " - pdb=" SG CYS B 313 " pdb="FE2 SF4 B 407 " - pdb=" SG CYS B 316 " pdb="FE3 SF4 B 407 " - pdb=" SG CYS B 289 " pdb="FE1 SF4 B 407 " - pdb=" SG CYS B 310 " pdb=" SF4 B 408 " pdb="FE1 SF4 B 408 " - pdb=" SG CYS B 320 " pdb="FE4 SF4 B 408 " - pdb=" SG CYS B 285 " pdb="FE3 SF4 B 408 " - pdb=" SG CYS B 282 " pdb="FE3 SF4 B 408 " - pdb=" SG CYS B 279 " pdb=" SF4 C 501 " pdb="FE2 SF4 C 501 " - pdb=" SG CYS C 372 " pdb="FE1 SF4 C 501 " - pdb=" SG CYS C 418 " pdb="FE3 SF4 C 501 " - pdb=" SG CYS C 369 " pdb="FE4 SF4 C 501 " - pdb=" SG CYS C 375 " pdb=" SF4 C 502 " pdb="FE2 SF4 C 502 " - pdb=" SG CYS C 411 " pdb="FE4 SF4 C 502 " - pdb=" SG CYS C 408 " pdb="FE3 SF4 C 502 " - pdb=" SG CYS C 379 " pdb="FE1 SF4 C 502 " - pdb=" SG CYS C 414 " Number of angles added : 120 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3050 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 12 sheets defined 49.3% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 1 through 12 Processing helix chain 'A' and resid 24 through 31 removed outlier: 3.844A pdb=" N SER A 31 " --> pdb=" O PHE A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 62 removed outlier: 4.263A pdb=" N ALA A 53 " --> pdb=" O ALA A 49 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ILE A 54 " --> pdb=" O LEU A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 67 removed outlier: 3.665A pdb=" N SER A 67 " --> pdb=" O ASP A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 70 No H-bonds generated for 'chain 'A' and resid 68 through 70' Processing helix chain 'A' and resid 71 through 94 removed outlier: 3.505A pdb=" N ALA A 75 " --> pdb=" O LEU A 71 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU A 86 " --> pdb=" O ALA A 82 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS A 92 " --> pdb=" O GLU A 88 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LYS A 93 " --> pdb=" O MET A 89 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER A 94 " --> pdb=" O ILE A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 100 Processing helix chain 'A' and resid 113 through 125 Processing helix chain 'A' and resid 128 through 160 removed outlier: 3.856A pdb=" N GLU A 155 " --> pdb=" O ALA A 151 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ARG A 156 " --> pdb=" O GLY A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 185 removed outlier: 3.782A pdb=" N ILE A 171 " --> pdb=" O GLU A 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 28 Proline residue: B 8 - end of helix removed outlier: 3.516A pdb=" N PHE B 19 " --> pdb=" O PHE B 15 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE B 21 " --> pdb=" O LEU B 17 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LYS B 28 " --> pdb=" O ALA B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 91 removed outlier: 3.825A pdb=" N CYS B 82 " --> pdb=" O GLY B 78 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N MET B 90 " --> pdb=" O VAL B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 131 removed outlier: 3.570A pdb=" N ALA B 131 " --> pdb=" O GLU B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 152 removed outlier: 3.581A pdb=" N ALA B 150 " --> pdb=" O GLY B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 213 Processing helix chain 'B' and resid 221 through 227 removed outlier: 3.950A pdb=" N LYS B 225 " --> pdb=" O GLY B 221 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA B 226 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N CYS B 227 " --> pdb=" O CYS B 223 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 221 through 227' Processing helix chain 'B' and resid 251 through 256 removed outlier: 4.031A pdb=" N LYS B 255 " --> pdb=" O GLU B 251 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N CYS B 256 " --> pdb=" O CYS B 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 251 through 256' Processing helix chain 'B' and resid 283 through 288 removed outlier: 4.319A pdb=" N LYS B 287 " --> pdb=" O GLY B 283 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ASN B 288 " --> pdb=" O LEU B 284 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 283 through 288' Processing helix chain 'B' and resid 314 through 318 Processing helix chain 'C' and resid 18 through 23 removed outlier: 4.529A pdb=" N GLU C 23 " --> pdb=" O GLU C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 134 removed outlier: 4.789A pdb=" N ASP C 123 " --> pdb=" O LEU C 119 " (cutoff:3.500A) removed outlier: 8.812A pdb=" N ALA C 124 " --> pdb=" O GLU C 120 " (cutoff:3.500A) removed outlier: 8.822A pdb=" N ASP C 125 " --> pdb=" O ASP C 121 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ALA C 126 " --> pdb=" O MET C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 150 removed outlier: 3.602A pdb=" N LYS C 149 " --> pdb=" O PRO C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 182 removed outlier: 3.548A pdb=" N HIS C 177 " --> pdb=" O THR C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 198 Processing helix chain 'C' and resid 210 through 222 removed outlier: 3.671A pdb=" N GLY C 222 " --> pdb=" O VAL C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 240 removed outlier: 3.785A pdb=" N GLN C 238 " --> pdb=" O LYS C 235 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N GLY C 239 " --> pdb=" O TYR C 236 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA C 240 " --> pdb=" O PRO C 237 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 235 through 240' Processing helix chain 'C' and resid 242 through 249 Processing helix chain 'C' and resid 258 through 262 Processing helix chain 'C' and resid 269 through 282 Processing helix chain 'C' and resid 310 through 318 removed outlier: 3.582A pdb=" N VAL C 314 " --> pdb=" O PRO C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 362 removed outlier: 3.914A pdb=" N LYS C 362 " --> pdb=" O GLU C 359 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 359 through 362' Processing helix chain 'C' and resid 373 through 379 removed outlier: 3.573A pdb=" N GLY C 377 " --> pdb=" O GLY C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 393 removed outlier: 3.607A pdb=" N ILE C 388 " --> pdb=" O GLN C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 403 Processing helix chain 'C' and resid 412 through 417 Processing helix chain 'C' and resid 423 through 439 removed outlier: 3.558A pdb=" N ARG C 439 " --> pdb=" O ILE C 435 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 43 removed outlier: 3.853A pdb=" N ILE D 23 " --> pdb=" O SER D 19 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N MET D 24 " --> pdb=" O THR D 20 " (cutoff:3.500A) Proline residue: D 33 - end of helix Processing helix chain 'D' and resid 44 through 68 removed outlier: 3.670A pdb=" N ALA D 48 " --> pdb=" O LEU D 44 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU D 49 " --> pdb=" O TRP D 45 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N VAL D 50 " --> pdb=" O ALA D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 76 removed outlier: 4.087A pdb=" N ASP D 76 " --> pdb=" O THR D 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 73 through 76' Processing helix chain 'D' and resid 77 through 88 removed outlier: 3.774A pdb=" N VAL D 81 " --> pdb=" O TRP D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 109 removed outlier: 4.343A pdb=" N GLY D 99 " --> pdb=" O PRO D 95 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL D 100 " --> pdb=" O TRP D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 136 removed outlier: 3.512A pdb=" N ARG D 129 " --> pdb=" O ALA D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 140 removed outlier: 3.648A pdb=" N MET D 140 " --> pdb=" O PRO D 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 137 through 140' Processing helix chain 'D' and resid 171 through 178 Processing helix chain 'D' and resid 192 through 197 removed outlier: 3.556A pdb=" N GLY D 197 " --> pdb=" O ALA D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 204 removed outlier: 3.777A pdb=" N LEU D 201 " --> pdb=" O GLY D 197 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE D 202 " --> pdb=" O GLY D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 226 removed outlier: 3.527A pdb=" N LEU D 216 " --> pdb=" O PRO D 212 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE D 219 " --> pdb=" O TYR D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 245 removed outlier: 3.527A pdb=" N PHE D 244 " --> pdb=" O MET D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 278 removed outlier: 3.645A pdb=" N ILE D 262 " --> pdb=" O LYS D 258 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA D 264 " --> pdb=" O GLN D 260 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR D 271 " --> pdb=" O CYS D 267 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N MET D 272 " --> pdb=" O GLY D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 292 Processing helix chain 'D' and resid 294 through 299 Processing helix chain 'E' and resid 2 through 10 removed outlier: 4.057A pdb=" N ASN E 6 " --> pdb=" O ASN E 2 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N GLY E 10 " --> pdb=" O ASN E 6 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 31 removed outlier: 4.133A pdb=" N THR E 27 " --> pdb=" O GLY E 23 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N THR E 31 " --> pdb=" O THR E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 35 through 58 removed outlier: 3.608A pdb=" N LEU E 58 " --> pdb=" O ALA E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 90 removed outlier: 3.809A pdb=" N VAL E 74 " --> pdb=" O ALA E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 97 Processing helix chain 'E' and resid 101 through 106 removed outlier: 3.553A pdb=" N ILE E 104 " --> pdb=" O ILE E 101 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N VAL E 105 " --> pdb=" O PRO E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 118 removed outlier: 3.566A pdb=" N ALA E 118 " --> pdb=" O ALA E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 154 removed outlier: 3.577A pdb=" N PHE E 127 " --> pdb=" O ILE E 123 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA E 128 " --> pdb=" O ALA E 124 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU E 151 " --> pdb=" O ILE E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 195 removed outlier: 3.694A pdb=" N ALA E 178 " --> pdb=" O LEU E 174 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N PHE E 179 " --> pdb=" O PRO E 175 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LEU E 180 " --> pdb=" O PRO E 176 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N THR E 181 " --> pdb=" O GLY E 177 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 6 removed outlier: 3.698A pdb=" N LYS G 6 " --> pdb=" O GLU G 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 2 through 6' Processing helix chain 'G' and resid 8 through 13 removed outlier: 3.783A pdb=" N LYS G 12 " --> pdb=" O GLN G 8 " (cutoff:3.500A) Processing helix chain 'G' and resid 13 through 59 removed outlier: 3.726A pdb=" N LEU G 19 " --> pdb=" O PHE G 15 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE G 20 " --> pdb=" O LYS G 16 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU G 21 " --> pdb=" O LEU G 17 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N LEU G 34 " --> pdb=" O CYS G 30 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N GLY G 41 " --> pdb=" O TYR G 37 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N THR G 42 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N VAL G 58 " --> pdb=" O ALA G 54 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU G 59 " --> pdb=" O ARG G 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 70 through 79 removed outlier: 3.681A pdb=" N GLU G 74 " --> pdb=" O ALA G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 144 through 148 removed outlier: 3.985A pdb=" N ALA G 147 " --> pdb=" O GLY G 144 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N SER G 148 " --> pdb=" O ALA G 145 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 144 through 148' Processing helix chain 'G' and resid 152 through 156 removed outlier: 3.614A pdb=" N THR G 156 " --> pdb=" O ASP G 153 " (cutoff:3.500A) Processing helix chain 'G' and resid 185 through 206 Processing sheet with id=AA1, first strand: chain 'B' and resid 100 through 104 Processing sheet with id=AA2, first strand: chain 'B' and resid 118 through 119 removed outlier: 6.297A pdb=" N GLU B 118 " --> pdb=" O VAL D 8 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 157 through 159 Processing sheet with id=AA4, first strand: chain 'B' and resid 232 through 235 Processing sheet with id=AA5, first strand: chain 'C' and resid 4 through 6 removed outlier: 6.108A pdb=" N LYS C 4 " --> pdb=" O SER C 231 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N GLY C 202 " --> pdb=" O GLU C 228 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N TYR C 230 " --> pdb=" O GLY C 202 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE C 204 " --> pdb=" O TYR C 230 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N LEU C 232 " --> pdb=" O ILE C 204 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL C 206 " --> pdb=" O LEU C 232 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N CYS C 160 " --> pdb=" O VAL C 265 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N MET C 267 " --> pdb=" O CYS C 160 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N VAL C 162 " --> pdb=" O MET C 267 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 27 through 28 removed outlier: 8.215A pdb=" N ILE C 353 " --> pdb=" O TYR C 289 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N THR C 291 " --> pdb=" O ILE C 353 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N CYS C 355 " --> pdb=" O THR C 291 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N THR C 293 " --> pdb=" O CYS C 355 " (cutoff:3.500A) removed outlier: 8.904A pdb=" N THR C 357 " --> pdb=" O THR C 293 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU C 354 " --> pdb=" O VAL C 328 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N VAL C 328 " --> pdb=" O LEU C 354 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N LEU C 356 " --> pdb=" O GLY C 326 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL C 337 " --> pdb=" O SER C 330 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 34 through 38 removed outlier: 3.770A pdb=" N ALA C 84 " --> pdb=" O VAL C 100 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N GLU C 102 " --> pdb=" O VAL C 82 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N VAL C 82 " --> pdb=" O GLU C 102 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY C 80 " --> pdb=" O VAL C 57 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 34 through 38 Processing sheet with id=AA9, first strand: chain 'C' and resid 48 through 49 removed outlier: 6.520A pdb=" N VAL C 74 " --> pdb=" O VAL C 63 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 155 through 156 Processing sheet with id=AB2, first strand: chain 'G' and resid 64 through 67 removed outlier: 3.524A pdb=" N GLY G 94 " --> pdb=" O GLY G 102 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N GLY G 102 " --> pdb=" O GLY G 94 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N SER G 96 " --> pdb=" O VAL G 100 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N VAL G 100 " --> pdb=" O SER G 96 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N GLN G 118 " --> pdb=" O ILE G 135 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY G 122 " --> pdb=" O GLY G 131 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLY G 131 " --> pdb=" O GLY G 122 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 165 through 167 536 hydrogen bonds defined for protein. 1560 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: 1.58 Time building geometry restraints manager: 1.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.42: 4949 1.42 - 1.64: 7678 1.64 - 1.85: 171 1.85 - 2.07: 0 2.07 - 2.28: 124 Bond restraints: 12922 Sorted by residual: bond pdb=" C4 FMN D 401 " pdb=" C4A FMN D 401 " ideal model delta sigma weight residual 1.485 1.407 0.078 2.00e-02 2.50e+03 1.52e+01 bond pdb=" C4 FMN C 503 " pdb=" C4A FMN C 503 " ideal model delta sigma weight residual 1.485 1.407 0.078 2.00e-02 2.50e+03 1.50e+01 bond pdb=" C4 FMN G 301 " pdb=" C4A FMN G 301 " ideal model delta sigma weight residual 1.485 1.408 0.077 2.00e-02 2.50e+03 1.50e+01 bond pdb=" O5' FMN C 503 " pdb=" P FMN C 503 " ideal model delta sigma weight residual 1.676 1.611 0.065 2.00e-02 2.50e+03 1.05e+01 bond pdb=" O5' FMN D 401 " pdb=" P FMN D 401 " ideal model delta sigma weight residual 1.676 1.617 0.059 2.00e-02 2.50e+03 8.61e+00 ... (remaining 12917 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.16: 17473 3.16 - 6.33: 128 6.33 - 9.49: 22 9.49 - 12.66: 2 12.66 - 15.82: 3 Bond angle restraints: 17628 Sorted by residual: angle pdb=" CA GLU G 86 " pdb=" CB GLU G 86 " pdb=" CG GLU G 86 " ideal model delta sigma weight residual 114.10 128.17 -14.07 2.00e+00 2.50e-01 4.95e+01 angle pdb=" C ILE B 65 " pdb=" N VAL B 66 " pdb=" CA VAL B 66 " ideal model delta sigma weight residual 121.97 134.43 -12.46 1.80e+00 3.09e-01 4.79e+01 angle pdb=" CA PRO B 290 " pdb=" CB PRO B 290 " pdb=" CG PRO B 290 " ideal model delta sigma weight residual 104.50 95.06 9.44 1.90e+00 2.77e-01 2.47e+01 angle pdb=" CB GLU G 86 " pdb=" CG GLU G 86 " pdb=" CD GLU G 86 " ideal model delta sigma weight residual 112.60 120.71 -8.11 1.70e+00 3.46e-01 2.27e+01 angle pdb=" N PRO B 290 " pdb=" CD PRO B 290 " pdb=" CG PRO B 290 " ideal model delta sigma weight residual 103.20 96.16 7.04 1.50e+00 4.44e-01 2.20e+01 ... (remaining 17623 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 6683 17.66 - 35.33: 764 35.33 - 52.99: 200 52.99 - 70.65: 23 70.65 - 88.32: 10 Dihedral angle restraints: 7680 sinusoidal: 2904 harmonic: 4776 Sorted by residual: dihedral pdb=" CA CYS B 289 " pdb=" C CYS B 289 " pdb=" N PRO B 290 " pdb=" CA PRO B 290 " ideal model delta harmonic sigma weight residual -180.00 -125.79 -54.21 0 5.00e+00 4.00e-02 1.18e+02 dihedral pdb=" CA ARG E 9 " pdb=" C ARG E 9 " pdb=" N GLY E 10 " pdb=" CA GLY E 10 " ideal model delta harmonic sigma weight residual 180.00 146.38 33.62 0 5.00e+00 4.00e-02 4.52e+01 dihedral pdb=" CA THR D 141 " pdb=" C THR D 141 " pdb=" N SER D 142 " pdb=" CA SER D 142 " ideal model delta harmonic sigma weight residual 180.00 156.63 23.37 0 5.00e+00 4.00e-02 2.18e+01 ... (remaining 7677 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1811 0.062 - 0.125: 304 0.125 - 0.187: 18 0.187 - 0.249: 1 0.249 - 0.311: 3 Chirality restraints: 2137 Sorted by residual: chirality pdb=" CA GLU G 86 " pdb=" N GLU G 86 " pdb=" C GLU G 86 " pdb=" CB GLU G 86 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.42e+00 chirality pdb=" CA ASP B 35 " pdb=" N ASP B 35 " pdb=" C ASP B 35 " pdb=" CB ASP B 35 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" CB VAL B 66 " pdb=" CA VAL B 66 " pdb=" CG1 VAL B 66 " pdb=" CG2 VAL B 66 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.84e+00 ... (remaining 2134 not shown) Planarity restraints: 2169 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS B 289 " 0.061 5.00e-02 4.00e+02 8.82e-02 1.24e+01 pdb=" N PRO B 290 " -0.152 5.00e-02 4.00e+02 pdb=" CA PRO B 290 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO B 290 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 35 " 0.048 5.00e-02 4.00e+02 7.11e-02 8.10e+00 pdb=" N PRO B 36 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO B 36 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 36 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER D 57 " 0.013 2.00e-02 2.50e+03 2.51e-02 6.32e+00 pdb=" C SER D 57 " -0.043 2.00e-02 2.50e+03 pdb=" O SER D 57 " 0.016 2.00e-02 2.50e+03 pdb=" N VAL D 58 " 0.015 2.00e-02 2.50e+03 ... (remaining 2166 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 3217 2.80 - 3.33: 10826 3.33 - 3.85: 18973 3.85 - 4.38: 21628 4.38 - 4.90: 39177 Nonbonded interactions: 93821 Sorted by model distance: nonbonded pdb=" O THR B 173 " pdb=" OG1 THR B 173 " model vdw 2.277 3.040 nonbonded pdb=" O SER G 206 " pdb=" OG SER G 206 " model vdw 2.284 3.040 nonbonded pdb=" O THR E 27 " pdb=" OG1 THR E 31 " model vdw 2.300 3.040 nonbonded pdb=" OD1 ASP C 208 " pdb=" OG1 THR C 234 " model vdw 2.304 3.040 nonbonded pdb=" O ALA E 178 " pdb=" OG1 THR E 181 " model vdw 2.335 3.040 ... (remaining 93816 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 3.870 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: 0.250 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.590 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 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:5.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 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 0.078 12966 Z= 0.200 Angle : 1.105 61.890 17748 Z= 0.423 Chirality : 0.046 0.311 2137 Planarity : 0.007 0.088 2169 Dihedral : 16.045 88.319 4630 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.48 % Allowed : 7.22 % Favored : 92.30 % Rotamer: Outliers : 1.41 % Allowed : 18.49 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.06 % 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: -1.42 (0.20), residues: 1676 helix: 0.17 (0.19), residues: 747 sheet: 0.07 (0.50), residues: 106 loop : -2.21 (0.20), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 228 TYR 0.018 0.001 TYR D 263 PHE 0.015 0.001 PHE E 179 TRP 0.009 0.001 TRP E 191 HIS 0.005 0.001 HIS C 5 Details of bonding type rmsd covalent geometry : bond 0.00366 (12922) covalent geometry : angle 0.76309 (17628) hydrogen bonds : bond 0.16585 ( 532) hydrogen bonds : angle 6.34931 ( 1560) metal coordination : bond 0.00537 ( 42) metal coordination : angle 9.74384 ( 120) Misc. bond : bond 0.04548 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 149 time to evaluate : 0.475 Fit side-chains revert: symmetry clash REVERT: A 164 LYS cc_start: 0.7623 (tptp) cc_final: 0.7385 (pmtt) REVERT: B 90 MET cc_start: 0.6322 (mpp) cc_final: 0.6086 (mpt) REVERT: E 64 ASP cc_start: 0.8175 (m-30) cc_final: 0.7797 (t0) REVERT: E 121 ASN cc_start: 0.8808 (m110) cc_final: 0.8579 (m110) outliers start: 19 outliers final: 4 residues processed: 164 average time/residue: 0.5105 time to fit residues: 91.4403 Evaluate side-chains 126 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 122 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain G residue 128 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.0170 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 0.9980 overall best weight: 0.9622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 112 ASN C 182 GLN G 118 GLN ** G 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 203 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.107289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.063949 restraints weight = 22750.752| |-----------------------------------------------------------------------------| r_work (start): 0.2735 rms_B_bonded: 3.30 r_work: 0.2616 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.1130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12966 Z= 0.137 Angle : 1.018 67.489 17748 Z= 0.331 Chirality : 0.044 0.256 2137 Planarity : 0.005 0.070 2169 Dihedral : 5.747 56.692 1817 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.48 % Allowed : 6.86 % Favored : 92.66 % Rotamer: Outliers : 3.41 % Allowed : 18.86 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.06 % 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: -0.68 (0.21), residues: 1676 helix: 1.08 (0.20), residues: 757 sheet: -0.00 (0.48), residues: 114 loop : -2.13 (0.20), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 55 TYR 0.018 0.001 TYR D 263 PHE 0.009 0.001 PHE D 131 TRP 0.005 0.001 TRP D 97 HIS 0.002 0.000 HIS C 5 Details of bonding type rmsd covalent geometry : bond 0.00303 (12922) covalent geometry : angle 0.62405 (17628) hydrogen bonds : bond 0.05732 ( 532) hydrogen bonds : angle 4.26644 ( 1560) metal coordination : bond 0.00623 ( 42) metal coordination : angle 9.80199 ( 120) Misc. bond : bond 0.00025 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 134 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 164 LYS cc_start: 0.8617 (tptp) cc_final: 0.7464 (pmtt) REVERT: B 31 GLU cc_start: 0.5106 (OUTLIER) cc_final: 0.4741 (mm-30) REVERT: C 33 GLU cc_start: 0.8837 (OUTLIER) cc_final: 0.8536 (pm20) REVERT: C 123 ASP cc_start: 0.5480 (OUTLIER) cc_final: 0.5245 (p0) REVERT: E 14 GLU cc_start: 0.8522 (mt-10) cc_final: 0.8236 (mt-10) REVERT: E 64 ASP cc_start: 0.8634 (m-30) cc_final: 0.7638 (t0) REVERT: E 121 ASN cc_start: 0.8204 (m110) cc_final: 0.7440 (m-40) REVERT: G 82 MET cc_start: 0.9117 (ttm) cc_final: 0.8318 (tmm) REVERT: G 139 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7588 (mt-10) outliers start: 46 outliers final: 18 residues processed: 161 average time/residue: 0.4696 time to fit residues: 82.8299 Evaluate side-chains 146 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 124 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 158 GLU Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 110 CYS Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 258 MET Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 282 CYS Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 192 LYS Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 139 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 51 optimal weight: 4.9990 chunk 131 optimal weight: 3.9990 chunk 119 optimal weight: 0.0980 chunk 32 optimal weight: 4.9990 chunk 76 optimal weight: 0.0170 chunk 29 optimal weight: 1.9990 chunk 149 optimal weight: 4.9990 chunk 139 optimal weight: 1.9990 chunk 142 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 84 optimal weight: 5.9990 overall best weight: 0.7420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 GLN ** G 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.107593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.064668 restraints weight = 22972.271| |-----------------------------------------------------------------------------| r_work (start): 0.2752 rms_B_bonded: 3.26 r_work: 0.2631 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12966 Z= 0.118 Angle : 0.996 68.993 17748 Z= 0.311 Chirality : 0.043 0.245 2137 Planarity : 0.005 0.055 2169 Dihedral : 5.427 55.181 1812 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.48 % Allowed : 6.62 % Favored : 92.90 % Rotamer: Outliers : 3.56 % Allowed : 19.38 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.06 % 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: -0.37 (0.21), residues: 1676 helix: 1.41 (0.20), residues: 760 sheet: 0.17 (0.50), residues: 107 loop : -2.04 (0.21), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 440 TYR 0.017 0.001 TYR D 263 PHE 0.009 0.001 PHE B 30 TRP 0.005 0.001 TRP D 97 HIS 0.002 0.000 HIS C 5 Details of bonding type rmsd covalent geometry : bond 0.00256 (12922) covalent geometry : angle 0.58731 (17628) hydrogen bonds : bond 0.04941 ( 532) hydrogen bonds : angle 3.92032 ( 1560) metal coordination : bond 0.00510 ( 42) metal coordination : angle 9.79838 ( 120) Misc. bond : bond 0.00022 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 134 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 ILE cc_start: 0.5370 (OUTLIER) cc_final: 0.4801 (tt) REVERT: A 164 LYS cc_start: 0.8573 (tptp) cc_final: 0.7447 (pmtt) REVERT: C 33 GLU cc_start: 0.8843 (OUTLIER) cc_final: 0.8531 (pm20) REVERT: C 123 ASP cc_start: 0.5423 (OUTLIER) cc_final: 0.5207 (p0) REVERT: E 14 GLU cc_start: 0.8439 (mt-10) cc_final: 0.8129 (mt-10) REVERT: E 64 ASP cc_start: 0.8588 (m-30) cc_final: 0.7558 (t0) REVERT: E 121 ASN cc_start: 0.8222 (m110) cc_final: 0.7849 (m110) outliers start: 48 outliers final: 21 residues processed: 164 average time/residue: 0.4618 time to fit residues: 83.3779 Evaluate side-chains 152 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 128 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 158 GLU Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain B residue 35 ASP Chi-restraints excluded: chain B residue 58 CYS Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 282 CYS Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 140 THR Chi-restraints excluded: chain G residue 153 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 154 optimal weight: 10.0000 chunk 125 optimal weight: 1.9990 chunk 111 optimal weight: 0.0980 chunk 114 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 101 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 chunk 127 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 22 optimal weight: 0.0870 chunk 76 optimal weight: 2.9990 overall best weight: 1.2162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 GLN D 89 ASN G 176 ASN G 203 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.105512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.062508 restraints weight = 22988.901| |-----------------------------------------------------------------------------| r_work (start): 0.2713 rms_B_bonded: 3.26 r_work: 0.2591 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12966 Z= 0.141 Angle : 1.022 69.825 17748 Z= 0.325 Chirality : 0.044 0.227 2137 Planarity : 0.005 0.069 2169 Dihedral : 5.459 55.136 1812 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.48 % Allowed : 7.10 % Favored : 92.42 % Rotamer: Outliers : 3.27 % Allowed : 20.56 % Favored : 76.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.06 % 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: -0.27 (0.21), residues: 1676 helix: 1.49 (0.20), residues: 760 sheet: 0.17 (0.49), residues: 114 loop : -2.00 (0.21), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 37 TYR 0.018 0.001 TYR D 263 PHE 0.010 0.001 PHE D 131 TRP 0.005 0.001 TRP D 97 HIS 0.002 0.001 HIS C 5 Details of bonding type rmsd covalent geometry : bond 0.00330 (12922) covalent geometry : angle 0.61366 (17628) hydrogen bonds : bond 0.05399 ( 532) hydrogen bonds : angle 3.94796 ( 1560) metal coordination : bond 0.00674 ( 42) metal coordination : angle 9.95922 ( 120) Misc. bond : bond 0.00047 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 123 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 164 LYS cc_start: 0.8607 (tptp) cc_final: 0.7469 (pmtt) REVERT: B 1 MET cc_start: 0.6189 (tpt) cc_final: 0.5904 (tpp) REVERT: C 33 GLU cc_start: 0.8871 (OUTLIER) cc_final: 0.8542 (pm20) REVERT: C 123 ASP cc_start: 0.5628 (OUTLIER) cc_final: 0.5406 (p0) REVERT: E 14 GLU cc_start: 0.8451 (mt-10) cc_final: 0.8123 (mt-10) REVERT: E 64 ASP cc_start: 0.8671 (m-30) cc_final: 0.7219 (t0) REVERT: E 121 ASN cc_start: 0.8288 (m110) cc_final: 0.7943 (m110) REVERT: G 176 ASN cc_start: 0.7411 (OUTLIER) cc_final: 0.7116 (p0) outliers start: 44 outliers final: 21 residues processed: 156 average time/residue: 0.4587 time to fit residues: 78.7045 Evaluate side-chains 146 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 122 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 158 GLU Chi-restraints excluded: chain B residue 58 CYS Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 282 CYS Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 140 THR Chi-restraints excluded: chain G residue 153 ASP Chi-restraints excluded: chain G residue 176 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- 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: 53.4698 > 50: distance: 50 - 107: 8.878 distance: 53 - 104: 6.791 distance: 58 - 64: 19.936 distance: 64 - 65: 46.503 distance: 65 - 66: 17.034 distance: 66 - 67: 43.041 distance: 66 - 68: 49.638 distance: 68 - 69: 17.615 distance: 69 - 70: 13.919 distance: 69 - 72: 22.412 distance: 70 - 71: 18.725 distance: 70 - 77: 20.477 distance: 72 - 73: 24.997 distance: 73 - 74: 11.611 distance: 74 - 75: 5.741 distance: 74 - 76: 4.613 distance: 77 - 78: 10.644 distance: 78 - 79: 7.814 distance: 78 - 81: 15.354 distance: 79 - 80: 10.087 distance: 79 - 85: 9.344 distance: 81 - 82: 18.486 distance: 82 - 83: 10.589 distance: 82 - 84: 10.690 distance: 85 - 86: 7.070 distance: 86 - 87: 18.256 distance: 87 - 88: 25.442 distance: 87 - 89: 21.409 distance: 89 - 90: 28.871 distance: 90 - 91: 5.601 distance: 90 - 93: 28.052 distance: 91 - 92: 30.988 distance: 91 - 97: 28.935 distance: 93 - 94: 16.455 distance: 94 - 95: 12.507 distance: 94 - 96: 11.846 distance: 97 - 98: 12.600 distance: 97 - 103: 9.298 distance: 98 - 99: 7.454 distance: 98 - 101: 21.602 distance: 99 - 100: 15.795 distance: 99 - 104: 13.358 distance: 101 - 102: 22.612 distance: 102 - 103: 10.900 distance: 104 - 105: 11.562 distance: 105 - 106: 4.783 distance: 105 - 108: 14.370 distance: 106 - 107: 15.965 distance: 106 - 113: 22.846 distance: 108 - 109: 13.677 distance: 110 - 111: 3.453 distance: 113 - 114: 30.067 distance: 114 - 115: 11.782 distance: 114 - 117: 15.546 distance: 115 - 116: 28.644 distance: 115 - 120: 18.486 distance: 117 - 118: 36.394 distance: 117 - 119: 31.183 distance: 120 - 121: 18.482 distance: 121 - 122: 17.503 distance: 121 - 124: 28.255 distance: 122 - 123: 24.573 distance: 122 - 128: 15.883 distance: 124 - 125: 15.776 distance: 125 - 126: 5.672 distance: 125 - 127: 13.280 distance: 128 - 129: 32.114 distance: 128 - 134: 23.215 distance: 129 - 130: 11.660 distance: 129 - 132: 8.346 distance: 130 - 131: 8.714 distance: 130 - 135: 11.525 distance: 132 - 133: 15.159 distance: 133 - 134: 13.431