Starting phenix.real_space_refine on Fri Jul 3 19:40:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cjc_45627/07_2026/9cjc_45627.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cjc_45627/07_2026/9cjc_45627.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9cjc_45627/07_2026/9cjc_45627.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cjc_45627/07_2026/9cjc_45627.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9cjc_45627/07_2026/9cjc_45627.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cjc_45627/07_2026/9cjc_45627.map" } resolution = 2.04 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= 0.069 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 Mo 2 10.26 5 Fe 32 7.16 5 S 134 5.16 5 C 9686 2.51 5 N 2571 2.21 5 O 3524 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 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: 15949 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 477, 3790 Classifications: {'peptide': 477} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 455} Chain: "B" Number of atoms: 4174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4174 Classifications: {'peptide': 522} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 495} Chain: "C" Number of atoms: 3026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3026 Classifications: {'peptide': 383} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 364} Chain breaks: 3 Chain: "D" Number of atoms: 4174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4174 Classifications: {'peptide': 522} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 495} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'HCA': 1, 'ICS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Ad-hoc single atom residues: {' FE': 1} Unusual residues: {'CLF': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "C" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'ICS': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Ad-hoc single atom residues: {' FE': 1} Unusual residues: {'CLF': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "A" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 120 Classifications: {'water': 120} Link IDs: {None: 119} Chain: "B" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 264 Classifications: {'water': 264} Link IDs: {None: 263} Chain: "C" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 69 Classifications: {'water': 69} Link IDs: {None: 68} Chain: "D" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 250 Classifications: {'water': 250} Link IDs: {None: 249} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2089 SG CYS A 275 50.131 58.526 26.292 1.00 13.57 S ATOM 1170 SG CYS A 154 31.001 46.800 25.387 1.00 6.37 S ATOM 4549 SG CYS B 95 32.655 43.677 29.438 1.00 17.94 S ATOM 465 SG CYS A 62 36.401 49.092 27.932 1.00 4.22 S ATOM 652 SG CYS A 88 30.550 49.187 31.443 1.00 13.23 S ATOM 652 SG CYS A 88 30.550 49.187 31.443 1.00 13.23 S ATOM 5002 SG CYS B 153 27.563 45.490 28.651 1.00 16.74 S ATOM 4369 SG CYS B 70 29.270 43.922 35.429 1.00 10.71 S ATOM 4549 SG CYS B 95 32.655 43.677 29.438 1.00 17.94 S ATOM 9666 SG CYS C 275 33.824 57.864 101.120 1.00 41.89 S ATOM 8747 SG CYS C 154 52.709 45.589 102.490 1.00 10.67 S ATOM 11749 SG CYS D 95 50.900 42.708 98.379 1.00 20.65 S ATOM 8042 SG CYS C 62 47.464 48.212 99.978 1.00 5.08 S ATOM 8229 SG CYS C 88 53.131 48.101 96.449 1.00 5.68 S ATOM 8229 SG CYS C 88 53.131 48.101 96.449 1.00 5.68 S ATOM 12202 SG CYS D 153 56.084 44.196 99.149 1.00 17.66 S ATOM 11569 SG CYS D 70 54.195 42.802 92.383 1.00 19.95 S ATOM 11749 SG CYS D 95 50.900 42.708 98.379 1.00 20.65 S Time building chain proxies: 3.43, per 1000 atoms: 0.22 Number of scatterers: 15949 At special positions: 0 Unit cell: (83.85, 94.9, 125.45, 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) Mo 2 41.97 Fe 32 26.01 S 134 16.00 O 3524 8.00 N 2571 7.00 C 9686 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=16, symmetry=0 Number of additional bonds: simple=16, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.32 Conformation dependent library (CDL) restraints added in 615.8 milliseconds 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3488 Finding SS restraints... Secondary structure from input PDB file: 101 helices and 12 sheets defined 58.3% alpha, 8.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 5 through 18 Processing helix chain 'A' and resid 21 through 30 removed outlier: 3.970A pdb=" N LYS A 30 " --> pdb=" O LYS A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 45 Processing helix chain 'A' and resid 62 through 68 Processing helix chain 'A' and resid 86 through 92 Processing helix chain 'A' and resid 119 through 126 Processing helix chain 'A' and resid 127 through 142 Processing helix chain 'A' and resid 154 through 158 removed outlier: 3.600A pdb=" N GLY A 157 " --> pdb=" O CYS A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 175 Processing helix chain 'A' and resid 190 through 206 removed outlier: 4.155A pdb=" N GLY A 194 " --> pdb=" O SER A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 232 No H-bonds generated for 'chain 'A' and resid 230 through 232' Processing helix chain 'A' and resid 233 through 245 removed outlier: 4.009A pdb=" N LEU A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 265 Processing helix chain 'A' and resid 266 through 268 No H-bonds generated for 'chain 'A' and resid 266 through 268' Processing helix chain 'A' and resid 275 through 291 removed outlier: 5.779A pdb=" N TYR A 281 " --> pdb=" O ARG A 277 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N ILE A 282 " --> pdb=" O SER A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 314 removed outlier: 4.230A pdb=" N LYS A 304 " --> pdb=" O PHE A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 347 Proline residue: A 333 - end of helix Proline residue: A 344 - end of helix Processing helix chain 'A' and resid 358 through 363 Processing helix chain 'A' and resid 363 through 370 removed outlier: 3.625A pdb=" N LEU A 370 " --> pdb=" O ALA A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 Processing helix chain 'A' and resid 405 through 417 Processing helix chain 'A' and resid 424 through 434 removed outlier: 4.589A pdb=" N PHE A 429 " --> pdb=" O ILE A 425 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N ILE A 430 " --> pdb=" O LYS A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 447 Processing helix chain 'A' and resid 451 through 468 removed outlier: 3.516A pdb=" N ALA A 457 " --> pdb=" O PHE A 453 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE A 458 " --> pdb=" O ASP A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 474 Processing helix chain 'B' and resid 10 through 15 Processing helix chain 'B' and resid 17 through 31 Processing helix chain 'B' and resid 36 through 48 Processing helix chain 'B' and resid 49 through 58 Processing helix chain 'B' and resid 70 through 81 removed outlier: 3.996A pdb=" N GLY B 74 " --> pdb=" O CYS B 70 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY B 81 " --> pdb=" O LEU B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 108 removed outlier: 4.168A pdb=" N VAL B 96 " --> pdb=" O SER B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 126 Processing helix chain 'B' and resid 127 through 143 Processing helix chain 'B' and resid 152 through 159 Processing helix chain 'B' and resid 161 through 172 Processing helix chain 'B' and resid 192 through 210 Processing helix chain 'B' and resid 211 through 213 No H-bonds generated for 'chain 'B' and resid 211 through 213' Processing helix chain 'B' and resid 233 through 247 removed outlier: 3.924A pdb=" N PHE B 237 " --> pdb=" O TYR B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 284 Processing helix chain 'B' and resid 285 through 287 No H-bonds generated for 'chain 'B' and resid 285 through 287' Processing helix chain 'B' and resid 294 through 297 Processing helix chain 'B' and resid 298 through 308 Processing helix chain 'B' and resid 320 through 337 removed outlier: 4.017A pdb=" N TRP B 324 " --> pdb=" O MET B 320 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR B 325 " --> pdb=" O GLY B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 363 removed outlier: 5.146A pdb=" N THR B 360 " --> pdb=" O THR B 356 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N TRP B 361 " --> pdb=" O ASP B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 386 Processing helix chain 'B' and resid 399 through 412 Processing helix chain 'B' and resid 413 through 417 removed outlier: 3.873A pdb=" N LYS B 417 " --> pdb=" O PRO B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 437 Processing helix chain 'B' and resid 447 through 459 removed outlier: 3.978A pdb=" N ILE B 451 " --> pdb=" O TYR B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 463 Processing helix chain 'B' and resid 478 through 482 Processing helix chain 'B' and resid 485 through 509 Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'C' and resid 62 through 68 Processing helix chain 'C' and resid 86 through 93 Processing helix chain 'C' and resid 119 through 126 Processing helix chain 'C' and resid 127 through 142 Processing helix chain 'C' and resid 154 through 158 Processing helix chain 'C' and resid 162 through 175 removed outlier: 3.542A pdb=" N VAL C 166 " --> pdb=" O ASP C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 206 Processing helix chain 'C' and resid 230 through 232 No H-bonds generated for 'chain 'C' and resid 230 through 232' Processing helix chain 'C' and resid 233 through 245 removed outlier: 3.891A pdb=" N LEU C 241 " --> pdb=" O SER C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 265 Processing helix chain 'C' and resid 266 through 268 No H-bonds generated for 'chain 'C' and resid 266 through 268' Processing helix chain 'C' and resid 280 through 291 Processing helix chain 'C' and resid 301 through 314 Processing helix chain 'C' and resid 317 through 347 Proline residue: C 333 - end of helix Proline residue: C 344 - end of helix Processing helix chain 'C' and resid 364 through 370 Processing helix chain 'C' and resid 413 through 417 removed outlier: 3.508A pdb=" N LYS C 417 " --> pdb=" O VAL C 413 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 413 through 417' Processing helix chain 'C' and resid 428 through 434 Processing helix chain 'C' and resid 451 through 468 removed outlier: 3.574A pdb=" N ALA C 457 " --> pdb=" O PHE C 453 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE C 458 " --> pdb=" O ASP C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 474 Processing helix chain 'D' and resid 4 through 8 removed outlier: 4.224A pdb=" N ILE D 8 " --> pdb=" O VAL D 5 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 15 Processing helix chain 'D' and resid 17 through 32 Processing helix chain 'D' and resid 36 through 48 Processing helix chain 'D' and resid 49 through 57 Processing helix chain 'D' and resid 70 through 81 removed outlier: 4.013A pdb=" N GLY D 74 " --> pdb=" O CYS D 70 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 108 removed outlier: 4.006A pdb=" N VAL D 96 " --> pdb=" O SER D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 126 Processing helix chain 'D' and resid 127 through 143 Processing helix chain 'D' and resid 152 through 158 Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 192 through 210 Processing helix chain 'D' and resid 211 through 213 No H-bonds generated for 'chain 'D' and resid 211 through 213' Processing helix chain 'D' and resid 233 through 247 removed outlier: 3.841A pdb=" N PHE D 237 " --> pdb=" O TYR D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 284 Processing helix chain 'D' and resid 285 through 287 No H-bonds generated for 'chain 'D' and resid 285 through 287' Processing helix chain 'D' and resid 294 through 297 Processing helix chain 'D' and resid 298 through 308 Processing helix chain 'D' and resid 320 through 337 removed outlier: 4.001A pdb=" N TRP D 324 " --> pdb=" O MET D 320 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N THR D 325 " --> pdb=" O GLY D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 341 through 363 removed outlier: 5.296A pdb=" N THR D 360 " --> pdb=" O THR D 356 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N TRP D 361 " --> pdb=" O ASP D 357 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 386 Processing helix chain 'D' and resid 399 through 412 Processing helix chain 'D' and resid 413 through 417 removed outlier: 3.650A pdb=" N LYS D 417 " --> pdb=" O PRO D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 437 Processing helix chain 'D' and resid 447 through 459 removed outlier: 4.301A pdb=" N ILE D 451 " --> pdb=" O TYR D 447 " (cutoff:3.500A) Processing helix chain 'D' and resid 460 through 463 Processing helix chain 'D' and resid 478 through 482 Processing helix chain 'D' and resid 485 through 509 Processing helix chain 'D' and resid 515 through 519 Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 34 removed outlier: 6.285A pdb=" N VAL A 351 " --> pdb=" O VAL A 374 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY A 376 " --> pdb=" O VAL A 351 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ARG A 350 " --> pdb=" O LEU A 420 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N GLY A 422 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N MET A 352 " --> pdb=" O GLY A 422 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ILE A 421 " --> pdb=" O ARG A 439 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 178 through 181 removed outlier: 4.155A pdb=" N PHE A 114 " --> pdb=" O HIS A 80 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 248 through 254 removed outlier: 6.482A pdb=" N VAL A 223 " --> pdb=" O CYS A 249 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA A 251 " --> pdb=" O VAL A 223 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 114 through 115 Processing sheet with id=AA5, first strand: chain 'B' and resid 251 through 253 removed outlier: 6.386A pdb=" N ASN B 225 " --> pdb=" O VAL B 291 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 420 through 423 removed outlier: 8.471A pdb=" N THR B 420 " --> pdb=" O GLU B 389 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N VAL B 391 " --> pdb=" O THR B 420 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N TYR B 422 " --> pdb=" O VAL B 391 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE B 393 " --> pdb=" O TYR B 422 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N PHE B 367 " --> pdb=" O VAL B 391 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N ILE B 393 " --> pdb=" O PHE B 367 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LEU B 369 " --> pdb=" O ILE B 393 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N CYS B 395 " --> pdb=" O LEU B 369 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ARG B 366 " --> pdb=" O PHE B 441 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N ILE B 443 " --> pdb=" O ARG B 366 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ALA B 368 " --> pdb=" O ILE B 443 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N MET B 442 " --> pdb=" O ILE B 467 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 178 through 181 removed outlier: 4.218A pdb=" N PHE C 114 " --> pdb=" O HIS C 80 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 248 through 254 removed outlier: 6.489A pdb=" N VAL C 223 " --> pdb=" O CYS C 249 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA C 251 " --> pdb=" O VAL C 223 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 373 through 375 removed outlier: 6.040A pdb=" N VAL C 351 " --> pdb=" O VAL C 375 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 114 through 115 Processing sheet with id=AB2, first strand: chain 'D' and resid 251 through 253 removed outlier: 6.344A pdb=" N ASN D 225 " --> pdb=" O VAL D 291 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 420 through 423 removed outlier: 8.565A pdb=" N THR D 420 " --> pdb=" O GLU D 389 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N VAL D 391 " --> pdb=" O THR D 420 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N TYR D 422 " --> pdb=" O VAL D 391 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ILE D 393 " --> pdb=" O TYR D 422 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N PHE D 367 " --> pdb=" O VAL D 391 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N ILE D 393 " --> pdb=" O PHE D 367 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N LEU D 369 " --> pdb=" O ILE D 393 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N CYS D 395 " --> pdb=" O LEU D 369 " (cutoff:3.500A) 755 hydrogen bonds defined for protein. 2154 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: 2.86 Time building geometry restraints manager: 1.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.56: 15378 1.56 - 1.91: 171 1.91 - 2.25: 36 2.25 - 2.60: 82 2.60 - 2.94: 18 Bond restraints: 15685 Sorted by residual: bond pdb="FE2 CLF D 601 " pdb="FE8 CLF D 601 " ideal model delta sigma weight residual 2.200 2.944 -0.744 2.00e-02 2.50e+03 1.38e+03 bond pdb="FE2 CLF B 601 " pdb="FE8 CLF B 601 " ideal model delta sigma weight residual 2.200 2.938 -0.738 2.00e-02 2.50e+03 1.36e+03 bond pdb="FE4 CLF B 601 " pdb="FE5 CLF B 601 " ideal model delta sigma weight residual 2.200 2.880 -0.680 2.00e-02 2.50e+03 1.15e+03 bond pdb="FE4 CLF D 601 " pdb="FE5 CLF D 601 " ideal model delta sigma weight residual 2.200 2.878 -0.678 2.00e-02 2.50e+03 1.15e+03 bond pdb="FE6 CLF D 601 " pdb="FE7 CLF D 601 " ideal model delta sigma weight residual 2.200 2.861 -0.661 2.00e-02 2.50e+03 1.09e+03 ... (remaining 15680 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.90: 21152 6.90 - 13.80: 2 13.80 - 20.70: 3 20.70 - 27.60: 0 27.60 - 34.50: 4 Bond angle restraints: 21161 Sorted by residual: angle pdb=" S1 CLF B 601 " pdb="FE2 CLF B 601 " pdb="FE4 CLF B 601 " ideal model delta sigma weight residual 90.00 55.50 34.50 3.00e+00 1.11e-01 1.32e+02 angle pdb=" S1 CLF D 601 " pdb="FE2 CLF D 601 " pdb="FE4 CLF D 601 " ideal model delta sigma weight residual 90.00 55.66 34.34 3.00e+00 1.11e-01 1.31e+02 angle pdb=" S1 CLF D 601 " pdb="FE2 CLF D 601 " pdb="FE1 CLF D 601 " ideal model delta sigma weight residual 90.00 56.82 33.18 3.00e+00 1.11e-01 1.22e+02 angle pdb=" S1 CLF B 601 " pdb="FE2 CLF B 601 " pdb="FE1 CLF B 601 " ideal model delta sigma weight residual 90.00 56.90 33.10 3.00e+00 1.11e-01 1.22e+02 angle pdb=" S1 CLF B 601 " pdb="FE2 CLF B 601 " pdb="FE3 CLF B 601 " ideal model delta sigma weight residual 90.00 106.98 -16.98 3.00e+00 1.11e-01 3.20e+01 ... (remaining 21156 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 8478 17.79 - 35.58: 813 35.58 - 53.38: 213 53.38 - 71.17: 64 71.17 - 88.96: 26 Dihedral angle restraints: 9594 sinusoidal: 4139 harmonic: 5455 Sorted by residual: dihedral pdb=" CA PHE D 367 " pdb=" C PHE D 367 " pdb=" N ALA D 368 " pdb=" CA ALA D 368 " ideal model delta harmonic sigma weight residual 180.00 155.41 24.59 0 5.00e+00 4.00e-02 2.42e+01 dihedral pdb=" CA ILE C 364 " pdb=" C ILE C 364 " pdb=" N GLY C 365 " pdb=" CA GLY C 365 " ideal model delta harmonic sigma weight residual 180.00 -157.98 -22.02 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CA ASP C 445 " pdb=" C ASP C 445 " pdb=" N TYR C 446 " pdb=" CA TYR C 446 " ideal model delta harmonic sigma weight residual -180.00 -158.81 -21.19 0 5.00e+00 4.00e-02 1.80e+01 ... (remaining 9591 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1122 0.030 - 0.060: 685 0.060 - 0.090: 270 0.090 - 0.121: 128 0.121 - 0.151: 18 Chirality restraints: 2223 Sorted by residual: chirality pdb=" CA ILE D 318 " pdb=" N ILE D 318 " pdb=" C ILE D 318 " pdb=" CB ILE D 318 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.68e-01 chirality pdb=" CA ILE B 318 " pdb=" N ILE B 318 " pdb=" C ILE B 318 " pdb=" CB ILE B 318 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.31e-01 chirality pdb=" CA ILE A 226 " pdb=" N ILE A 226 " pdb=" C ILE A 226 " pdb=" CB ILE A 226 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.78e-01 ... (remaining 2220 not shown) Planarity restraints: 2712 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG B 453 " 0.008 2.00e-02 2.50e+03 1.65e-02 2.73e+00 pdb=" C ARG B 453 " -0.029 2.00e-02 2.50e+03 pdb=" O ARG B 453 " 0.011 2.00e-02 2.50e+03 pdb=" N ASP B 454 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY C 73 " -0.025 5.00e-02 4.00e+02 3.74e-02 2.24e+00 pdb=" N PRO C 74 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO C 74 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 74 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG D 453 " -0.007 2.00e-02 2.50e+03 1.47e-02 2.17e+00 pdb=" C ARG D 453 " 0.025 2.00e-02 2.50e+03 pdb=" O ARG D 453 " -0.010 2.00e-02 2.50e+03 pdb=" N ASP D 454 " -0.009 2.00e-02 2.50e+03 ... (remaining 2709 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 458 2.65 - 3.21: 15566 3.21 - 3.78: 31096 3.78 - 4.34: 43021 4.34 - 4.90: 64974 Nonbonded interactions: 155115 Sorted by model distance: nonbonded pdb=" OD2 ASP B 357 " pdb="FE FE B 602 " model vdw 2.091 3.000 nonbonded pdb=" OE2 GLU B 109 " pdb="FE FE D 602 " model vdw 2.129 3.000 nonbonded pdb=" O ARG B 108 " pdb="FE FE D 602 " model vdw 2.147 3.000 nonbonded pdb=" O ARG D 108 " pdb="FE FE B 602 " model vdw 2.173 3.000 nonbonded pdb=" OD2 ASP C 117 " pdb=" O HOH C 701 " model vdw 2.177 3.040 ... (remaining 155110 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 'B' selection = chain 'D' } 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: 21.950 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: 0.310 Check model and map are aligned: 0.110 Set scattering table: 0.050 Process input model: 14.400 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 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:6.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8900 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 : 0.024 0.744 15701 Z= 1.206 Angle : 0.793 34.500 21161 Z= 0.375 Chirality : 0.046 0.151 2223 Planarity : 0.005 0.058 2712 Dihedral : 16.087 88.961 6106 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.85 % Allowed : 11.78 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.74 % Cis-general : 0.11 % 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: 0.71 (0.19), residues: 1890 helix: 1.30 (0.17), residues: 935 sheet: -0.86 (0.37), residues: 164 loop : -0.12 (0.21), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 96 TYR 0.022 0.003 TYR B 142 PHE 0.019 0.002 PHE A 431 TRP 0.020 0.002 TRP C 444 HIS 0.008 0.002 HIS D 297 Details of bonding type rmsd/Z covalent geometry : bond 0.02411 / 1.20 (15685) covalent geometry : angle 0.79320 / 0.38 (21161) hydrogen bonds : bond 0.12871 / 8.98 ( 755) hydrogen bonds : angle 6.70267 / 4.81 ( 2154) Misc. bond : bond 0.03936 / 2.54 ( 16) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 184 time to evaluate : 0.609 Fit side-chains REVERT: A 391 MET cc_start: 0.7694 (mmm) cc_final: 0.7493 (mmm) REVERT: D 503 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.7682 (mp0) outliers start: 14 outliers final: 9 residues processed: 195 average time/residue: 0.7462 time to fit residues: 157.9940 Evaluate side-chains 190 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 180 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 503 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.0980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 8.9990 chunk 149 optimal weight: 4.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 29 ASN A 53 GLN A 98 ASN B 518 ASN C 298 ASN C 451 HIS C 476 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.127396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.108561 restraints weight = 10053.433| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 0.68 r_work: 0.3121 rms_B_bonded: 1.00 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 1.70 restraints_weight: 0.2500 r_work: 0.2836 rms_B_bonded: 4.55 restraints_weight: 0.1250 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8877 moved from start: 0.0517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.260 15701 Z= 0.206 Angle : 0.748 29.085 21161 Z= 0.361 Chirality : 0.046 0.150 2223 Planarity : 0.005 0.066 2712 Dihedral : 5.958 59.373 2408 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.83 % Allowed : 10.87 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.74 % Cis-general : 0.11 % 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: 0.71 (0.19), residues: 1890 helix: 1.31 (0.17), residues: 958 sheet: -0.92 (0.35), residues: 169 loop : -0.14 (0.22), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 96 TYR 0.021 0.002 TYR A 379 PHE 0.017 0.002 PHE A 431 TRP 0.015 0.002 TRP C 335 HIS 0.009 0.001 HIS D 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.19 (15685) covalent geometry : angle 0.74761 / 0.36 (21161) hydrogen bonds : bond 0.05672 / 3.88 ( 755) hydrogen bonds : angle 5.92422 / 4.25 ( 2154) Misc. bond : bond 0.12197 / 7.85 ( 16) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 182 time to evaluate : 0.432 Fit side-chains revert: symmetry clash REVERT: A 168 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.8183 (mtpt) REVERT: B 120 GLU cc_start: 0.7795 (mt-10) cc_final: 0.7471 (mt-10) REVERT: C 53 GLN cc_start: 0.7526 (OUTLIER) cc_final: 0.6997 (tt0) REVERT: C 318 GLU cc_start: 0.7754 (mm-30) cc_final: 0.7167 (mm-30) REVERT: C 349 LYS cc_start: 0.8112 (OUTLIER) cc_final: 0.7908 (mttt) REVERT: D 146 MET cc_start: 0.9038 (OUTLIER) cc_final: 0.8723 (ttp) REVERT: D 211 LYS cc_start: 0.8417 (OUTLIER) cc_final: 0.8125 (mmtm) outliers start: 30 outliers final: 15 residues processed: 202 average time/residue: 0.6945 time to fit residues: 152.4301 Evaluate side-chains 196 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 176 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 168 LYS Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain C residue 53 GLN Chi-restraints excluded: chain C residue 60 ARG Chi-restraints excluded: chain C residue 88 CYS Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 349 LYS Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 428 LYS Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 146 MET Chi-restraints excluded: chain D residue 211 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 122 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 chunk 144 optimal weight: 5.9990 chunk 123 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 chunk 181 optimal weight: 5.9990 chunk 149 optimal weight: 6.9990 chunk 125 optimal weight: 0.7980 chunk 90 optimal weight: 0.6980 chunk 64 optimal weight: 0.5980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 29 ASN A 53 GLN A 98 ASN C 451 HIS C 476 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.127676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.108832 restraints weight = 10199.573| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 0.69 r_work: 0.3131 rms_B_bonded: 1.01 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 1.71 restraints_weight: 0.2500 r_work: 0.2846 rms_B_bonded: 4.60 restraints_weight: 0.1250 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8867 moved from start: 0.0628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.230 15701 Z= 0.181 Angle : 0.726 29.280 21161 Z= 0.346 Chirality : 0.045 0.149 2223 Planarity : 0.004 0.062 2712 Dihedral : 5.643 59.793 2402 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.83 % Allowed : 10.81 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.74 % Cis-general : 0.11 % 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: 0.77 (0.19), residues: 1890 helix: 1.36 (0.17), residues: 960 sheet: -0.93 (0.35), residues: 169 loop : -0.13 (0.22), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 359 TYR 0.020 0.002 TYR C 229 PHE 0.015 0.002 PHE A 431 TRP 0.015 0.002 TRP C 335 HIS 0.009 0.001 HIS D 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.17 (15685) covalent geometry : angle 0.72614 / 0.35 (21161) hydrogen bonds : bond 0.05318 / 3.64 ( 755) hydrogen bonds : angle 5.80360 / 4.15 ( 2154) Misc. bond : bond 0.10715 / 6.91 ( 16) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 182 time to evaluate : 0.545 Fit side-chains revert: symmetry clash REVERT: A 168 LYS cc_start: 0.8611 (OUTLIER) cc_final: 0.8171 (mtpt) REVERT: A 401 TYR cc_start: 0.8052 (OUTLIER) cc_final: 0.6630 (p90) REVERT: B 120 GLU cc_start: 0.7768 (mt-10) cc_final: 0.7427 (mt-10) REVERT: B 121 ASP cc_start: 0.7817 (OUTLIER) cc_final: 0.7438 (p0) REVERT: C 53 GLN cc_start: 0.7499 (OUTLIER) cc_final: 0.6969 (tt0) REVERT: C 318 GLU cc_start: 0.7709 (mm-30) cc_final: 0.6928 (mp0) REVERT: C 349 LYS cc_start: 0.8079 (OUTLIER) cc_final: 0.7869 (mttt) REVERT: D 146 MET cc_start: 0.9041 (OUTLIER) cc_final: 0.8742 (ttp) REVERT: D 503 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.8010 (mp0) outliers start: 30 outliers final: 13 residues processed: 202 average time/residue: 0.7552 time to fit residues: 165.7989 Evaluate side-chains 197 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 177 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 168 LYS Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 401 TYR Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain C residue 53 GLN Chi-restraints excluded: chain C residue 60 ARG Chi-restraints excluded: chain C residue 88 CYS Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 349 LYS Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 428 LYS Chi-restraints excluded: chain D residue 146 MET Chi-restraints excluded: chain D residue 503 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 75 optimal weight: 1.9990 chunk 96 optimal weight: 6.9990 chunk 149 optimal weight: 7.9990 chunk 48 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 139 optimal weight: 0.9980 chunk 84 optimal weight: 0.8980 chunk 93 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 chunk 147 optimal weight: 0.6980 chunk 132 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 29 ASN A 53 GLN A 98 ASN A 321 GLN C 451 HIS C 476 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.130252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.111518 restraints weight = 10187.793| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 0.69 r_work: 0.3163 rms_B_bonded: 1.02 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 1.73 restraints_weight: 0.2500 r_work: 0.2880 rms_B_bonded: 4.64 restraints_weight: 0.1250 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.0794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.195 15701 Z= 0.151 Angle : 0.694 29.198 21161 Z= 0.326 Chirality : 0.044 0.157 2223 Planarity : 0.004 0.052 2712 Dihedral : 5.433 59.539 2401 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.71 % Allowed : 11.29 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.74 % Cis-general : 0.11 % 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: 0.89 (0.19), residues: 1890 helix: 1.48 (0.17), residues: 960 sheet: -0.90 (0.36), residues: 169 loop : -0.10 (0.22), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 359 TYR 0.017 0.002 TYR C 229 PHE 0.013 0.001 PHE A 431 TRP 0.015 0.002 TRP C 335 HIS 0.009 0.001 HIS D 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.14 (15685) covalent geometry : angle 0.69360 / 0.33 (21161) hydrogen bonds : bond 0.04680 / 3.20 ( 755) hydrogen bonds : angle 5.66251 / 4.04 ( 2154) Misc. bond : bond 0.09213 / 5.93 ( 16) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 182 time to evaluate : 0.656 Fit side-chains revert: symmetry clash REVERT: A 401 TYR cc_start: 0.8032 (OUTLIER) cc_final: 0.6641 (p90) REVERT: B 120 GLU cc_start: 0.7749 (mt-10) cc_final: 0.7408 (mt-10) REVERT: B 121 ASP cc_start: 0.7809 (m-30) cc_final: 0.7454 (p0) REVERT: B 417 LYS cc_start: 0.8215 (OUTLIER) cc_final: 0.7840 (mmpt) REVERT: C 53 GLN cc_start: 0.7490 (OUTLIER) cc_final: 0.6960 (tt0) REVERT: C 318 GLU cc_start: 0.7682 (mm-30) cc_final: 0.6874 (mp0) REVERT: C 349 LYS cc_start: 0.8072 (OUTLIER) cc_final: 0.7815 (mtpt) REVERT: D 146 MET cc_start: 0.9004 (OUTLIER) cc_final: 0.8743 (ttp) REVERT: D 503 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8022 (mp0) outliers start: 28 outliers final: 13 residues processed: 200 average time/residue: 0.7500 time to fit residues: 163.1463 Evaluate side-chains 192 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 173 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 401 TYR Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain C residue 53 GLN Chi-restraints excluded: chain C residue 60 ARG Chi-restraints excluded: chain C residue 88 CYS Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 349 LYS Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 428 LYS Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 146 MET Chi-restraints excluded: chain D residue 503 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- 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: 55.6763 > 50: distance: 107 - 111: 21.861 distance: 111 - 112: 17.072 distance: 112 - 113: 26.265 distance: 112 - 115: 14.891 distance: 113 - 114: 8.998 distance: 113 - 117: 33.272 distance: 114 - 139: 3.367 distance: 115 - 116: 37.995 distance: 117 - 118: 13.431 distance: 118 - 119: 4.863 distance: 118 - 121: 18.534 distance: 119 - 120: 9.603 distance: 119 - 131: 16.013 distance: 120 - 151: 7.673 distance: 121 - 122: 6.386 distance: 122 - 123: 4.173 distance: 122 - 124: 4.995 distance: 123 - 125: 9.630 distance: 124 - 126: 5.801 distance: 124 - 127: 5.469 distance: 126 - 128: 5.951 distance: 127 - 129: 6.268 distance: 129 - 130: 5.828 distance: 131 - 132: 3.592 distance: 132 - 133: 13.319 distance: 132 - 135: 18.797 distance: 133 - 134: 14.338 distance: 133 - 139: 10.120 distance: 135 - 136: 19.556 distance: 136 - 137: 7.983 distance: 136 - 138: 4.782 distance: 139 - 140: 8.376 distance: 140 - 141: 16.261 distance: 140 - 143: 6.569 distance: 141 - 142: 9.229 distance: 141 - 151: 8.863 distance: 143 - 144: 12.993 distance: 144 - 145: 14.475 distance: 144 - 146: 8.874 distance: 146 - 148: 14.284 distance: 147 - 149: 5.615 distance: 148 - 149: 9.880 distance: 149 - 150: 4.684 distance: 151 - 152: 10.061 distance: 152 - 153: 33.178 distance: 152 - 155: 5.560 distance: 153 - 154: 19.873 distance: 153 - 157: 12.338 distance: 155 - 156: 10.789 distance: 157 - 158: 3.541 distance: 158 - 159: 8.948 distance: 159 - 160: 13.829 distance: 159 - 161: 17.826 distance: 161 - 162: 6.315 distance: 161 - 167: 12.656 distance: 162 - 163: 41.721 distance: 162 - 165: 26.277 distance: 163 - 164: 43.227 distance: 163 - 168: 50.846 distance: 165 - 166: 8.872 distance: 168 - 169: 18.730 distance: 169 - 170: 16.005 distance: 169 - 172: 17.775 distance: 170 - 171: 31.432 distance: 170 - 180: 23.563 distance: 172 - 173: 20.008 distance: 173 - 174: 10.241 distance: 173 - 175: 14.080 distance: 174 - 176: 7.204 distance: 175 - 177: 16.438 distance: 176 - 178: 13.480 distance: 177 - 178: 12.769 distance: 178 - 179: 11.704 distance: 180 - 181: 15.744 distance: 181 - 182: 21.004 distance: 181 - 184: 22.549 distance: 182 - 183: 23.123 distance: 182 - 190: 12.740 distance: 183 - 207: 21.025 distance: 184 - 185: 11.826 distance: 185 - 186: 17.165 distance: 185 - 187: 20.825 distance: 186 - 188: 26.026 distance: 187 - 189: 23.886 distance: 188 - 189: 14.039 distance: 190 - 191: 14.666 distance: 191 - 192: 18.493 distance: 192 - 193: 12.796 distance: 192 - 194: 17.726 distance: 193 - 211: 32.615