Starting phenix.real_space_refine on Fri Aug 22 22:03:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dsn_30839/08_2025/7dsn_30839_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dsn_30839/08_2025/7dsn_30839.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7dsn_30839/08_2025/7dsn_30839.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dsn_30839/08_2025/7dsn_30839.map" model { file = "/net/cci-nas-00/data/ceres_data/7dsn_30839/08_2025/7dsn_30839_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dsn_30839/08_2025/7dsn_30839_neut.cif" } resolution = 3.1 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= 0.005 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 27 5.16 5 C 4939 2.51 5 N 1192 2.21 5 O 1375 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7534 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3670 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 22, 'TRANS': 448} Chain: "B" Number of atoms: 3586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3586 Classifications: {'peptide': 464} Link IDs: {'PTRANS': 24, 'TRANS': 439} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'3PH': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 118 Unusual residues: {'HO9': 1, 'Y01': 2} Classifications: {'undetermined': 3, 'water': 17} Link IDs: {None: 19} Time building chain proxies: 1.84, per 1000 atoms: 0.24 Number of scatterers: 7534 At special positions: 0 Unit cell: (83.699, 86.96, 126.092, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 27 16.00 P 1 15.00 O 1375 8.00 N 1192 7.00 C 4939 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 211 " - pdb=" SG CYS B 164 " distance=2.19 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG C 1 " - " ASN A 507 " " NAG D 1 " - " ASN A 366 " " NAG E 1 " - " ASN A 382 " " NAG F 1 " - " ASN A 425 " Time building additional restraints: 0.62 Conformation dependent library (CDL) restraints added in 379.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1722 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 6 sheets defined 55.6% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 166 through 174 Processing helix chain 'A' and resid 178 through 207 removed outlier: 3.671A pdb=" N ARG A 183 " --> pdb=" O TRP A 179 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA A 199 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG A 207 " --> pdb=" O VAL A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 236 removed outlier: 3.778A pdb=" N GLN A 235 " --> pdb=" O LEU A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 246 removed outlier: 3.799A pdb=" N LYS A 246 " --> pdb=" O LEU A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 249 No H-bonds generated for 'chain 'A' and resid 247 through 249' Processing helix chain 'A' and resid 250 through 255 Processing helix chain 'A' and resid 287 through 300 removed outlier: 3.821A pdb=" N SER A 293 " --> pdb=" O GLU A 289 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS A 300 " --> pdb=" O GLN A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 342 removed outlier: 3.725A pdb=" N VAL A 331 " --> pdb=" O VAL A 327 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLU A 336 " --> pdb=" O LYS A 332 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE A 337 " --> pdb=" O ASP A 333 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA A 341 " --> pdb=" O PHE A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 370 removed outlier: 3.751A pdb=" N ALA A 362 " --> pdb=" O SER A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 393 removed outlier: 3.698A pdb=" N LEU A 392 " --> pdb=" O GLN A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 427 removed outlier: 3.670A pdb=" N THR A 416 " --> pdb=" O THR A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 445 removed outlier: 3.621A pdb=" N SER A 444 " --> pdb=" O LEU A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 459 Processing helix chain 'A' and resid 509 through 514 Processing helix chain 'A' and resid 520 through 532 removed outlier: 3.558A pdb=" N ARG A 526 " --> pdb=" O SER A 522 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER A 532 " --> pdb=" O SER A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 539 Processing helix chain 'B' and resid 51 through 64 removed outlier: 3.563A pdb=" N GLY B 55 " --> pdb=" O THR B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 78 Processing helix chain 'B' and resid 81 through 110 removed outlier: 3.681A pdb=" N LEU B 86 " --> pdb=" O PRO B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 125 removed outlier: 3.632A pdb=" N GLY B 125 " --> pdb=" O LEU B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 139 Processing helix chain 'B' and resid 139 through 158 Processing helix chain 'B' and resid 159 through 161 No H-bonds generated for 'chain 'B' and resid 159 through 161' Processing helix chain 'B' and resid 167 through 189 removed outlier: 3.681A pdb=" N LEU B 173 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL B 174 " --> pdb=" O ALA B 170 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU B 177 " --> pdb=" O LEU B 173 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL B 179 " --> pdb=" O ALA B 175 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU B 180 " --> pdb=" O CYS B 176 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA B 184 " --> pdb=" O LEU B 180 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER B 189 " --> pdb=" O VAL B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 220 removed outlier: 3.932A pdb=" N ALA B 193 " --> pdb=" O SER B 189 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN B 197 " --> pdb=" O ALA B 193 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU B 210 " --> pdb=" O LEU B 206 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE B 211 " --> pdb=" O ALA B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 248 removed outlier: 3.609A pdb=" N ALA B 246 " --> pdb=" O ASN B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 263 Processing helix chain 'B' and resid 269 through 274 Processing helix chain 'B' and resid 274 through 300 Proline residue: B 283 - end of helix removed outlier: 3.624A pdb=" N LEU B 287 " --> pdb=" O PRO B 283 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL B 290 " --> pdb=" O THR B 286 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA B 295 " --> pdb=" O LEU B 291 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N THR B 299 " --> pdb=" O ALA B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 306 removed outlier: 3.651A pdb=" N LEU B 306 " --> pdb=" O THR B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 320 Processing helix chain 'B' and resid 325 through 333 removed outlier: 3.504A pdb=" N VAL B 329 " --> pdb=" O TRP B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 356 removed outlier: 3.606A pdb=" N ASN B 340 " --> pdb=" O PHE B 336 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY B 341 " --> pdb=" O GLY B 337 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER B 342 " --> pdb=" O SER B 338 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N THR B 345 " --> pdb=" O GLY B 341 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER B 347 " --> pdb=" O LEU B 343 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ARG B 348 " --> pdb=" O PHE B 344 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU B 356 " --> pdb=" O VAL B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 386 removed outlier: 3.583A pdb=" N PHE B 379 " --> pdb=" O PRO B 375 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR B 384 " --> pdb=" O THR B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 390 removed outlier: 3.610A pdb=" N SER B 390 " --> pdb=" O TYR B 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 387 through 390' Processing helix chain 'B' and resid 393 through 397 removed outlier: 3.834A pdb=" N ILE B 397 " --> pdb=" O PHE B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 420 removed outlier: 4.098A pdb=" N VAL B 408 " --> pdb=" O ASN B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 448 removed outlier: 3.584A pdb=" N LEU B 441 " --> pdb=" O VAL B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 453 removed outlier: 3.567A pdb=" N LYS B 453 " --> pdb=" O VAL B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 476 removed outlier: 3.530A pdb=" N THR B 463 " --> pdb=" O GLY B 459 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE B 464 " --> pdb=" O ILE B 460 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE B 465 " --> pdb=" O GLY B 461 " (cutoff:3.500A) Proline residue: B 470 - end of helix Processing helix chain 'B' and resid 482 through 501 removed outlier: 3.860A pdb=" N GLN B 487 " --> pdb=" O LYS B 483 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N GLY B 488 " --> pdb=" O TRP B 484 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 400 through 402 removed outlier: 6.548A pdb=" N LEU A 377 " --> pdb=" O LEU A 400 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N THR A 402 " --> pdb=" O LEU A 377 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ALA A 379 " --> pdb=" O THR A 402 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N PHE A 346 " --> pdb=" O ILE A 378 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N GLY A 380 " --> pdb=" O PHE A 346 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N VAL A 348 " --> pdb=" O GLY A 380 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLY A 345 " --> pdb=" O VAL A 305 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N LEU A 260 " --> pdb=" O ILE A 306 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ASP A 308 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N LEU A 262 " --> pdb=" O ASP A 308 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 266 through 268 Processing sheet with id=AA3, first strand: chain 'A' and resid 541 through 545 removed outlier: 4.547A pdb=" N SER A 553 " --> pdb=" O PHE A 545 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 575 through 576 Processing sheet with id=AA5, first strand: chain 'A' and resid 593 through 594 Processing sheet with id=AA6, first strand: chain 'B' and resid 365 through 366 334 hydrogen bonds defined for protein. 972 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.24 Time building geometry restraints manager: 0.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1168 1.31 - 1.43: 2050 1.43 - 1.56: 4424 1.56 - 1.68: 25 1.68 - 1.81: 40 Bond restraints: 7707 Sorted by residual: bond pdb=" CAI Y01 B 603 " pdb=" CAZ Y01 B 603 " ideal model delta sigma weight residual 1.332 1.555 -0.223 2.00e-02 2.50e+03 1.24e+02 bond pdb=" CAI Y01 B 602 " pdb=" CAZ Y01 B 602 " ideal model delta sigma weight residual 1.332 1.554 -0.222 2.00e-02 2.50e+03 1.23e+02 bond pdb=" C22 HO9 B 601 " pdb=" C25 HO9 B 601 " ideal model delta sigma weight residual 1.380 1.564 -0.184 2.00e-02 2.50e+03 8.46e+01 bond pdb=" C23 HO9 B 601 " pdb=" C28 HO9 B 601 " ideal model delta sigma weight residual 1.390 1.565 -0.175 2.00e-02 2.50e+03 7.68e+01 bond pdb=" CBG Y01 B 602 " pdb=" CBI Y01 B 602 " ideal model delta sigma weight residual 1.537 1.385 0.152 2.00e-02 2.50e+03 5.78e+01 ... (remaining 7702 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.66: 10135 2.66 - 5.32: 287 5.32 - 7.98: 58 7.98 - 10.64: 14 10.64 - 13.30: 3 Bond angle restraints: 10497 Sorted by residual: angle pdb=" N VAL B 396 " pdb=" CA VAL B 396 " pdb=" C VAL B 396 " ideal model delta sigma weight residual 112.83 106.26 6.57 9.90e-01 1.02e+00 4.40e+01 angle pdb=" C PRO A 209 " pdb=" N ARG A 210 " pdb=" CA ARG A 210 " ideal model delta sigma weight residual 121.54 131.91 -10.37 1.91e+00 2.74e-01 2.95e+01 angle pdb=" N ILE B 68 " pdb=" CA ILE B 68 " pdb=" C ILE B 68 " ideal model delta sigma weight residual 112.83 107.51 5.32 9.90e-01 1.02e+00 2.89e+01 angle pdb=" N THR A 163 " pdb=" CA THR A 163 " pdb=" C THR A 163 " ideal model delta sigma weight residual 111.71 105.32 6.39 1.34e+00 5.57e-01 2.27e+01 angle pdb=" C THR B 71 " pdb=" N PRO B 72 " pdb=" CA PRO B 72 " ideal model delta sigma weight residual 119.84 114.06 5.78 1.25e+00 6.40e-01 2.14e+01 ... (remaining 10492 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.07: 4553 35.07 - 70.15: 126 70.15 - 105.22: 20 105.22 - 140.29: 31 140.29 - 175.37: 7 Dihedral angle restraints: 4737 sinusoidal: 2057 harmonic: 2680 Sorted by residual: dihedral pdb=" CA GLY A 410 " pdb=" C GLY A 410 " pdb=" N SER A 411 " pdb=" CA SER A 411 " ideal model delta harmonic sigma weight residual -180.00 -154.75 -25.25 0 5.00e+00 4.00e-02 2.55e+01 dihedral pdb=" CA THR B 264 " pdb=" C THR B 264 " pdb=" N GLU B 265 " pdb=" CA GLU B 265 " ideal model delta harmonic sigma weight residual 180.00 -155.82 -24.18 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" CA ARG A 210 " pdb=" C ARG A 210 " pdb=" N CYS A 211 " pdb=" CA CYS A 211 " ideal model delta harmonic sigma weight residual 180.00 156.52 23.48 0 5.00e+00 4.00e-02 2.20e+01 ... (remaining 4734 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.192: 1223 1.192 - 2.383: 0 2.383 - 3.575: 0 3.575 - 4.766: 0 4.766 - 5.958: 10 Chirality restraints: 1233 Sorted by residual: chirality pdb=" CBI Y01 B 602 " pdb=" CAU Y01 B 602 " pdb=" CBE Y01 B 602 " pdb=" CBG Y01 B 602 " both_signs ideal model delta sigma weight residual False 2.94 -3.02 5.96 2.00e-01 2.50e+01 8.87e+02 chirality pdb=" CBI Y01 B 603 " pdb=" CAU Y01 B 603 " pdb=" CBE Y01 B 603 " pdb=" CBG Y01 B 603 " both_signs ideal model delta sigma weight residual False 2.94 -3.00 5.94 2.00e-01 2.50e+01 8.82e+02 chirality pdb=" CBH Y01 B 602 " pdb=" CAT Y01 B 602 " pdb=" CAZ Y01 B 602 " pdb=" CBF Y01 B 602 " both_signs ideal model delta sigma weight residual False -2.85 2.64 -5.50 2.00e-01 2.50e+01 7.56e+02 ... (remaining 1230 not shown) Planarity restraints: 1286 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS B 164 " -0.073 5.00e-02 4.00e+02 1.13e-01 2.04e+01 pdb=" N PRO B 165 " 0.195 5.00e-02 4.00e+02 pdb=" CA PRO B 165 " -0.062 5.00e-02 4.00e+02 pdb=" CD PRO B 165 " -0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 618 " -0.052 5.00e-02 4.00e+02 7.76e-02 9.63e+00 pdb=" N PRO A 619 " 0.134 5.00e-02 4.00e+02 pdb=" CA PRO A 619 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 619 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 282 " -0.038 5.00e-02 4.00e+02 5.69e-02 5.18e+00 pdb=" N PRO B 283 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO B 283 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 283 " -0.032 5.00e-02 4.00e+02 ... (remaining 1283 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 199 2.69 - 3.24: 6731 3.24 - 3.79: 11474 3.79 - 4.35: 15599 4.35 - 4.90: 25421 Nonbonded interactions: 59424 Sorted by model distance: nonbonded pdb=" O VAL B 70 " pdb=" OG1 THR B 71 " model vdw 2.132 3.040 nonbonded pdb=" OG SER A 407 " pdb=" O LEU A 436 " model vdw 2.216 3.040 nonbonded pdb=" CG2 ILE B 397 " pdb=" O21 HO9 B 601 " model vdw 2.254 3.460 nonbonded pdb=" CG2 ILE B 147 " pdb=" C27 HO9 B 601 " model vdw 2.265 3.760 nonbonded pdb=" OG SER B 113 " pdb=" O THR B 264 " model vdw 2.271 3.040 ... (remaining 59419 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 'C' selection = chain 'D' selection = chain 'E' 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: 1.190 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: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 8.350 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 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 : 0.012 0.223 7716 Z= 0.583 Angle : 1.168 13.297 10523 Z= 0.603 Chirality : 0.490 5.958 1233 Planarity : 0.008 0.113 1282 Dihedral : 22.156 175.366 3012 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.97 % Allowed : 6.66 % Favored : 92.37 % Rotamer: Outliers : 1.52 % Allowed : 5.70 % Favored : 92.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.42 (0.21), residues: 931 helix: -2.79 (0.17), residues: 486 sheet: -1.73 (0.59), residues: 63 loop : -3.19 (0.25), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 556 TYR 0.022 0.002 TYR B 103 PHE 0.022 0.002 PHE A 497 TRP 0.013 0.002 TRP A 220 HIS 0.005 0.001 HIS B 367 Details of bonding type rmsd covalent geometry : bond 0.01174 ( 7707) covalent geometry : angle 1.14298 (10497) SS BOND : bond 0.15911 ( 1) SS BOND : angle 5.72543 ( 2) hydrogen bonds : bond 0.21417 ( 334) hydrogen bonds : angle 7.35577 ( 972) link_BETA1-4 : bond 0.00722 ( 4) link_BETA1-4 : angle 4.44714 ( 12) link_NAG-ASN : bond 0.00789 ( 4) link_NAG-ASN : angle 5.23570 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 150 time to evaluate : 0.319 Fit side-chains REVERT: B 51 THR cc_start: 0.8410 (m) cc_final: 0.8194 (m) REVERT: B 195 ARG cc_start: 0.7498 (mtp180) cc_final: 0.7056 (mtm180) REVERT: B 365 MET cc_start: 0.8597 (mtt) cc_final: 0.8290 (mtt) REVERT: B 401 SER cc_start: 0.7524 (OUTLIER) cc_final: 0.7022 (p) REVERT: B 438 PHE cc_start: 0.7291 (t80) cc_final: 0.7078 (t80) REVERT: B 496 CYS cc_start: 0.7983 (m) cc_final: 0.7733 (m) REVERT: B 500 MET cc_start: 0.8380 (mtt) cc_final: 0.8051 (mtm) outliers start: 12 outliers final: 5 residues processed: 155 average time/residue: 0.0849 time to fit residues: 17.5845 Evaluate side-chains 115 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 109 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 164 CYS Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 401 SER Chi-restraints excluded: chain B residue 505 GLN 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: 67.5834 > 50: distance: 12 - 18: 3.270 distance: 46 - 64: 31.582 distance: 51 - 72: 37.309 distance: 54 - 57: 19.378 distance: 55 - 83: 24.483 distance: 57 - 58: 24.176 distance: 58 - 59: 7.444 distance: 58 - 61: 18.627 distance: 59 - 60: 6.015 distance: 59 - 64: 10.385 distance: 60 - 87: 40.767 distance: 61 - 62: 45.377 distance: 61 - 63: 15.053 distance: 64 - 65: 19.366 distance: 65 - 66: 6.425 distance: 65 - 68: 9.012 distance: 66 - 67: 11.068 distance: 66 - 72: 12.063 distance: 67 - 95: 55.599 distance: 68 - 69: 4.718 distance: 69 - 70: 23.860 distance: 69 - 71: 4.790 distance: 72 - 73: 28.676 distance: 73 - 74: 30.233 distance: 73 - 76: 23.880 distance: 74 - 75: 27.761 distance: 74 - 83: 33.561 distance: 75 - 107: 25.983 distance: 76 - 77: 34.710 distance: 77 - 78: 17.842 distance: 77 - 79: 5.583 distance: 78 - 80: 5.859 distance: 79 - 81: 19.071 distance: 81 - 82: 9.493 distance: 83 - 84: 25.978 distance: 84 - 85: 12.278 distance: 85 - 86: 26.552 distance: 85 - 87: 7.618 distance: 86 - 117: 38.773 distance: 88 - 89: 39.520 distance: 89 - 90: 10.744 distance: 89 - 95: 19.734 distance: 92 - 93: 3.467 distance: 92 - 94: 56.646 distance: 95 - 96: 4.406 distance: 96 - 99: 39.547 distance: 97 - 98: 24.051 distance: 97 - 107: 10.704 distance: 99 - 100: 16.882 distance: 100 - 101: 5.896 distance: 100 - 102: 7.233 distance: 101 - 103: 10.840 distance: 102 - 104: 5.881 distance: 103 - 105: 18.579 distance: 104 - 105: 15.297 distance: 105 - 106: 21.176 distance: 107 - 108: 42.383 distance: 108 - 109: 36.221 distance: 108 - 111: 22.651 distance: 109 - 117: 56.637 distance: 112 - 113: 22.852 distance: 112 - 114: 22.522 distance: 113 - 115: 40.057 distance: 114 - 116: 45.775 distance: 115 - 116: 26.455 distance: 117 - 118: 7.261 distance: 118 - 119: 40.979 distance: 118 - 121: 17.582 distance: 119 - 120: 12.767 distance: 119 - 125: 27.075 distance: 121 - 122: 37.208 distance: 122 - 123: 6.808 distance: 122 - 124: 48.267 distance: 126 - 127: 3.379 distance: 127 - 128: 32.065 distance: 127 - 129: 4.655 distance: 129 - 130: 22.914 distance: 130 - 131: 10.682 distance: 130 - 133: 27.097 distance: 131 - 132: 8.977 distance: 131 - 136: 25.891 distance: 133 - 134: 18.556 distance: 133 - 135: 7.769