Starting phenix.real_space_refine on Sat Jul 4 11:14:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8thd_41254/07_2026/8thd_41254.cif Found real_map, /net/cci-nas-00/data/ceres_data/8thd_41254/07_2026/8thd_41254.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8thd_41254/07_2026/8thd_41254.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8thd_41254/07_2026/8thd_41254.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8thd_41254/07_2026/8thd_41254.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8thd_41254/07_2026/8thd_41254.map" } resolution = 3.25 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= 0.026 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: 6 Type Number sf(0) Gaussians P 14 5.49 5 Mg 3 5.21 5 S 98 5.16 5 C 12905 2.51 5 N 3437 2.21 5 O 3939 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20396 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 3863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3863 Classifications: {'peptide': 474} Link IDs: {'PTRANS': 21, 'TRANS': 452} Chain breaks: 4 Chain: "B" Number of atoms: 2495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2495 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 9, 'TRANS': 308} Chain: "C" Number of atoms: 2571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2571 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 12, 'TRANS': 312} Chain: "D" Number of atoms: 2629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2629 Classifications: {'peptide': 332} Link IDs: {'PTRANS': 12, 'TRANS': 319} Chain: "E" Number of atoms: 2675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2675 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 14, 'TRANS': 324} Chain breaks: 1 Chain: "F" Number of atoms: 1995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1995 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 8, 'TRANS': 245} Chain: "G" Number of atoms: 2011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2011 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 8, 'TRANS': 247} Chain: "H" Number of atoms: 2003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 2003 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 8, 'TRANS': 246} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.17, per 1000 atoms: 0.20 Number of scatterers: 20396 At special positions: 0 Unit cell: (115.92, 119.232, 150.696, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 98 16.00 P 14 15.00 Mg 3 11.99 O 3939 8.00 N 3437 7.00 C 12905 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: 1.66 Conformation dependent library (CDL) restraints added in 827.6 milliseconds 5054 Ramachandran restraints generated. 2527 Oldfield, 0 Emsley, 2527 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4898 Finding SS restraints... Secondary structure from input PDB file: 106 helices and 16 sheets defined 50.0% alpha, 14.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'A' and resid 203 through 209 Processing helix chain 'A' and resid 240 through 245 Processing helix chain 'A' and resid 256 through 276 removed outlier: 3.586A pdb=" N LYS A 276 " --> pdb=" O HIS A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 356 Processing helix chain 'A' and resid 373 through 387 removed outlier: 6.616A pdb=" N ASP A 379 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N ILE A 380 " --> pdb=" O ASP A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 429 Processing helix chain 'A' and resid 445 through 455 removed outlier: 3.514A pdb=" N GLN A 455 " --> pdb=" O LEU A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 481 removed outlier: 3.521A pdb=" N VAL A 469 " --> pdb=" O SER A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 496 Processing helix chain 'A' and resid 499 through 511 Processing helix chain 'A' and resid 535 through 557 removed outlier: 3.660A pdb=" N ILE A 539 " --> pdb=" O SER A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 581 Processing helix chain 'A' and resid 585 through 592 removed outlier: 3.518A pdb=" N PHE A 592 " --> pdb=" O MET A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 629 removed outlier: 3.786A pdb=" N HIS A 620 " --> pdb=" O ASN A 616 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARG A 628 " --> pdb=" O GLN A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 639 removed outlier: 3.996A pdb=" N ARG A 633 " --> pdb=" O TYR A 629 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N HIS A 637 " --> pdb=" O ARG A 633 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N LEU A 639 " --> pdb=" O ALA A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 661 Processing helix chain 'A' and resid 700 through 708 removed outlier: 4.138A pdb=" N LEU A 706 " --> pdb=" O GLU A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 716 Processing helix chain 'A' and resid 716 through 735 Processing helix chain 'A' and resid 773 through 781 Processing helix chain 'B' and resid 10 through 15 Processing helix chain 'B' and resid 26 through 40 Processing helix chain 'B' and resid 54 through 68 Processing helix chain 'B' and resid 70 through 74 Processing helix chain 'B' and resid 85 through 99 removed outlier: 4.052A pdb=" N ILE B 93 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N LYS B 94 " --> pdb=" O ARG B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 119 Processing helix chain 'B' and resid 120 through 134 removed outlier: 4.027A pdb=" N ARG B 129 " --> pdb=" O GLN B 125 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR B 130 " --> pdb=" O ALA B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 150 removed outlier: 3.742A pdb=" N LYS B 149 " --> pdb=" O GLN B 146 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE B 150 " --> pdb=" O SER B 147 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 146 through 150' Processing helix chain 'B' and resid 151 through 156 Processing helix chain 'B' and resid 167 through 183 Processing helix chain 'B' and resid 187 through 199 Processing helix chain 'B' and resid 201 through 217 Processing helix chain 'B' and resid 220 through 225 Processing helix chain 'B' and resid 232 through 242 Processing helix chain 'B' and resid 244 through 255 Processing helix chain 'B' and resid 262 through 277 Processing helix chain 'B' and resid 281 through 302 Processing helix chain 'B' and resid 305 through 322 removed outlier: 3.786A pdb=" N LEU B 309 " --> pdb=" O THR B 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 19 Processing helix chain 'C' and resid 23 through 27 removed outlier: 3.671A pdb=" N VAL C 27 " --> pdb=" O LEU C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 44 Processing helix chain 'C' and resid 58 through 72 Processing helix chain 'C' and resid 74 through 78 Processing helix chain 'C' and resid 88 through 102 removed outlier: 3.871A pdb=" N VAL C 92 " --> pdb=" O ARG C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 137 Processing helix chain 'C' and resid 149 through 153 removed outlier: 3.735A pdb=" N LYS C 152 " --> pdb=" O TYR C 149 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU C 153 " --> pdb=" O ALA C 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 149 through 153' Processing helix chain 'C' and resid 154 through 159 Processing helix chain 'C' and resid 170 through 186 removed outlier: 3.525A pdb=" N HIS C 184 " --> pdb=" O ASN C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 202 removed outlier: 3.923A pdb=" N ASN C 202 " --> pdb=" O ILE C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 219 Processing helix chain 'C' and resid 228 through 236 removed outlier: 3.574A pdb=" N ILE C 232 " --> pdb=" O SER C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 254 Processing helix chain 'C' and resid 255 through 271 Processing helix chain 'C' and resid 273 through 288 removed outlier: 3.651A pdb=" N ASP C 287 " --> pdb=" O LYS C 283 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR C 288 " --> pdb=" O ILE C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 313 Processing helix chain 'C' and resid 315 through 334 removed outlier: 3.578A pdb=" N GLU C 334 " --> pdb=" O SER C 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 31 Processing helix chain 'D' and resid 42 through 55 removed outlier: 4.124A pdb=" N VAL D 48 " --> pdb=" O HIS D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 83 Processing helix chain 'D' and resid 84 through 92 removed outlier: 4.344A pdb=" N LYS D 89 " --> pdb=" O PRO D 85 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N SER D 90 " --> pdb=" O ASP D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 115 Processing helix chain 'D' and resid 153 through 160 Processing helix chain 'D' and resid 193 through 208 Processing helix chain 'D' and resid 215 through 225 Processing helix chain 'D' and resid 227 through 246 Processing helix chain 'D' and resid 252 through 261 removed outlier: 3.519A pdb=" N VAL D 256 " --> pdb=" O THR D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 278 Processing helix chain 'D' and resid 279 through 292 removed outlier: 3.844A pdb=" N LYS D 292 " --> pdb=" O ASN D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 310 removed outlier: 3.563A pdb=" N VAL D 300 " --> pdb=" O SER D 296 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR D 310 " --> pdb=" O GLU D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 335 removed outlier: 3.589A pdb=" N TRP D 324 " --> pdb=" O ASN D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 353 Processing helix chain 'E' and resid 3 through 8 Processing helix chain 'E' and resid 19 through 32 removed outlier: 3.897A pdb=" N GLN E 32 " --> pdb=" O SER E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 61 Processing helix chain 'E' and resid 62 through 67 Processing helix chain 'E' and resid 97 through 105 removed outlier: 7.971A pdb=" N ASN E 103 " --> pdb=" O ASP E 100 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASN E 104 " --> pdb=" O MET E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 119 removed outlier: 4.044A pdb=" N MET E 119 " --> pdb=" O GLU E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 146 Processing helix chain 'E' and resid 147 through 161 removed outlier: 3.517A pdb=" N GLU E 159 " --> pdb=" O ARG E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 184 Processing helix chain 'E' and resid 194 through 210 Processing helix chain 'E' and resid 216 through 227 removed outlier: 3.720A pdb=" N LYS E 220 " --> pdb=" O LYS E 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 245 Processing helix chain 'E' and resid 257 through 273 Processing helix chain 'E' and resid 275 through 292 Processing helix chain 'E' and resid 295 through 308 Processing helix chain 'E' and resid 314 through 334 Processing helix chain 'E' and resid 337 through 354 removed outlier: 4.092A pdb=" N HIS E 341 " --> pdb=" O LYS E 337 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASP E 354 " --> pdb=" O MET E 350 " (cutoff:3.500A) Processing helix chain 'F' and resid 8 through 19 removed outlier: 4.257A pdb=" N PHE F 12 " --> pdb=" O GLU F 8 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N PHE F 19 " --> pdb=" O ILE F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 72 through 81 Processing helix chain 'F' and resid 141 through 155 removed outlier: 3.624A pdb=" N GLN F 153 " --> pdb=" O ARG F 149 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LEU F 154 " --> pdb=" O ASP F 150 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER F 155 " --> pdb=" O LEU F 151 " (cutoff:3.500A) Processing helix chain 'F' and resid 163 through 166 Processing helix chain 'F' and resid 209 through 216 Processing helix chain 'F' and resid 217 through 221 removed outlier: 3.812A pdb=" N SER F 220 " --> pdb=" O LYS F 217 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 21 removed outlier: 3.507A pdb=" N LYS G 13 " --> pdb=" O ALA G 9 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ASP G 21 " --> pdb=" O ASP G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 57 No H-bonds generated for 'chain 'G' and resid 55 through 57' Processing helix chain 'G' and resid 72 through 80 Processing helix chain 'G' and resid 141 through 152 Processing helix chain 'G' and resid 209 through 217 Processing helix chain 'G' and resid 218 through 221 Processing helix chain 'H' and resid 9 through 18 removed outlier: 3.633A pdb=" N LYS H 13 " --> pdb=" O ALA H 9 " (cutoff:3.500A) Processing helix chain 'H' and resid 72 through 80 Processing helix chain 'H' and resid 141 through 152 Processing helix chain 'H' and resid 190 through 194 Processing helix chain 'H' and resid 209 through 216 Processing helix chain 'H' and resid 217 through 219 No H-bonds generated for 'chain 'H' and resid 217 through 219' Processing sheet with id=AA1, first strand: chain 'A' and resid 227 through 228 removed outlier: 3.749A pdb=" N VAL A 227 " --> pdb=" O GLU A 483 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 362 through 365 removed outlier: 3.664A pdb=" N CYS A 438 " --> pdb=" O LEU A 336 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N ILE A 335 " --> pdb=" O PHE A 459 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N THR A 461 " --> pdb=" O ILE A 335 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N HIS A 337 " --> pdb=" O THR A 461 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 600 through 601 removed outlier: 6.411A pdb=" N LEU A 600 " --> pdb=" O VAL E 76 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 75 through 77 removed outlier: 6.033A pdb=" N LYS B 109 " --> pdb=" O ARG B 139 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N ALA B 141 " --> pdb=" O LYS B 109 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N VAL B 111 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N ALA B 143 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N LEU B 113 " --> pdb=" O ALA B 143 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N MET B 45 " --> pdb=" O PHE B 142 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N CYS B 144 " --> pdb=" O MET B 45 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ILE B 47 " --> pdb=" O CYS B 144 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 49 through 52 removed outlier: 6.281A pdb=" N LEU C 50 " --> pdb=" O PHE C 164 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 79 through 83 removed outlier: 6.116A pdb=" N LYS C 112 " --> pdb=" O ARG C 142 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 63 through 64 Processing sheet with id=AA8, first strand: chain 'D' and resid 135 through 140 removed outlier: 5.544A pdb=" N LYS D 135 " --> pdb=" O ARG D 165 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N CYS D 167 " --> pdb=" O LYS D 135 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N ILE D 137 " --> pdb=" O CYS D 167 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ILE D 169 " --> pdb=" O ILE D 137 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N LEU D 139 " --> pdb=" O ILE D 169 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'E' and resid 93 through 96 removed outlier: 6.498A pdb=" N LEU E 94 " --> pdb=" O ILE E 139 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N ASN E 141 " --> pdb=" O LEU E 94 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ILE E 96 " --> pdb=" O ASN E 141 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N LYS E 136 " --> pdb=" O ARG E 166 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N ILE E 168 " --> pdb=" O LYS E 136 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N VAL E 138 " --> pdb=" O ILE E 168 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N VAL E 170 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ILE E 140 " --> pdb=" O VAL E 170 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU E 39 " --> pdb=" O MET E 169 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N CYS E 171 " --> pdb=" O LEU E 39 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N LEU E 41 " --> pdb=" O CYS E 171 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 57 through 60 removed outlier: 3.597A pdb=" N GLU F 59 " --> pdb=" O LYS F 5 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N LEU F 88 " --> pdb=" O PHE F 6 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 66 through 71 removed outlier: 3.751A pdb=" N MET F 70 " --> pdb=" O VAL F 26 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N VAL F 26 " --> pdb=" O MET F 70 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N LEU F 25 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N VAL F 40 " --> pdb=" O LEU F 25 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ASN F 27 " --> pdb=" O GLN F 38 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLN F 38 " --> pdb=" O ASN F 27 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU F 250 " --> pdb=" O ALA F 235 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ASP F 240 " --> pdb=" O ARG F 224 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N ARG F 224 " --> pdb=" O ASP F 240 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR F 136 " --> pdb=" O GLU F 198 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS F 196 " --> pdb=" O SER F 138 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 204 through 208 removed outlier: 3.759A pdb=" N LEU F 205 " --> pdb=" O ILE F 160 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N SER F 157 " --> pdb=" O ASP F 172 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N ASP F 172 " --> pdb=" O SER F 157 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA F 171 " --> pdb=" O GLY F 178 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLY F 178 " --> pdb=" O ALA F 171 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER F 177 " --> pdb=" O SER G 115 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER F 179 " --> pdb=" O GLU G 113 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLU G 113 " --> pdb=" O SER F 179 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE G 100 " --> pdb=" O ILE G 91 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU G 2 " --> pdb=" O ALA G 92 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 66 through 71 removed outlier: 3.792A pdb=" N MET G 70 " --> pdb=" O VAL G 26 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N VAL G 26 " --> pdb=" O MET G 70 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N LEU G 25 " --> pdb=" O VAL G 40 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N VAL G 40 " --> pdb=" O LEU G 25 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N ASN G 27 " --> pdb=" O GLN G 38 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N GLN G 38 " --> pdb=" O ASN G 27 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ASP G 240 " --> pdb=" O ARG G 224 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ARG G 224 " --> pdb=" O ASP G 240 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 206 through 208 removed outlier: 6.028A pdb=" N SER G 157 " --> pdb=" O ASP G 172 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ASP G 172 " --> pdb=" O SER G 157 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE G 181 " --> pdb=" O ILE H 111 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE H 111 " --> pdb=" O ILE G 181 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LEU H 88 " --> pdb=" O PHE H 6 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU H 59 " --> pdb=" O LYS H 5 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 66 through 71 removed outlier: 5.936A pdb=" N LEU H 25 " --> pdb=" O VAL H 40 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N VAL H 40 " --> pdb=" O LEU H 25 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASN H 27 " --> pdb=" O GLN H 38 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N SER H 230 " --> pdb=" O PRO H 234 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ASP H 240 " --> pdb=" O ARG H 224 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ARG H 224 " --> pdb=" O ASP H 240 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU H 139 " --> pdb=" O VAL H 225 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 177 through 182 removed outlier: 3.548A pdb=" N GLY H 178 " --> pdb=" O ALA H 171 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA H 171 " --> pdb=" O GLY H 178 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N ASP H 172 " --> pdb=" O SER H 157 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N SER H 157 " --> pdb=" O ASP H 172 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N LEU H 205 " --> pdb=" O ILE H 160 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ILE H 162 " --> pdb=" O VAL H 203 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N VAL H 203 " --> pdb=" O ILE H 162 " (cutoff:3.500A) 1047 hydrogen bonds defined for protein. 3015 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: 4.05 Time building geometry restraints manager: 2.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 6749 1.36 - 1.51: 5016 1.51 - 1.65: 8806 1.65 - 1.80: 75 1.80 - 1.95: 77 Bond restraints: 20723 Sorted by residual: bond pdb=" O3B AGS D 401 " pdb=" PB AGS D 401 " ideal model delta sigma weight residual 1.673 1.584 0.089 2.00e-02 2.50e+03 2.00e+01 bond pdb=" O3B AGS B 401 " pdb=" PB AGS B 401 " ideal model delta sigma weight residual 1.673 1.585 0.088 2.00e-02 2.50e+03 1.93e+01 bond pdb=" O3B AGS A 801 " pdb=" PB AGS A 801 " ideal model delta sigma weight residual 1.673 1.586 0.087 2.00e-02 2.50e+03 1.89e+01 bond pdb=" O3B AGS C 401 " pdb=" PB AGS C 401 " ideal model delta sigma weight residual 1.673 1.588 0.085 2.00e-02 2.50e+03 1.81e+01 bond pdb=" O3A AGS C 401 " pdb=" PA AGS C 401 " ideal model delta sigma weight residual 1.664 1.587 0.077 2.00e-02 2.50e+03 1.50e+01 ... (remaining 20718 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 27454 2.13 - 4.26: 471 4.26 - 6.40: 74 6.40 - 8.53: 22 8.53 - 10.66: 17 Bond angle restraints: 28038 Sorted by residual: angle pdb=" CA ILE E 96 " pdb=" C ILE E 96 " pdb=" O ILE E 96 " ideal model delta sigma weight residual 121.64 117.90 3.74 9.80e-01 1.04e+00 1.46e+01 angle pdb=" N ILE F 128 " pdb=" CA ILE F 128 " pdb=" C ILE F 128 " ideal model delta sigma weight residual 111.91 108.62 3.29 8.90e-01 1.26e+00 1.37e+01 angle pdb=" N LYS G 20 " pdb=" CA LYS G 20 " pdb=" C LYS G 20 " ideal model delta sigma weight residual 111.02 115.53 -4.51 1.22e+00 6.72e-01 1.37e+01 angle pdb=" CA CYS H 81 " pdb=" C CYS H 81 " pdb=" O CYS H 81 " ideal model delta sigma weight residual 122.63 117.87 4.76 1.29e+00 6.01e-01 1.36e+01 angle pdb=" O3A AGS D 401 " pdb=" PB AGS D 401 " pdb=" O3B AGS D 401 " ideal model delta sigma weight residual 100.38 111.04 -10.66 3.00e+00 1.11e-01 1.26e+01 ... (remaining 28033 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.19: 12398 35.19 - 70.37: 426 70.37 - 105.56: 36 105.56 - 140.75: 1 140.75 - 175.94: 5 Dihedral angle restraints: 12866 sinusoidal: 5364 harmonic: 7502 Sorted by residual: dihedral pdb=" O1B ADP E 401 " pdb=" O3A ADP E 401 " pdb=" PB ADP E 401 " pdb=" PA ADP E 401 " ideal model delta sinusoidal sigma weight residual 300.00 174.65 125.35 1 2.00e+01 2.50e-03 3.79e+01 dihedral pdb=" O1A AGS C 401 " pdb=" O3A AGS C 401 " pdb=" PA AGS C 401 " pdb=" PB AGS C 401 " ideal model delta sinusoidal sigma weight residual 82.37 -93.57 175.94 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O2B AGS C 401 " pdb=" O3B AGS C 401 " pdb=" PB AGS C 401 " pdb=" PG AGS C 401 " ideal model delta sinusoidal sigma weight residual 7.37 -178.90 -173.73 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 12863 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 2740 0.055 - 0.111: 470 0.111 - 0.166: 61 0.166 - 0.221: 7 0.221 - 0.276: 5 Chirality restraints: 3283 Sorted by residual: chirality pdb=" C3' AGS D 401 " pdb=" C2' AGS D 401 " pdb=" C4' AGS D 401 " pdb=" O3' AGS D 401 " both_signs ideal model delta sigma weight residual False -2.37 -2.65 0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" CB ILE F 162 " pdb=" CA ILE F 162 " pdb=" CG1 ILE F 162 " pdb=" CG2 ILE F 162 " both_signs ideal model delta sigma weight residual False 2.64 2.91 -0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" C3' AGS C 401 " pdb=" C2' AGS C 401 " pdb=" C4' AGS C 401 " pdb=" O3' AGS C 401 " both_signs ideal model delta sigma weight residual False -2.37 -2.63 0.26 2.00e-01 2.50e+01 1.74e+00 ... (remaining 3280 not shown) Planarity restraints: 3551 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO D 66 " 0.060 5.00e-02 4.00e+02 9.03e-02 1.31e+01 pdb=" N PRO D 67 " -0.156 5.00e-02 4.00e+02 pdb=" CA PRO D 67 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO D 67 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 196 " -0.044 5.00e-02 4.00e+02 6.40e-02 6.56e+00 pdb=" N PRO A 197 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 197 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 197 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA CYS C 144 " 0.012 2.00e-02 2.50e+03 2.41e-02 5.82e+00 pdb=" C CYS C 144 " -0.042 2.00e-02 2.50e+03 pdb=" O CYS C 144 " 0.016 2.00e-02 2.50e+03 pdb=" N VAL C 145 " 0.014 2.00e-02 2.50e+03 ... (remaining 3548 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 301 2.67 - 3.22: 19112 3.22 - 3.78: 31860 3.78 - 4.34: 43124 4.34 - 4.90: 71679 Nonbonded interactions: 166076 Sorted by model distance: nonbonded pdb=" O GLY D 70 " pdb=" OG1 THR D 74 " model vdw 2.107 3.040 nonbonded pdb=" OG1 THR B 56 " pdb="MG MG B 402 " model vdw 2.142 2.170 nonbonded pdb=" OD2 ASP D 140 " pdb="MG MG D 402 " model vdw 2.210 2.170 nonbonded pdb=" O LYS F 31 " pdb=" OH TYR F 60 " model vdw 2.252 3.040 nonbonded pdb=" O2B AGS D 401 " pdb="MG MG D 402 " model vdw 2.255 2.170 ... (remaining 166071 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 'F' selection = (chain 'G' and resid 1 through 254) selection = (chain 'H' and resid 1 through 254) } 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: 5.020 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: 0.020 Extract box with map and model: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 18.840 Find NCS groups from input model: 0.240 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 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 0.099 20723 Z= 0.218 Angle : 0.724 10.661 28038 Z= 0.384 Chirality : 0.043 0.276 3283 Planarity : 0.005 0.090 3551 Dihedral : 17.508 175.937 7968 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.43 % Allowed : 18.06 % Favored : 81.50 % 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 are not related in a simple way. whole: 0.17 (0.16), residues: 2527 helix: 1.22 (0.15), residues: 1144 sheet: 0.11 (0.25), residues: 471 loop : -1.28 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 149 TYR 0.016 0.001 TYR D 64 PHE 0.025 0.001 PHE A 509 TRP 0.009 0.001 TRP A 488 HIS 0.004 0.001 HIS D 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.22 (20723) covalent geometry : angle 0.72389 / 0.38 (28038) hydrogen bonds : bond 0.17325 / 11.55 ( 1047) hydrogen bonds : angle 6.77174 / 4.76 ( 3015) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5054 Ramachandran restraints generated. 2527 Oldfield, 0 Emsley, 2527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5054 Ramachandran restraints generated. 2527 Oldfield, 0 Emsley, 2527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 663 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 653 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 GLN cc_start: 0.6874 (OUTLIER) cc_final: 0.6582 (tp40) REVERT: A 359 ASN cc_start: 0.7637 (p0) cc_final: 0.7185 (t0) REVERT: A 361 TYR cc_start: 0.8663 (p90) cc_final: 0.8170 (p90) REVERT: A 505 MET cc_start: 0.8954 (tpp) cc_final: 0.8424 (mmt) REVERT: A 588 MET cc_start: 0.7567 (mmp) cc_final: 0.6882 (mtm) REVERT: C 15 TRP cc_start: 0.8650 (m-10) cc_final: 0.8228 (m-10) REVERT: C 30 GLN cc_start: 0.8102 (mm-40) cc_final: 0.7671 (mm-40) REVERT: C 109 LYS cc_start: 0.6745 (OUTLIER) cc_final: 0.6031 (mptt) REVERT: D 49 LEU cc_start: 0.8525 (mt) cc_final: 0.8256 (mt) REVERT: D 83 TYR cc_start: 0.5684 (m-10) cc_final: 0.5181 (m-10) REVERT: D 132 PRO cc_start: 0.7948 (Cg_exo) cc_final: 0.7743 (Cg_endo) REVERT: D 134 TYR cc_start: 0.5532 (p90) cc_final: 0.5141 (p90) REVERT: D 343 LEU cc_start: 0.8749 (tp) cc_final: 0.8323 (tp) REVERT: F 70 MET cc_start: 0.1808 (mtp) cc_final: 0.1353 (mtp) REVERT: F 137 LEU cc_start: 0.1989 (pp) cc_final: 0.1704 (pp) REVERT: F 180 VAL cc_start: 0.2749 (t) cc_final: 0.2439 (m) REVERT: F 196 LYS cc_start: 0.3868 (mmtt) cc_final: 0.3565 (tptp) REVERT: G 8 GLU cc_start: 0.5159 (tp30) cc_final: 0.4905 (tm-30) REVERT: G 36 ILE cc_start: 0.6974 (pt) cc_final: 0.6738 (mt) REVERT: G 63 ASP cc_start: 0.4360 (p0) cc_final: 0.4106 (p0) REVERT: H 7 GLU cc_start: 0.6904 (mp0) cc_final: 0.6518 (tt0) REVERT: H 58 GLN cc_start: 0.7925 (tt0) cc_final: 0.7479 (mt0) REVERT: H 124 ASP cc_start: 0.6315 (t70) cc_final: 0.4742 (p0) REVERT: H 196 LYS cc_start: 0.6118 (mmtm) cc_final: 0.5737 (ttpp) outliers start: 10 outliers final: 2 residues processed: 660 average time/residue: 0.1667 time to fit residues: 163.8627 Evaluate side-chains 364 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 360 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 109 LYS Chi-restraints excluded: chain H residue 79 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 216 optimal weight: 7.9990 chunk 98 optimal weight: 8.9990 chunk 194 optimal weight: 9.9990 chunk 227 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 247 optimal weight: 5.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.9980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 243 GLN A 406 ASN ** A 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 496 ASN ** A 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 HIS B 220 ASN D 42 GLN D 313 ASN E 32 GLN G 94 ASN G 153 GLN H 29 GLN H 153 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.188686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.126466 restraints weight = 28108.721| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 2.43 r_work: 0.3393 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 20723 Z= 0.195 Angle : 0.666 11.428 28038 Z= 0.331 Chirality : 0.044 0.260 3283 Planarity : 0.005 0.053 3551 Dihedral : 11.934 169.477 2897 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.82 % Allowed : 18.02 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.16), residues: 2527 helix: 1.41 (0.15), residues: 1154 sheet: 0.09 (0.25), residues: 455 loop : -1.06 (0.19), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 80 TYR 0.019 0.002 TYR E 8 PHE 0.031 0.002 PHE D 63 TRP 0.008 0.001 TRP A 420 HIS 0.006 0.001 HIS G 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.19 (20723) covalent geometry : angle 0.66647 / 0.33 (28038) hydrogen bonds : bond 0.04348 / 2.97 ( 1047) hydrogen bonds : angle 5.04881 / 3.55 ( 3015) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5054 Ramachandran restraints generated. 2527 Oldfield, 0 Emsley, 2527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5054 Ramachandran restraints generated. 2527 Oldfield, 0 Emsley, 2527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 383 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 GLN cc_start: 0.7056 (OUTLIER) cc_final: 0.6841 (tp40) REVERT: A 359 ASN cc_start: 0.7627 (p0) cc_final: 0.7227 (t0) REVERT: A 361 TYR cc_start: 0.8971 (p90) cc_final: 0.8532 (p90) REVERT: A 379 ASP cc_start: 0.7798 (m-30) cc_final: 0.7512 (m-30) REVERT: A 505 MET cc_start: 0.9014 (tpp) cc_final: 0.8449 (mmt) REVERT: A 588 MET cc_start: 0.7501 (mmp) cc_final: 0.6753 (mtm) REVERT: B 115 GLU cc_start: 0.8333 (mt-10) cc_final: 0.8129 (mt-10) REVERT: C 109 LYS cc_start: 0.6694 (OUTLIER) cc_final: 0.5839 (mptt) REVERT: C 139 LYS cc_start: 0.8893 (tppt) cc_final: 0.8568 (mptt) REVERT: C 140 ASN cc_start: 0.7996 (t0) cc_final: 0.7715 (t0) REVERT: C 316 ASP cc_start: 0.8027 (OUTLIER) cc_final: 0.7755 (t0) REVERT: D 132 PRO cc_start: 0.8052 (Cg_exo) cc_final: 0.7435 (Cg_endo) REVERT: D 154 ARG cc_start: 0.6924 (tpt90) cc_final: 0.6723 (tpt90) REVERT: D 157 MET cc_start: 0.7152 (ptt) cc_final: 0.6605 (ptt) REVERT: D 249 LYS cc_start: 0.8522 (mttt) cc_final: 0.8024 (mtpt) REVERT: E 8 TYR cc_start: 0.8270 (m-80) cc_final: 0.7724 (m-10) REVERT: E 20 GLU cc_start: 0.7481 (tm-30) cc_final: 0.7278 (tm-30) REVERT: E 217 ASP cc_start: 0.8015 (t0) cc_final: 0.7748 (t0) REVERT: F 70 MET cc_start: 0.1942 (mtp) cc_final: 0.1454 (mtp) REVERT: F 174 ASP cc_start: 0.6563 (p0) cc_final: 0.6283 (m-30) REVERT: F 196 LYS cc_start: 0.4279 (mmtt) cc_final: 0.3833 (tptp) REVERT: F 249 PHE cc_start: 0.5556 (m-80) cc_final: 0.3974 (m-80) REVERT: G 1 MET cc_start: 0.3404 (mtt) cc_final: 0.3147 (mtt) REVERT: G 8 GLU cc_start: 0.5855 (tp30) cc_final: 0.5218 (tm-30) REVERT: G 63 ASP cc_start: 0.5389 (p0) cc_final: 0.5077 (p0) REVERT: G 149 ARG cc_start: 0.8322 (mtm-85) cc_final: 0.7355 (mtm-85) REVERT: G 190 HIS cc_start: 0.4817 (p90) cc_final: 0.4573 (p-80) REVERT: H 7 GLU cc_start: 0.7411 (mp0) cc_final: 0.6798 (tt0) REVERT: H 24 GLN cc_start: 0.8084 (tt0) cc_final: 0.7776 (mt0) REVERT: H 58 GLN cc_start: 0.8035 (tt0) cc_final: 0.7594 (mt0) REVERT: H 146 LYS cc_start: 0.8075 (tptm) cc_final: 0.7846 (tptm) REVERT: H 196 LYS cc_start: 0.5370 (mmtm) cc_final: 0.4831 (ttmm) REVERT: H 245 PHE cc_start: 0.7326 (OUTLIER) cc_final: 0.6938 (p90) outliers start: 88 outliers final: 41 residues processed: 445 average time/residue: 0.1456 time to fit residues: 101.0363 Evaluate side-chains 361 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 316 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 406 ASN Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 485 CYS Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain C residue 73 LYS Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 109 LYS Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 215 CYS Chi-restraints excluded: chain C residue 316 ASP Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 63 PHE Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 89 SER Chi-restraints excluded: chain E residue 93 HIS Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 208 ASN Chi-restraints excluded: chain F residue 28 PHE Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 119 MET Chi-restraints excluded: chain F residue 181 ILE Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain F residue 246 LEU Chi-restraints excluded: chain G residue 3 GLU Chi-restraints excluded: chain G residue 28 PHE Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 206 THR Chi-restraints excluded: chain H residue 67 THR Chi-restraints excluded: chain H residue 95 THR Chi-restraints excluded: chain H residue 113 GLU Chi-restraints excluded: chain H residue 139 LEU Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 225 VAL Chi-restraints excluded: chain H residue 245 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 146 optimal weight: 1.9990 chunk 174 optimal weight: 1.9990 chunk 222 optimal weight: 2.9990 chunk 8 optimal weight: 0.3980 chunk 104 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 chunk 109 optimal weight: 0.5980 chunk 224 optimal weight: 7.9990 chunk 225 optimal weight: 0.9990 chunk 161 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 549 ASN A 622 GLN A 711 GLN B 41 ASN C 140 ASN D 42 GLN D 313 ASN E 18 HIS E 317 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.184192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.136564 restraints weight = 28169.867| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 2.95 r_work: 0.3295 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.3565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20723 Z= 0.151 Angle : 0.583 10.000 28038 Z= 0.289 Chirality : 0.042 0.206 3283 Planarity : 0.004 0.039 3551 Dihedral : 10.857 161.557 2893 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.69 % Allowed : 19.02 % Favored : 77.29 % 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 are not related in a simple way. whole: 0.60 (0.17), residues: 2527 helix: 1.56 (0.15), residues: 1158 sheet: 0.10 (0.24), residues: 458 loop : -0.93 (0.19), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 91 TYR 0.015 0.002 TYR D 134 PHE 0.022 0.001 PHE A 509 TRP 0.007 0.001 TRP B 11 HIS 0.004 0.001 HIS A 506 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (20723) covalent geometry : angle 0.58328 / 0.29 (28038) hydrogen bonds : bond 0.03936 / 2.65 ( 1047) hydrogen bonds : angle 4.73212 / 3.34 ( 3015) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5054 Ramachandran restraints generated. 2527 Oldfield, 0 Emsley, 2527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5054 Ramachandran restraints generated. 2527 Oldfield, 0 Emsley, 2527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 345 time to evaluate : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 SER cc_start: 0.8360 (m) cc_final: 0.8154 (p) REVERT: A 361 TYR cc_start: 0.8974 (p90) cc_final: 0.8679 (p90) REVERT: A 383 ASP cc_start: 0.8085 (m-30) cc_final: 0.7883 (m-30) REVERT: A 505 MET cc_start: 0.8842 (tpp) cc_final: 0.8305 (mmt) REVERT: A 528 LEU cc_start: 0.6619 (OUTLIER) cc_final: 0.6186 (tp) REVERT: A 550 ASP cc_start: 0.8849 (t70) cc_final: 0.8632 (t0) REVERT: A 588 MET cc_start: 0.7609 (mmp) cc_final: 0.6863 (mtm) REVERT: B 94 LYS cc_start: 0.9034 (ttpp) cc_final: 0.8810 (tttp) REVERT: C 99 ASP cc_start: 0.8478 (m-30) cc_final: 0.8257 (m-30) REVERT: C 109 LYS cc_start: 0.6617 (OUTLIER) cc_final: 0.5773 (mptt) REVERT: C 139 LYS cc_start: 0.8780 (tppt) cc_final: 0.8531 (mptt) REVERT: C 316 ASP cc_start: 0.7936 (OUTLIER) cc_final: 0.7681 (t0) REVERT: D 157 MET cc_start: 0.6976 (ptt) cc_final: 0.6662 (ptt) REVERT: E 249 LYS cc_start: 0.7750 (mtpp) cc_final: 0.7161 (mmmt) REVERT: F 126 LEU cc_start: 0.3061 (mt) cc_final: 0.2659 (tp) REVERT: F 131 LEU cc_start: 0.1281 (mm) cc_final: 0.0979 (pt) REVERT: F 174 ASP cc_start: 0.6588 (p0) cc_final: 0.6326 (m-30) REVERT: F 196 LYS cc_start: 0.4322 (mmtt) cc_final: 0.3820 (tptp) REVERT: F 249 PHE cc_start: 0.5398 (m-80) cc_final: 0.3814 (m-80) REVERT: G 63 ASP cc_start: 0.5386 (p0) cc_final: 0.5174 (p0) REVERT: G 161 MET cc_start: 0.7286 (ttm) cc_final: 0.7061 (mtp) REVERT: G 190 HIS cc_start: 0.4976 (p90) cc_final: 0.4659 (p-80) REVERT: H 7 GLU cc_start: 0.7386 (mp0) cc_final: 0.6868 (tt0) REVERT: H 24 GLN cc_start: 0.8210 (tt0) cc_final: 0.7941 (mt0) REVERT: H 44 ARG cc_start: 0.8308 (mtt90) cc_final: 0.8105 (mtt180) REVERT: H 58 GLN cc_start: 0.7962 (tt0) cc_final: 0.7634 (mt0) REVERT: H 196 LYS cc_start: 0.5422 (mmtm) cc_final: 0.5010 (ttmm) REVERT: H 245 PHE cc_start: 0.7569 (OUTLIER) cc_final: 0.7208 (p90) outliers start: 85 outliers final: 49 residues processed: 408 average time/residue: 0.1460 time to fit residues: 92.3524 Evaluate side-chains 374 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 321 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 485 CYS Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 558 ASN Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 109 LYS Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 215 CYS Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 316 ASP Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 89 SER Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 254 ILE Chi-restraints excluded: chain E residue 333 SER Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 119 MET Chi-restraints excluded: chain F residue 188 MET Chi-restraints excluded: chain F residue 246 LEU Chi-restraints excluded: chain G residue 3 GLU Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 36 ILE Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 181 ILE Chi-restraints excluded: chain G residue 206 THR Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 67 THR Chi-restraints excluded: chain H residue 95 THR Chi-restraints excluded: chain H residue 139 LEU Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 225 VAL Chi-restraints excluded: chain H residue 245 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.4536 > 50: distance: 80 - 90: 34.993 distance: 90 - 91: 39.770 distance: 91 - 92: 45.639 distance: 91 - 94: 23.141 distance: 92 - 93: 29.846 distance: 92 - 99: 16.084 distance: 94 - 95: 57.431 distance: 95 - 96: 67.795 distance: 96 - 97: 41.258 distance: 97 - 98: 51.731 distance: 99 - 100: 9.096 distance: 100 - 101: 39.114 distance: 100 - 103: 41.126 distance: 101 - 102: 40.876 distance: 101 - 107: 40.948 distance: 103 - 104: 19.374 distance: 104 - 105: 58.757 distance: 104 - 106: 43.964 distance: 107 - 108: 57.617 distance: 109 - 110: 39.918 distance: 109 - 117: 57.486 distance: 111 - 112: 38.765 distance: 112 - 113: 55.885 distance: 112 - 114: 39.765 distance: 113 - 115: 45.153 distance: 114 - 116: 62.729 distance: 115 - 116: 42.702 distance: 118 - 119: 39.443 distance: 118 - 121: 11.549 distance: 119 - 120: 4.811 distance: 119 - 125: 56.726 distance: 121 - 122: 36.563 distance: 122 - 123: 34.677 distance: 122 - 124: 42.180 distance: 126 - 127: 62.923 distance: 126 - 129: 34.109 distance: 127 - 128: 9.200 distance: 127 - 133: 49.436 distance: 129 - 130: 35.307 distance: 130 - 131: 39.272 distance: 133 - 134: 23.190 distance: 134 - 135: 29.677 distance: 134 - 137: 23.731 distance: 135 - 136: 56.565 distance: 135 - 141: 66.242 distance: 137 - 138: 60.862 distance: 138 - 139: 58.902 distance: 138 - 140: 21.065 distance: 141 - 142: 39.863 distance: 141 - 147: 49.436 distance: 142 - 143: 41.468 distance: 142 - 145: 11.112 distance: 143 - 144: 20.196 distance: 143 - 148: 39.945 distance: 145 - 146: 62.230 distance: 146 - 147: 49.005 distance: 148 - 149: 14.846 distance: 149 - 150: 40.086 distance: 149 - 152: 40.248 distance: 150 - 156: 40.263 distance: 152 - 153: 6.015 distance: 153 - 154: 32.684 distance: 153 - 155: 34.541 distance: 157 - 158: 68.624 distance: 157 - 160: 41.185 distance: 158 - 159: 40.744 distance: 160 - 161: 30.236 distance: 161 - 162: 57.586 distance: 162 - 163: 49.989 distance: 163 - 164: 8.321 distance: 164 - 165: 56.556 distance: 164 - 166: 39.800 distance: 167 - 168: 7.227 distance: 168 - 169: 40.698 distance: 168 - 171: 51.043 distance: 169 - 170: 40.075 distance: 169 - 176: 34.794 distance: 171 - 172: 39.176 distance: 173 - 174: 56.020 distance: 173 - 175: 10.811