Starting phenix.real_space_refine on Mon Aug 25 04:15:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yry_34066/08_2025/7yry_34066.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yry_34066/08_2025/7yry_34066.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yry_34066/08_2025/7yry_34066.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yry_34066/08_2025/7yry_34066.map" model { file = "/net/cci-nas-00/data/ceres_data/7yry_34066/08_2025/7yry_34066.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yry_34066/08_2025/7yry_34066.cif" } resolution = 3.0 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= 0.001 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 12 5.49 5 Mg 4 5.21 5 S 99 5.16 5 C 15741 2.51 5 N 4306 2.21 5 O 4894 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25056 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 3702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3702 Classifications: {'peptide': 489} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 471} Chain: "B" Number of atoms: 3703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3703 Classifications: {'peptide': 489} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 471} Chain: "C" Number of atoms: 3703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3703 Classifications: {'peptide': 489} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 471} Chain: "D" Number of atoms: 3525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3525 Classifications: {'peptide': 463} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 440} Chain: "E" Number of atoms: 3525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3525 Classifications: {'peptide': 463} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 440} Chain: "F" Number of atoms: 3525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3525 Classifications: {'peptide': 463} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 440} Chain: "e" Number of atoms: 1010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1010 Classifications: {'peptide': 138} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 132} Chain: "g" Number of atoms: 2234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2234 Classifications: {'peptide': 288} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 8, 'TRANS': 279} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 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, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.86, per 1000 atoms: 0.23 Number of scatterers: 25056 At special positions: 0 Unit cell: (154.512, 131.335, 133.91, 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 99 16.00 P 12 15.00 Mg 4 11.99 O 4894 8.00 N 4306 7.00 C 15741 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: 2.01 Conformation dependent library (CDL) restraints added in 908.6 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5970 Finding SS restraints... Secondary structure from input PDB file: 133 helices and 27 sheets defined 47.6% alpha, 16.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'A' and resid 79 through 83 removed outlier: 4.366A pdb=" N SER A 82 " --> pdb=" O ASN A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 105 removed outlier: 3.627A pdb=" N LEU A 104 " --> pdb=" O GLY A 101 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU A 105 " --> pdb=" O PRO A 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 101 through 105' Processing helix chain 'A' and resid 151 through 158 removed outlier: 3.549A pdb=" N THR A 156 " --> pdb=" O LYS A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 186 removed outlier: 3.586A pdb=" N MET A 179 " --> pdb=" O GLY A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 216 removed outlier: 3.504A pdb=" N THR A 216 " --> pdb=" O LYS A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 220 Processing helix chain 'A' and resid 232 through 252 Proline residue: A 240 - end of helix removed outlier: 3.865A pdb=" N TYR A 249 " --> pdb=" O THR A 245 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N PHE A 250 " --> pdb=" O MET A 246 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ARG A 251 " --> pdb=" O GLY A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 278 removed outlier: 4.049A pdb=" N GLN A 267 " --> pdb=" O ASP A 263 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA A 268 " --> pdb=" O LEU A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 287 Processing helix chain 'A' and resid 290 through 300 removed outlier: 3.857A pdb=" N HIS A 295 " --> pdb=" O VAL A 291 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU A 298 " --> pdb=" O LEU A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 315 Processing helix chain 'A' and resid 340 through 348 Processing helix chain 'A' and resid 357 through 363 Processing helix chain 'A' and resid 378 through 383 removed outlier: 4.290A pdb=" N SER A 381 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA A 382 " --> pdb=" O GLY A 379 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLN A 383 " --> pdb=" O GLY A 380 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 378 through 383' Processing helix chain 'A' and resid 384 through 391 Processing helix chain 'A' and resid 393 through 408 Processing helix chain 'A' and resid 415 through 432 removed outlier: 3.546A pdb=" N ARG A 427 " --> pdb=" O GLU A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 454 Processing helix chain 'A' and resid 461 through 463 No H-bonds generated for 'chain 'A' and resid 461 through 463' Processing helix chain 'A' and resid 464 through 480 Processing helix chain 'A' and resid 480 through 491 Processing helix chain 'A' and resid 494 through 512 Processing helix chain 'B' and resid 101 through 105 removed outlier: 3.750A pdb=" N LEU B 104 " --> pdb=" O GLY B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 140 removed outlier: 3.697A pdb=" N ARG B 140 " --> pdb=" O VAL B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 158 Processing helix chain 'B' and resid 176 through 187 Processing helix chain 'B' and resid 202 through 217 Processing helix chain 'B' and resid 218 through 220 No H-bonds generated for 'chain 'B' and resid 218 through 220' Processing helix chain 'B' and resid 232 through 252 Proline residue: B 240 - end of helix removed outlier: 3.699A pdb=" N TYR B 249 " --> pdb=" O THR B 245 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N PHE B 250 " --> pdb=" O MET B 246 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ARG B 251 " --> pdb=" O GLY B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 278 removed outlier: 3.832A pdb=" N GLN B 267 " --> pdb=" O ASP B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 287 Processing helix chain 'B' and resid 290 through 300 removed outlier: 3.679A pdb=" N ARG B 297 " --> pdb=" O TYR B 293 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU B 298 " --> pdb=" O LEU B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 315 Processing helix chain 'B' and resid 340 through 348 Processing helix chain 'B' and resid 357 through 362 removed outlier: 3.545A pdb=" N PHE B 361 " --> pdb=" O GLU B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 383 removed outlier: 3.971A pdb=" N SER B 381 " --> pdb=" O VAL B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 404 removed outlier: 4.672A pdb=" N GLY B 392 " --> pdb=" O LYS B 388 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N GLY B 393 " --> pdb=" O LYS B 389 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ILE B 394 " --> pdb=" O LEU B 390 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU B 404 " --> pdb=" O GLN B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 408 removed outlier: 3.889A pdb=" N ALA B 408 " --> pdb=" O ALA B 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 405 through 408' Processing helix chain 'B' and resid 415 through 432 Processing helix chain 'B' and resid 441 through 454 removed outlier: 3.761A pdb=" N GLN B 445 " --> pdb=" O SER B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 463 No H-bonds generated for 'chain 'B' and resid 461 through 463' Processing helix chain 'B' and resid 464 through 480 Processing helix chain 'B' and resid 480 through 491 Processing helix chain 'B' and resid 494 through 512 removed outlier: 4.101A pdb=" N ALA B 510 " --> pdb=" O GLU B 506 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN B 512 " --> pdb=" O PHE B 508 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 140 Processing helix chain 'C' and resid 151 through 158 Processing helix chain 'C' and resid 175 through 186 Processing helix chain 'C' and resid 202 through 216 removed outlier: 3.559A pdb=" N ILE C 206 " --> pdb=" O LYS C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 220 removed outlier: 4.182A pdb=" N ALA C 220 " --> pdb=" O GLY C 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 217 through 220' Processing helix chain 'C' and resid 232 through 252 Proline residue: C 240 - end of helix removed outlier: 4.348A pdb=" N PHE C 250 " --> pdb=" O MET C 246 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG C 251 " --> pdb=" O GLY C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 278 removed outlier: 3.862A pdb=" N GLN C 267 " --> pdb=" O ASP C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 287 Processing helix chain 'C' and resid 290 through 300 removed outlier: 3.753A pdb=" N LEU C 298 " --> pdb=" O LEU C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 315 Processing helix chain 'C' and resid 340 through 350 removed outlier: 3.694A pdb=" N THR C 344 " --> pdb=" O ALA C 340 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ASN C 345 " --> pdb=" O PHE C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 363 Processing helix chain 'C' and resid 378 through 383 removed outlier: 3.717A pdb=" N SER C 381 " --> pdb=" O VAL C 378 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALA C 382 " --> pdb=" O GLY C 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 403 removed outlier: 4.708A pdb=" N GLY C 392 " --> pdb=" O LYS C 388 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N GLY C 393 " --> pdb=" O LYS C 389 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ILE C 394 " --> pdb=" O LEU C 390 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 411 removed outlier: 3.706A pdb=" N PHE C 407 " --> pdb=" O LEU C 404 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLN C 409 " --> pdb=" O ALA C 406 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ALA C 411 " --> pdb=" O ALA C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 432 Processing helix chain 'C' and resid 441 through 454 Processing helix chain 'C' and resid 464 through 480 Processing helix chain 'C' and resid 480 through 490 Processing helix chain 'C' and resid 494 through 510 removed outlier: 3.848A pdb=" N ALA C 510 " --> pdb=" O GLU C 506 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 83 Processing helix chain 'D' and resid 129 through 136 Processing helix chain 'D' and resid 153 through 166 Processing helix chain 'D' and resid 167 through 169 No H-bonds generated for 'chain 'D' and resid 167 through 169' Processing helix chain 'D' and resid 181 through 195 removed outlier: 3.533A pdb=" N SER D 195 " --> pdb=" O GLU D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 199 No H-bonds generated for 'chain 'D' and resid 197 through 199' Processing helix chain 'D' and resid 211 through 231 removed outlier: 3.661A pdb=" N ARG D 217 " --> pdb=" O GLY D 213 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N ALA D 219 " --> pdb=" O ARG D 215 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N LEU D 220 " --> pdb=" O LEU D 216 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N THR D 221 " --> pdb=" O ARG D 217 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLY D 222 " --> pdb=" O VAL D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 259 removed outlier: 3.901A pdb=" N THR D 253 " --> pdb=" O ILE D 249 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL D 259 " --> pdb=" O ALA D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 264 Processing helix chain 'D' and resid 275 through 285 removed outlier: 3.850A pdb=" N LEU D 283 " --> pdb=" O GLU D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 307 Processing helix chain 'D' and resid 310 through 317 Processing helix chain 'D' and resid 318 through 320 No H-bonds generated for 'chain 'D' and resid 318 through 320' Processing helix chain 'D' and resid 327 through 332 Processing helix chain 'D' and resid 350 through 355 Processing helix chain 'D' and resid 355 through 382 removed outlier: 3.556A pdb=" N TYR D 359 " --> pdb=" O GLY D 355 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N ASP D 377 " --> pdb=" O LYS D 373 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N ILE D 378 " --> pdb=" O GLU D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 388 through 405 Processing helix chain 'D' and resid 412 through 417 Processing helix chain 'D' and resid 424 through 438 Processing helix chain 'D' and resid 444 through 449 removed outlier: 3.635A pdb=" N PHE D 448 " --> pdb=" O GLU D 445 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N TYR D 449 " --> pdb=" O GLN D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 453 through 464 Processing helix chain 'E' and resid 79 through 83 Processing helix chain 'E' and resid 129 through 135 Processing helix chain 'E' and resid 153 through 169 removed outlier: 3.572A pdb=" N ASN E 157 " --> pdb=" O GLY E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 194 Processing helix chain 'E' and resid 195 through 199 removed outlier: 5.320A pdb=" N LEU E 198 " --> pdb=" O SER E 195 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ASP E 199 " --> pdb=" O ASN E 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 195 through 199' Processing helix chain 'E' and resid 211 through 231 removed outlier: 3.584A pdb=" N ARG E 215 " --> pdb=" O PRO E 211 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N ALA E 219 " --> pdb=" O ARG E 215 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LEU E 220 " --> pdb=" O LEU E 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 263 removed outlier: 3.776A pdb=" N TYR E 252 " --> pdb=" O ASN E 248 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 285 Processing helix chain 'E' and resid 303 through 307 removed outlier: 3.552A pdb=" N ASP E 306 " --> pdb=" O VAL E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 310 through 318 removed outlier: 3.925A pdb=" N THR E 316 " --> pdb=" O SER E 312 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ALA E 318 " --> pdb=" O ALA E 314 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 333 Processing helix chain 'E' and resid 350 through 355 Processing helix chain 'E' and resid 355 through 382 removed outlier: 3.912A pdb=" N LYS E 376 " --> pdb=" O TYR E 372 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ASP E 377 " --> pdb=" O LYS E 373 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ILE E 378 " --> pdb=" O GLU E 374 " (cutoff:3.500A) Processing helix chain 'E' and resid 391 through 405 removed outlier: 3.563A pdb=" N PHE E 405 " --> pdb=" O ILE E 401 " (cutoff:3.500A) Processing helix chain 'E' and resid 424 through 438 removed outlier: 3.662A pdb=" N THR E 428 " --> pdb=" O PRO E 424 " (cutoff:3.500A) Processing helix chain 'E' and resid 444 through 449 removed outlier: 4.073A pdb=" N TYR E 449 " --> pdb=" O GLN E 446 " (cutoff:3.500A) Processing helix chain 'E' and resid 453 through 464 Processing helix chain 'F' and resid 79 through 83 removed outlier: 3.812A pdb=" N THR F 82 " --> pdb=" O GLY F 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 118 removed outlier: 3.559A pdb=" N GLN F 118 " --> pdb=" O TYR F 115 " (cutoff:3.500A) Processing helix chain 'F' and resid 129 through 136 Processing helix chain 'F' and resid 154 through 168 Processing helix chain 'F' and resid 181 through 195 Processing helix chain 'F' and resid 197 through 201 removed outlier: 3.691A pdb=" N VAL F 201 " --> pdb=" O LEU F 198 " (cutoff:3.500A) Processing helix chain 'F' and resid 211 through 217 removed outlier: 3.522A pdb=" N ARG F 215 " --> pdb=" O PRO F 211 " (cutoff:3.500A) Processing helix chain 'F' and resid 218 through 232 removed outlier: 3.766A pdb=" N GLY F 222 " --> pdb=" O VAL F 218 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 238 removed outlier: 4.176A pdb=" N LYS F 238 " --> pdb=" O GLU F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 248 through 264 Processing helix chain 'F' and resid 275 through 285 Processing helix chain 'F' and resid 303 through 307 removed outlier: 3.558A pdb=" N ASP F 306 " --> pdb=" O VAL F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 310 through 318 Processing helix chain 'F' and resid 327 through 333 removed outlier: 3.615A pdb=" N ALA F 331 " --> pdb=" O SER F 327 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER F 333 " --> pdb=" O ASP F 329 " (cutoff:3.500A) Processing helix chain 'F' and resid 350 through 355 Processing helix chain 'F' and resid 355 through 383 removed outlier: 3.948A pdb=" N TYR F 359 " --> pdb=" O GLY F 355 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ASP F 377 " --> pdb=" O LYS F 373 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ILE F 378 " --> pdb=" O GLU F 374 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY F 383 " --> pdb=" O ILE F 379 " (cutoff:3.500A) Processing helix chain 'F' and resid 389 through 405 Processing helix chain 'F' and resid 412 through 417 Processing helix chain 'F' and resid 424 through 438 removed outlier: 3.643A pdb=" N THR F 428 " --> pdb=" O PRO F 424 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE F 429 " --> pdb=" O LEU F 425 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG F 430 " --> pdb=" O LYS F 426 " (cutoff:3.500A) Processing helix chain 'F' and resid 444 through 449 Processing helix chain 'F' and resid 453 through 464 Processing helix chain 'e' and resid 91 through 125 removed outlier: 4.574A pdb=" N ALA e 97 " --> pdb=" O ALA e 93 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ARG e 98 " --> pdb=" O ILE e 94 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ALA e 119 " --> pdb=" O ALA e 115 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ALA e 120 " --> pdb=" O ALA e 116 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA e 122 " --> pdb=" O LEU e 118 " (cutoff:3.500A) Processing helix chain 'e' and resid 128 through 133 removed outlier: 3.595A pdb=" N ARG e 132 " --> pdb=" O LEU e 128 " (cutoff:3.500A) Processing helix chain 'g' and resid 3 through 37 Processing helix chain 'g' and resid 42 through 60 removed outlier: 3.968A pdb=" N ALA g 46 " --> pdb=" O GLY g 42 " (cutoff:3.500A) Processing helix chain 'g' and resid 65 through 69 removed outlier: 3.749A pdb=" N MET g 68 " --> pdb=" O HIS g 65 " (cutoff:3.500A) Processing helix chain 'g' and resid 90 through 108 removed outlier: 3.692A pdb=" N GLU g 108 " --> pdb=" O LYS g 104 " (cutoff:3.500A) Processing helix chain 'g' and resid 119 through 128 Processing helix chain 'g' and resid 150 through 161 Processing helix chain 'g' and resid 213 through 242 removed outlier: 4.401A pdb=" N LEU g 217 " --> pdb=" O GLU g 213 " (cutoff:3.500A) Processing helix chain 'g' and resid 244 through 288 Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 67 removed outlier: 4.840A pdb=" N GLU A 52 " --> pdb=" O ALA A 64 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N ARG A 94 " --> pdb=" O MET A 53 " (cutoff:3.500A) removed outlier: 8.523A pdb=" N GLU A 55 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N THR A 92 " --> pdb=" O GLU A 55 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ARG A 41 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N VAL A 35 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ILE A 39 " --> pdb=" O VAL A 35 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N GLY A 73 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ARG D 51 " --> pdb=" O GLN D 42 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N GLN D 44 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N VAL D 49 " --> pdb=" O GLN D 44 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLN D 8 " --> pdb=" O ASP D 15 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N GLU D 17 " --> pdb=" O ILE D 6 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ILE D 6 " --> pdb=" O GLU D 17 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 100 removed outlier: 3.628A pdb=" N VAL A 100 " --> pdb=" O LEU A 126 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LEU A 126 " --> pdb=" O VAL A 100 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 108 through 109 removed outlier: 3.670A pdb=" N ILE A 199 " --> pdb=" O ASP A 262 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA A 257 " --> pdb=" O SER A 324 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LEU A 167 " --> pdb=" O ILE A 354 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N LEU A 356 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ILE A 169 " --> pdb=" O LEU A 356 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 146 through 147 removed outlier: 4.651A pdb=" N VAL A 160 " --> pdb=" O VAL A 147 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 61 through 67 removed outlier: 4.606A pdb=" N GLU B 52 " --> pdb=" O ALA B 64 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N MET B 53 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ARG B 41 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N VAL B 35 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ILE B 39 " --> pdb=" O VAL B 35 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N GLY B 73 " --> pdb=" O LEU B 65 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N THR F 38 " --> pdb=" O MET F 55 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N ARG F 51 " --> pdb=" O GLN F 42 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N GLN F 44 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N VAL F 49 " --> pdb=" O GLN F 44 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN F 8 " --> pdb=" O ASP F 15 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N GLU F 17 " --> pdb=" O ILE F 6 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N ILE F 6 " --> pdb=" O GLU F 17 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 97 through 100 removed outlier: 4.565A pdb=" N LEU B 126 " --> pdb=" O VAL B 100 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 108 through 109 Processing sheet with id=AA8, first strand: chain 'B' and resid 146 through 147 removed outlier: 4.454A pdb=" N VAL B 160 " --> pdb=" O VAL B 147 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 330 through 332 removed outlier: 10.333A pdb=" N GLN B 353 " --> pdb=" O GLY B 372 " (cutoff:3.500A) removed outlier: 8.594A pdb=" N GLY B 372 " --> pdb=" O GLN B 353 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N PHE B 355 " --> pdb=" O ASN B 370 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 61 through 67 removed outlier: 6.672A pdb=" N ARG C 41 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N VAL C 35 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ILE C 39 " --> pdb=" O VAL C 35 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N SER C 71 " --> pdb=" O LEU C 67 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N LEU C 67 " --> pdb=" O SER C 71 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N GLY C 73 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ARG E 51 " --> pdb=" O GLN E 42 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N GLN E 44 " --> pdb=" O VAL E 49 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N VAL E 49 " --> pdb=" O GLN E 44 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N VAL E 13 " --> pdb=" O ILE E 9 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ILE E 9 " --> pdb=" O VAL E 13 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ASP E 15 " --> pdb=" O ILE E 7 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 97 through 100 removed outlier: 4.110A pdb=" N LEU C 126 " --> pdb=" O VAL C 100 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 107 through 109 removed outlier: 6.504A pdb=" N ARG C 107 " --> pdb=" O VAL C 224 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N ALA C 226 " --> pdb=" O ARG C 107 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL C 109 " --> pdb=" O ALA C 226 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N ALA C 228 " --> pdb=" O VAL C 109 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR C 261 " --> pdb=" O LEU C 328 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLY C 323 " --> pdb=" O VAL C 305 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 107 through 109 removed outlier: 6.504A pdb=" N ARG C 107 " --> pdb=" O VAL C 224 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N ALA C 226 " --> pdb=" O ARG C 107 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL C 109 " --> pdb=" O ALA C 226 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N ALA C 228 " --> pdb=" O VAL C 109 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR C 261 " --> pdb=" O LEU C 328 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N GLU C 166 " --> pdb=" O PRO C 329 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N ILE C 331 " --> pdb=" O GLU C 166 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ILE C 168 " --> pdb=" O ILE C 331 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LEU C 167 " --> pdb=" O ILE C 354 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 146 through 147 removed outlier: 4.550A pdb=" N VAL C 160 " --> pdb=" O VAL C 147 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 75 through 77 Processing sheet with id=AB7, first strand: chain 'D' and resid 86 through 87 removed outlier: 3.531A pdb=" N VAL D 178 " --> pdb=" O ASP D 247 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N VAL D 144 " --> pdb=" O GLN D 299 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N VAL D 301 " --> pdb=" O VAL D 144 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N LEU D 146 " --> pdb=" O VAL D 301 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 124 through 125 removed outlier: 3.555A pdb=" N LEU D 125 " --> pdb=" O PHE D 138 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N PHE D 138 " --> pdb=" O LEU D 125 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'E' and resid 75 through 77 Processing sheet with id=AC1, first strand: chain 'E' and resid 86 through 87 removed outlier: 6.483A pdb=" N LEU E 244 " --> pdb=" O ILE E 298 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N ALA E 300 " --> pdb=" O LEU E 244 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N VAL E 246 " --> pdb=" O ALA E 300 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 124 through 125 removed outlier: 4.334A pdb=" N PHE E 138 " --> pdb=" O LEU E 125 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 241 through 242 Processing sheet with id=AC4, first strand: chain 'F' and resid 75 through 77 Processing sheet with id=AC5, first strand: chain 'F' and resid 86 through 87 removed outlier: 6.793A pdb=" N MET F 87 " --> pdb=" O TYR F 205 " (cutoff:3.500A) removed outlier: 8.659A pdb=" N GLN F 207 " --> pdb=" O MET F 87 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU F 172 " --> pdb=" O ASP F 241 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA F 300 " --> pdb=" O VAL F 246 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N LYS F 143 " --> pdb=" O ALA F 322 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N VAL F 324 " --> pdb=" O LYS F 143 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N GLY F 145 " --> pdb=" O VAL F 324 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'e' and resid 17 through 20 removed outlier: 3.851A pdb=" N VAL e 76 " --> pdb=" O GLN e 5 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'e' and resid 31 through 34 removed outlier: 4.150A pdb=" N LEU e 23 " --> pdb=" O ILE e 34 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG e 51 " --> pdb=" O ILE e 24 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N LYS e 26 " --> pdb=" O PRO e 49 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL e 52 " --> pdb=" O GLU e 60 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'e' and resid 44 through 45 removed outlier: 3.592A pdb=" N GLY e 67 " --> pdb=" O LEU e 45 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'g' and resid 113 through 118 removed outlier: 6.485A pdb=" N VAL g 76 " --> pdb=" O GLN g 114 " (cutoff:3.500A) removed outlier: 8.623A pdb=" N ALA g 116 " --> pdb=" O VAL g 76 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N TYR g 78 " --> pdb=" O ALA g 116 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N ILE g 118 " --> pdb=" O TYR g 78 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ILE g 80 " --> pdb=" O ILE g 118 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE g 79 " --> pdb=" O TYR g 169 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL g 81 " --> pdb=" O VAL g 171 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ASN g 173 " --> pdb=" O VAL g 81 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLU g 186 " --> pdb=" O LEU g 170 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER g 172 " --> pdb=" O LYS g 184 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS g 184 " --> pdb=" O SER g 172 " (cutoff:3.500A) 1237 hydrogen bonds defined for protein. 3537 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: 4.25 Time building geometry restraints manager: 2.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8453 1.34 - 1.46: 4816 1.46 - 1.58: 11968 1.58 - 1.70: 15 1.70 - 1.82: 184 Bond restraints: 25436 Sorted by residual: bond pdb=" C VAL g 176 " pdb=" N ASN g 177 " ideal model delta sigma weight residual 1.332 1.264 0.068 1.40e-02 5.10e+03 2.35e+01 bond pdb=" O3 PO4 E 601 " pdb=" P PO4 E 601 " ideal model delta sigma weight residual 1.569 1.509 0.060 2.00e-02 2.50e+03 8.94e+00 bond pdb=" O4 PO4 E 601 " pdb=" P PO4 E 601 " ideal model delta sigma weight residual 1.568 1.510 0.058 2.00e-02 2.50e+03 8.40e+00 bond pdb=" O2 PO4 E 601 " pdb=" P PO4 E 601 " ideal model delta sigma weight residual 1.567 1.510 0.057 2.00e-02 2.50e+03 8.17e+00 bond pdb=" O1 PO4 E 601 " pdb=" P PO4 E 601 " ideal model delta sigma weight residual 1.565 1.510 0.055 2.00e-02 2.50e+03 7.58e+00 ... (remaining 25431 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.54: 34222 2.54 - 5.08: 217 5.08 - 7.61: 24 7.61 - 10.15: 9 10.15 - 12.69: 2 Bond angle restraints: 34474 Sorted by residual: angle pdb=" CB MET E 55 " pdb=" CG MET E 55 " pdb=" SD MET E 55 " ideal model delta sigma weight residual 112.70 125.39 -12.69 3.00e+00 1.11e-01 1.79e+01 angle pdb=" C GLU F 389 " pdb=" CA GLU F 389 " pdb=" CB GLU F 389 " ideal model delta sigma weight residual 110.42 118.14 -7.72 1.99e+00 2.53e-01 1.51e+01 angle pdb=" CA ILE g 226 " pdb=" CB ILE g 226 " pdb=" CG1 ILE g 226 " ideal model delta sigma weight residual 110.40 116.71 -6.31 1.70e+00 3.46e-01 1.38e+01 angle pdb=" N ILE e 94 " pdb=" CA ILE e 94 " pdb=" C ILE e 94 " ideal model delta sigma weight residual 111.81 108.72 3.09 8.60e-01 1.35e+00 1.29e+01 angle pdb=" CA GLU F 389 " pdb=" CB GLU F 389 " pdb=" CG GLU F 389 " ideal model delta sigma weight residual 114.10 120.71 -6.61 2.00e+00 2.50e-01 1.09e+01 ... (remaining 34469 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.87: 14879 35.87 - 71.74: 582 71.74 - 107.61: 51 107.61 - 143.49: 1 143.49 - 179.36: 1 Dihedral angle restraints: 15514 sinusoidal: 6145 harmonic: 9369 Sorted by residual: dihedral pdb=" C5' ADP D 502 " pdb=" O5' ADP D 502 " pdb=" PA ADP D 502 " pdb=" O2A ADP D 502 " ideal model delta sinusoidal sigma weight residual -60.00 119.36 -179.36 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O1B ADP D 502 " pdb=" O3A ADP D 502 " pdb=" PB ADP D 502 " pdb=" PA ADP D 502 " ideal model delta sinusoidal sigma weight residual -60.00 61.57 -121.57 1 2.00e+01 2.50e-03 3.66e+01 dihedral pdb=" CA MET F 203 " pdb=" C MET F 203 " pdb=" N VAL F 204 " pdb=" CA VAL F 204 " ideal model delta harmonic sigma weight residual 180.00 157.71 22.29 0 5.00e+00 4.00e-02 1.99e+01 ... (remaining 15511 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 2867 0.040 - 0.080: 775 0.080 - 0.120: 295 0.120 - 0.161: 40 0.161 - 0.201: 2 Chirality restraints: 3979 Sorted by residual: chirality pdb=" CB ILE e 24 " pdb=" CA ILE e 24 " pdb=" CG1 ILE e 24 " pdb=" CG2 ILE e 24 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CA GLU F 389 " pdb=" N GLU F 389 " pdb=" C GLU F 389 " pdb=" CB GLU F 389 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.46e-01 chirality pdb=" CB ILE g 226 " pdb=" CA ILE g 226 " pdb=" CG1 ILE g 226 " pdb=" CG2 ILE g 226 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.93e-01 ... (remaining 3976 not shown) Planarity restraints: 4494 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL g 176 " 0.017 2.00e-02 2.50e+03 3.30e-02 1.09e+01 pdb=" C VAL g 176 " -0.057 2.00e-02 2.50e+03 pdb=" O VAL g 176 " 0.021 2.00e-02 2.50e+03 pdb=" N ASN g 177 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN g 177 " -0.014 2.00e-02 2.50e+03 2.70e-02 7.30e+00 pdb=" C ASN g 177 " 0.047 2.00e-02 2.50e+03 pdb=" O ASN g 177 " -0.017 2.00e-02 2.50e+03 pdb=" N ALA g 178 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP F 310 " 0.030 5.00e-02 4.00e+02 4.51e-02 3.25e+00 pdb=" N PRO F 311 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO F 311 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO F 311 " 0.025 5.00e-02 4.00e+02 ... (remaining 4491 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 207 2.61 - 3.18: 21105 3.18 - 3.76: 37313 3.76 - 4.33: 50646 4.33 - 4.90: 86049 Nonbonded interactions: 195320 Sorted by model distance: nonbonded pdb=" O2G ATP B 601 " pdb="MG MG B 602 " model vdw 2.041 2.170 nonbonded pdb="MG MG C 601 " pdb=" O2B ATP C 602 " model vdw 2.051 2.170 nonbonded pdb=" OG1 THR A 177 " pdb="MG MG A 602 " model vdw 2.066 2.170 nonbonded pdb=" N GLU D 104 " pdb=" OE1 GLU D 104 " model vdw 2.167 3.120 nonbonded pdb="MG MG D 501 " pdb=" O3B ADP D 502 " model vdw 2.171 2.170 ... (remaining 195315 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 26 through 514) selection = (chain 'B' and (resid 26 through 513 or (resid 514 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name \ CE2 or name CZ or name OH )))) selection = (chain 'C' and (resid 26 through 513 or (resid 514 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name \ CE2 or name CZ or name OH )))) } ncs_group { reference = (chain 'D' and resid 2 through 464) selection = (chain 'E' and resid 2 through 464) selection = chain 'F' } 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: 2.700 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: 0.270 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.560 Find NCS groups from input model: 0.540 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:6.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 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 : 0.002 0.068 25436 Z= 0.120 Angle : 0.544 12.692 34474 Z= 0.280 Chirality : 0.043 0.201 3979 Planarity : 0.003 0.045 4494 Dihedral : 17.926 179.358 9544 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.35 % Allowed : 26.64 % Favored : 70.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.15), residues: 3266 helix: 1.60 (0.15), residues: 1310 sheet: 0.20 (0.24), residues: 491 loop : -0.98 (0.15), residues: 1465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 20 TYR 0.023 0.001 TYR g 63 PHE 0.011 0.001 PHE F 415 TRP 0.027 0.002 TRP g 206 HIS 0.002 0.000 HIS D 190 Details of bonding type rmsd covalent geometry : bond 0.00248 (25436) covalent geometry : angle 0.54361 (34474) hydrogen bonds : bond 0.18291 ( 1221) hydrogen bonds : angle 6.90789 ( 3537) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 213 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 266 MET cc_start: 0.7148 (mpt) cc_final: 0.6892 (mpp) REVERT: E 404 PHE cc_start: 0.5689 (OUTLIER) cc_final: 0.5429 (t80) REVERT: e 22 MET cc_start: 0.3467 (tmm) cc_final: 0.3228 (tpp) REVERT: g 6 GLU cc_start: 0.6541 (tm-30) cc_final: 0.6334 (tp30) REVERT: g 39 MET cc_start: 0.7600 (mmp) cc_final: 0.6803 (tpp) REVERT: g 115 PHE cc_start: 0.8722 (p90) cc_final: 0.8262 (p90) REVERT: g 229 MET cc_start: 0.7984 (mmt) cc_final: 0.7758 (mmm) outliers start: 88 outliers final: 74 residues processed: 296 average time/residue: 0.5876 time to fit residues: 203.7111 Evaluate side-chains 268 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 193 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 507 SER Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 507 SER Chi-restraints excluded: chain B residue 509 LYS Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain D residue 9 ILE Chi-restraints excluded: chain D residue 62 LYS Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 123 ASP Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain D residue 416 THR Chi-restraints excluded: chain E residue 5 ARG Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 404 PHE Chi-restraints excluded: chain E residue 409 PHE Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 257 THR Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 289 SER Chi-restraints excluded: chain F residue 353 VAL Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 423 VAL Chi-restraints excluded: chain e residue 10 SER Chi-restraints excluded: chain e residue 44 LEU Chi-restraints excluded: chain e residue 77 THR Chi-restraints excluded: chain e residue 114 SER Chi-restraints excluded: chain e residue 130 THR Chi-restraints excluded: chain g residue 16 SER Chi-restraints excluded: chain g residue 18 GLN Chi-restraints excluded: chain g residue 60 ASN Chi-restraints excluded: chain g residue 92 ASN Chi-restraints excluded: chain g residue 129 TYR Chi-restraints excluded: chain g residue 166 ASP Chi-restraints excluded: chain g residue 198 ASP Chi-restraints excluded: chain g residue 206 TRP Chi-restraints excluded: chain g residue 228 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 61.0452 > 50: distance: 28 - 33: 15.792 distance: 33 - 34: 11.358 distance: 34 - 35: 14.605 distance: 34 - 37: 22.301 distance: 35 - 36: 20.649 distance: 35 - 41: 19.206 distance: 37 - 38: 10.512 distance: 38 - 39: 23.036 distance: 38 - 40: 13.806 distance: 41 - 42: 34.141 distance: 42 - 43: 37.641 distance: 42 - 45: 27.306 distance: 43 - 44: 5.883 distance: 43 - 46: 13.217 distance: 46 - 47: 32.778 distance: 46 - 52: 29.862 distance: 47 - 48: 21.873 distance: 47 - 50: 29.029 distance: 48 - 49: 42.800 distance: 48 - 53: 24.237 distance: 50 - 51: 15.147 distance: 51 - 52: 12.905 distance: 53 - 54: 48.864 distance: 54 - 55: 12.022 distance: 54 - 57: 16.211 distance: 55 - 56: 33.681 distance: 55 - 61: 31.075 distance: 57 - 58: 20.259 distance: 57 - 59: 38.416 distance: 58 - 60: 25.328 distance: 61 - 62: 16.691 distance: 62 - 63: 12.143 distance: 62 - 65: 27.172 distance: 63 - 64: 6.657 distance: 63 - 67: 26.545 distance: 65 - 66: 40.577 distance: 67 - 68: 18.693 distance: 67 - 147: 15.186 distance: 68 - 69: 15.117 distance: 68 - 71: 26.100 distance: 69 - 70: 19.671 distance: 69 - 74: 9.090 distance: 70 - 144: 14.726 distance: 71 - 72: 13.177 distance: 71 - 73: 29.864 distance: 74 - 75: 15.825 distance: 74 - 80: 17.209 distance: 75 - 76: 6.383 distance: 75 - 78: 9.090 distance: 76 - 77: 27.167 distance: 76 - 81: 38.231 distance: 78 - 79: 12.552 distance: 79 - 80: 31.976 distance: 81 - 82: 18.597 distance: 82 - 83: 9.106 distance: 82 - 85: 18.221 distance: 83 - 84: 12.885 distance: 83 - 88: 14.086 distance: 85 - 86: 20.191 distance: 85 - 87: 22.670 distance: 88 - 89: 9.082 distance: 89 - 90: 22.667 distance: 90 - 91: 24.639 distance: 90 - 92: 24.149 distance: 91 - 104: 7.958 distance: 92 - 93: 4.193 distance: 93 - 94: 6.509 distance: 93 - 96: 7.005 distance: 94 - 95: 4.482 distance: 94 - 99: 3.649 distance: 95 - 110: 7.190 distance: 96 - 97: 7.971 distance: 96 - 98: 4.058 distance: 163 - 171: 3.034