Starting phenix.real_space_refine on Sat Aug 23 02:31:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zdk_14652/08_2025/7zdk_14652.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zdk_14652/08_2025/7zdk_14652.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7zdk_14652/08_2025/7zdk_14652.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zdk_14652/08_2025/7zdk_14652.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7zdk_14652/08_2025/7zdk_14652.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zdk_14652/08_2025/7zdk_14652.map" } resolution = 3.01 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= 0.007 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 6 5.49 5 Mg 2 5.21 5 S 30 5.16 5 C 5804 2.51 5 N 1600 2.21 5 O 1647 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 88 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: 9089 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 4433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4433 Classifications: {'peptide': 573} Link IDs: {'PTRANS': 18, 'TRANS': 554} Chain: "D" Number of atoms: 4592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 588, 4592 Classifications: {'peptide': 588} Link IDs: {'PTRANS': 27, 'TRANS': 560} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.14, per 1000 atoms: 0.24 Number of scatterers: 9089 At special positions: 0 Unit cell: (117.18, 80.352, 114.669, 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 30 16.00 P 6 15.00 Mg 2 11.99 O 1647 8.00 N 1600 7.00 C 5804 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: 0.78 Conformation dependent library (CDL) restraints added in 243.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2148 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 6 sheets defined 68.3% alpha, 9.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'C' and resid 4 through 9 Processing helix chain 'C' and resid 14 through 50 Processing helix chain 'C' and resid 59 through 104 removed outlier: 3.556A pdb=" N ARG C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR C 74 " --> pdb=" O ALA C 70 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N HIS C 94 " --> pdb=" O ARG C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 132 removed outlier: 3.513A pdb=" N LEU C 120 " --> pdb=" O GLN C 116 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ASN C 121 " --> pdb=" O GLY C 117 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG C 122 " --> pdb=" O GLU C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 137 Processing helix chain 'C' and resid 137 through 157 removed outlier: 3.849A pdb=" N PHE C 157 " --> pdb=" O ILE C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 176 removed outlier: 3.612A pdb=" N THR C 165 " --> pdb=" O THR C 161 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE C 169 " --> pdb=" O THR C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 185 Processing helix chain 'C' and resid 185 through 209 Processing helix chain 'C' and resid 209 through 216 Processing helix chain 'C' and resid 218 through 269 removed outlier: 3.586A pdb=" N LEU C 243 " --> pdb=" O ARG C 239 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER C 267 " --> pdb=" O LEU C 263 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY C 268 " --> pdb=" O TRP C 264 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY C 269 " --> pdb=" O MET C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 290 removed outlier: 4.347A pdb=" N ALA C 281 " --> pdb=" O GLY C 277 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU C 282 " --> pdb=" O ALA C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 293 No H-bonds generated for 'chain 'C' and resid 291 through 293' Processing helix chain 'C' and resid 294 through 319 removed outlier: 4.335A pdb=" N GLY C 299 " --> pdb=" O ALA C 295 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA C 300 " --> pdb=" O PRO C 296 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N PHE C 301 " --> pdb=" O VAL C 297 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N GLN C 302 " --> pdb=" O THR C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 387 removed outlier: 3.665A pdb=" N GLN C 385 " --> pdb=" O THR C 381 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU C 386 " --> pdb=" O LEU C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 407 No H-bonds generated for 'chain 'C' and resid 405 through 407' Processing helix chain 'C' and resid 408 through 415 Processing helix chain 'C' and resid 429 through 436 removed outlier: 3.815A pdb=" N LEU C 436 " --> pdb=" O ASP C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 442 through 453 Processing helix chain 'C' and resid 456 through 460 Processing helix chain 'C' and resid 462 through 466 removed outlier: 3.622A pdb=" N ASN C 465 " --> pdb=" O ALA C 462 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER C 466 " --> pdb=" O GLY C 463 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 462 through 466' Processing helix chain 'C' and resid 476 through 492 removed outlier: 3.675A pdb=" N LEU C 483 " --> pdb=" O GLU C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 506 through 521 removed outlier: 3.675A pdb=" N GLN C 512 " --> pdb=" O THR C 508 " (cutoff:3.500A) Processing helix chain 'C' and resid 555 through 562 Processing helix chain 'C' and resid 564 through 572 Processing helix chain 'D' and resid 2 through 17 removed outlier: 3.556A pdb=" N GLU D 8 " --> pdb=" O SER D 4 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLN D 15 " --> pdb=" O ARG D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 54 removed outlier: 3.584A pdb=" N PHE D 32 " --> pdb=" O ARG D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 61 Processing helix chain 'D' and resid 62 through 110 Processing helix chain 'D' and resid 110 through 115 Processing helix chain 'D' and resid 118 through 127 Processing helix chain 'D' and resid 127 through 132 Processing helix chain 'D' and resid 133 through 139 removed outlier: 3.620A pdb=" N TYR D 137 " --> pdb=" O MET D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 162 removed outlier: 3.670A pdb=" N VAL D 148 " --> pdb=" O MET D 144 " (cutoff:3.500A) Proline residue: D 151 - end of helix Proline residue: D 160 - end of helix Processing helix chain 'D' and resid 162 through 173 removed outlier: 3.605A pdb=" N THR D 172 " --> pdb=" O ILE D 168 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA D 173 " --> pdb=" O LEU D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 203 removed outlier: 3.643A pdb=" N LEU D 178 " --> pdb=" O PRO D 174 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASP D 189 " --> pdb=" O MET D 185 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N LEU D 196 " --> pdb=" O ARG D 192 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N ALA D 197 " --> pdb=" O ARG D 193 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLY D 203 " --> pdb=" O ALA D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 210 Processing helix chain 'D' and resid 211 through 218 Processing helix chain 'D' and resid 220 through 274 removed outlier: 3.784A pdb=" N GLU D 226 " --> pdb=" O GLU D 222 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER D 227 " --> pdb=" O ALA D 223 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU D 241 " --> pdb=" O GLN D 237 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL D 242 " --> pdb=" O ARG D 238 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU D 245 " --> pdb=" O GLU D 241 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU D 248 " --> pdb=" O ARG D 244 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LEU D 253 " --> pdb=" O SER D 249 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLU D 254 " --> pdb=" O SER D 250 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER D 258 " --> pdb=" O GLU D 254 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU D 273 " --> pdb=" O GLY D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 310 removed outlier: 3.532A pdb=" N GLY D 290 " --> pdb=" O THR D 286 " (cutoff:3.500A) Proline residue: D 298 - end of helix removed outlier: 4.098A pdb=" N PHE D 301 " --> pdb=" O ALA D 297 " (cutoff:3.500A) Proline residue: D 303 - end of helix removed outlier: 3.538A pdb=" N THR D 309 " --> pdb=" O ARG D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 330 removed outlier: 3.795A pdb=" N ALA D 315 " --> pdb=" O TYR D 311 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA D 317 " --> pdb=" O ALA D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 388 through 397 Processing helix chain 'D' and resid 417 through 422 Processing helix chain 'D' and resid 438 through 444 Processing helix chain 'D' and resid 451 through 462 Processing helix chain 'D' and resid 473 through 477 removed outlier: 3.598A pdb=" N THR D 477 " --> pdb=" O GLY D 474 " (cutoff:3.500A) Processing helix chain 'D' and resid 487 through 501 Processing helix chain 'D' and resid 517 through 532 Processing helix chain 'D' and resid 566 through 573 removed outlier: 3.739A pdb=" N VAL D 572 " --> pdb=" O ALA D 568 " (cutoff:3.500A) Processing helix chain 'D' and resid 575 through 583 Processing sheet with id=AA1, first strand: chain 'C' and resid 362 through 363 Processing sheet with id=AA2, first strand: chain 'C' and resid 344 through 347 removed outlier: 6.709A pdb=" N VAL C 344 " --> pdb=" O LYS C 357 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LYS C 357 " --> pdb=" O VAL C 344 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N PHE C 346 " --> pdb=" O ALA C 355 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 416 through 419 removed outlier: 6.455A pdb=" N VAL C 496 " --> pdb=" O LEU C 527 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N VAL C 529 " --> pdb=" O VAL C 496 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N LEU C 498 " --> pdb=" O VAL C 529 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU C 552 " --> pdb=" O VAL C 544 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ASP C 546 " --> pdb=" O ILE C 550 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N ILE C 550 " --> pdb=" O ASP C 546 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 364 through 373 removed outlier: 6.477A pdb=" N ILE D 357 " --> pdb=" O LEU D 365 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N GLY D 367 " --> pdb=" O LEU D 355 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N LEU D 355 " --> pdb=" O GLY D 367 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N LEU D 369 " --> pdb=" O GLU D 353 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLU D 353 " --> pdb=" O LEU D 369 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N PHE D 371 " --> pdb=" O GLU D 351 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N GLU D 351 " --> pdb=" O PHE D 371 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N SER D 401 " --> pdb=" O THR D 358 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 364 through 373 removed outlier: 6.477A pdb=" N ILE D 357 " --> pdb=" O LEU D 365 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N GLY D 367 " --> pdb=" O LEU D 355 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N LEU D 355 " --> pdb=" O GLY D 367 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N LEU D 369 " --> pdb=" O GLU D 353 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLU D 353 " --> pdb=" O LEU D 369 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N PHE D 371 " --> pdb=" O GLU D 351 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N GLU D 351 " --> pdb=" O PHE D 371 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 425 through 428 removed outlier: 6.889A pdb=" N SER D 426 " --> pdb=" O LEU D 508 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N ASP D 510 " --> pdb=" O SER D 426 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N VAL D 428 " --> pdb=" O ASP D 510 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LEU D 507 " --> pdb=" O LEU D 538 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N VAL D 540 " --> pdb=" O LEU D 507 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N LEU D 509 " --> pdb=" O VAL D 540 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ARG D 378 " --> pdb=" O VAL D 552 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N TRP D 554 " --> pdb=" O ARG D 378 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N VAL D 380 " --> pdb=" O TRP D 554 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N MET D 556 " --> pdb=" O VAL D 380 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL D 382 " --> pdb=" O MET D 556 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE D 553 " --> pdb=" O GLN D 564 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLN D 564 " --> pdb=" O ILE D 553 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N VAL D 555 " --> pdb=" O ILE D 562 " (cutoff:3.500A) 570 hydrogen bonds defined for protein. 1677 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: 1.15 Time building geometry restraints manager: 0.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2482 1.33 - 1.45: 1557 1.45 - 1.57: 5163 1.57 - 1.69: 10 1.69 - 1.81: 57 Bond restraints: 9269 Sorted by residual: bond pdb=" N3B ANP D 602 " pdb=" PG ANP D 602 " ideal model delta sigma weight residual 1.795 1.626 0.169 2.00e-02 2.50e+03 7.12e+01 bond pdb=" N3B ANP C 602 " pdb=" PG ANP C 602 " ideal model delta sigma weight residual 1.795 1.628 0.167 2.00e-02 2.50e+03 6.99e+01 bond pdb=" O3A ANP C 602 " pdb=" PB ANP C 602 " ideal model delta sigma weight residual 1.700 1.596 0.104 2.00e-02 2.50e+03 2.70e+01 bond pdb=" O3A ANP D 602 " pdb=" PB ANP D 602 " ideal model delta sigma weight residual 1.700 1.602 0.098 2.00e-02 2.50e+03 2.41e+01 bond pdb=" N GLU C 500 " pdb=" CA GLU C 500 " ideal model delta sigma weight residual 1.458 1.488 -0.030 7.40e-03 1.83e+04 1.69e+01 ... (remaining 9264 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 12316 2.27 - 4.55: 242 4.55 - 6.82: 38 6.82 - 9.09: 7 9.09 - 11.36: 1 Bond angle restraints: 12604 Sorted by residual: angle pdb=" N GLU C 515 " pdb=" CA GLU C 515 " pdb=" C GLU C 515 " ideal model delta sigma weight residual 111.36 105.54 5.82 1.09e+00 8.42e-01 2.86e+01 angle pdb=" C GLU C 500 " pdb=" CA GLU C 500 " pdb=" CB GLU C 500 " ideal model delta sigma weight residual 111.00 114.48 -3.48 8.70e-01 1.32e+00 1.60e+01 angle pdb=" N TYR C 11 " pdb=" CA TYR C 11 " pdb=" C TYR C 11 " ideal model delta sigma weight residual 112.89 108.04 4.85 1.24e+00 6.50e-01 1.53e+01 angle pdb=" N LYS C 12 " pdb=" CA LYS C 12 " pdb=" C LYS C 12 " ideal model delta sigma weight residual 111.28 107.08 4.20 1.09e+00 8.42e-01 1.48e+01 angle pdb=" N ARG D 11 " pdb=" CA ARG D 11 " pdb=" C ARG D 11 " ideal model delta sigma weight residual 111.82 107.40 4.42 1.16e+00 7.43e-01 1.45e+01 ... (remaining 12599 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.57: 5037 19.57 - 39.13: 412 39.13 - 58.70: 71 58.70 - 78.27: 26 78.27 - 97.83: 18 Dihedral angle restraints: 5564 sinusoidal: 2233 harmonic: 3331 Sorted by residual: dihedral pdb=" CA LEU D 209 " pdb=" C LEU D 209 " pdb=" N ARG D 210 " pdb=" CA ARG D 210 " ideal model delta harmonic sigma weight residual 180.00 154.97 25.03 0 5.00e+00 4.00e-02 2.51e+01 dihedral pdb=" O2' ANP D 602 " pdb=" C2' ANP D 602 " pdb=" C3' ANP D 602 " pdb=" O3' ANP D 602 " ideal model delta sinusoidal sigma weight residual 47.90 -49.93 97.83 1 3.00e+01 1.11e-03 1.21e+01 dihedral pdb=" C1' ANP D 602 " pdb=" C2' ANP D 602 " pdb=" C3' ANP D 602 " pdb=" O3' ANP D 602 " ideal model delta sinusoidal sigma weight residual 164.59 69.72 94.87 1 3.00e+01 1.11e-03 1.16e+01 ... (remaining 5561 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 1348 0.089 - 0.179: 103 0.179 - 0.268: 8 0.268 - 0.357: 0 0.357 - 0.446: 2 Chirality restraints: 1461 Sorted by residual: chirality pdb=" C3' ANP C 602 " pdb=" C2' ANP C 602 " pdb=" C4' ANP C 602 " pdb=" O3' ANP C 602 " both_signs ideal model delta sigma weight residual False -2.36 -2.80 0.45 2.00e-01 2.50e+01 4.98e+00 chirality pdb=" C3' ANP D 602 " pdb=" C2' ANP D 602 " pdb=" C4' ANP D 602 " pdb=" O3' ANP D 602 " both_signs ideal model delta sigma weight residual False -2.36 -2.80 0.44 2.00e-01 2.50e+01 4.81e+00 chirality pdb=" CA VAL D 428 " pdb=" N VAL D 428 " pdb=" C VAL D 428 " pdb=" CB VAL D 428 " both_signs ideal model delta sigma weight residual False 2.44 2.70 -0.26 2.00e-01 2.50e+01 1.71e+00 ... (remaining 1458 not shown) Planarity restraints: 1604 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL D 428 " 0.012 2.00e-02 2.50e+03 2.55e-02 6.51e+00 pdb=" C VAL D 428 " -0.044 2.00e-02 2.50e+03 pdb=" O VAL D 428 " 0.017 2.00e-02 2.50e+03 pdb=" N GLY D 429 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 497 " 0.008 2.00e-02 2.50e+03 1.70e-02 2.89e+00 pdb=" C LEU C 497 " -0.029 2.00e-02 2.50e+03 pdb=" O LEU C 497 " 0.011 2.00e-02 2.50e+03 pdb=" N LEU C 498 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU D 511 " 0.027 5.00e-02 4.00e+02 4.00e-02 2.56e+00 pdb=" N PRO D 512 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO D 512 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 512 " 0.022 5.00e-02 4.00e+02 ... (remaining 1601 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1431 2.75 - 3.29: 8840 3.29 - 3.83: 14871 3.83 - 4.36: 19151 4.36 - 4.90: 32283 Nonbonded interactions: 76576 Sorted by model distance: nonbonded pdb=" OG1 THR D 438 " pdb=" OD1 ASP D 441 " model vdw 2.219 3.040 nonbonded pdb="MG MG D 601 " pdb=" O1G ANP D 602 " model vdw 2.220 2.170 nonbonded pdb="MG MG C 601 " pdb=" O1B ANP C 602 " model vdw 2.222 2.170 nonbonded pdb=" OG SER C 380 " pdb="MG MG C 601 " model vdw 2.223 2.170 nonbonded pdb="MG MG C 601 " pdb=" O2G ANP C 602 " model vdw 2.224 2.170 ... (remaining 76571 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.570 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: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.210 Find NCS groups from input model: 0.060 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 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 : 0.007 0.169 9269 Z= 0.346 Angle : 0.783 11.363 12604 Z= 0.460 Chirality : 0.051 0.446 1461 Planarity : 0.004 0.040 1604 Dihedral : 16.142 97.831 3416 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % 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: -1.50 (0.23), residues: 1157 helix: -1.19 (0.18), residues: 723 sheet: 0.39 (0.63), residues: 62 loop : -0.40 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 96 TYR 0.012 0.002 TYR D 88 PHE 0.014 0.002 PHE D 467 TRP 0.013 0.002 TRP D 81 HIS 0.004 0.001 HIS C 14 Details of bonding type rmsd covalent geometry : bond 0.00667 ( 9269) covalent geometry : angle 0.78259 (12604) hydrogen bonds : bond 0.25314 ( 569) hydrogen bonds : angle 8.49162 ( 1677) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.348 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.1357 time to fit residues: 19.4683 Evaluate side-chains 104 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 108 optimal weight: 0.0670 chunk 49 optimal weight: 0.4980 chunk 97 optimal weight: 0.4980 chunk 113 optimal weight: 0.9990 chunk 53 optimal weight: 0.0030 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 4.9990 overall best weight: 0.3528 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 225 GLN D 2 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.114251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.092050 restraints weight = 11094.008| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 1.51 r_work: 0.2828 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2693 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.1325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9269 Z= 0.139 Angle : 0.581 6.788 12604 Z= 0.297 Chirality : 0.040 0.151 1461 Planarity : 0.004 0.042 1604 Dihedral : 10.058 74.178 1329 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.95 % Allowed : 4.98 % Favored : 94.06 % 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: 0.49 (0.24), residues: 1157 helix: 0.77 (0.19), residues: 721 sheet: 0.44 (0.65), residues: 61 loop : -0.39 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 493 TYR 0.012 0.001 TYR D 88 PHE 0.016 0.001 PHE C 164 TRP 0.020 0.001 TRP D 427 HIS 0.003 0.001 HIS D 93 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 9269) covalent geometry : angle 0.58142 (12604) hydrogen bonds : bond 0.05948 ( 569) hydrogen bonds : angle 4.63477 ( 1677) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 120 time to evaluate : 0.242 Fit side-chains REVERT: C 515 GLU cc_start: 0.7805 (tm-30) cc_final: 0.7423 (tm-30) REVERT: D 15 GLN cc_start: 0.8401 (mt0) cc_final: 0.7907 (tp-100) REVERT: D 108 GLN cc_start: 0.8215 (tt0) cc_final: 0.7964 (mt0) REVERT: D 154 ILE cc_start: 0.9084 (OUTLIER) cc_final: 0.8564 (mt) REVERT: D 207 ASP cc_start: 0.8180 (t0) cc_final: 0.7920 (t0) REVERT: D 240 MET cc_start: 0.8742 (mmm) cc_final: 0.8329 (mmm) REVERT: D 277 ASP cc_start: 0.7605 (t0) cc_final: 0.7318 (t0) outliers start: 9 outliers final: 5 residues processed: 126 average time/residue: 0.1037 time to fit residues: 16.8621 Evaluate side-chains 108 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 102 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 360 SER Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 233 GLU Chi-restraints excluded: chain D residue 475 VAL Chi-restraints excluded: chain D residue 487 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 37 optimal weight: 2.9990 chunk 10 optimal weight: 0.4980 chunk 57 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 chunk 60 optimal weight: 1.9990 chunk 2 optimal weight: 0.0980 chunk 30 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 42 optimal weight: 4.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 303 HIS C 306 GLN C 474 GLN C 541 GLN C 553 GLN D 143 GLN D 482 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.114574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.092532 restraints weight = 11013.745| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 1.50 r_work: 0.2859 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2722 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9269 Z= 0.130 Angle : 0.525 6.524 12604 Z= 0.264 Chirality : 0.039 0.153 1461 Planarity : 0.004 0.042 1604 Dihedral : 7.845 67.369 1329 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.06 % Allowed : 8.91 % Favored : 90.03 % 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: 1.31 (0.25), residues: 1157 helix: 1.57 (0.19), residues: 718 sheet: 0.31 (0.66), residues: 58 loop : -0.31 (0.32), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 139 TYR 0.016 0.001 TYR D 88 PHE 0.013 0.001 PHE D 467 TRP 0.020 0.001 TRP D 81 HIS 0.003 0.001 HIS C 424 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 9269) covalent geometry : angle 0.52508 (12604) hydrogen bonds : bond 0.05162 ( 569) hydrogen bonds : angle 4.18689 ( 1677) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 112 time to evaluate : 0.246 Fit side-chains REVERT: C 183 ARG cc_start: 0.8017 (ttm110) cc_final: 0.7750 (ttm170) REVERT: C 515 GLU cc_start: 0.7840 (tm-30) cc_final: 0.7444 (tm-30) REVERT: D 15 GLN cc_start: 0.8475 (mt0) cc_final: 0.7968 (tp-100) REVERT: D 154 ILE cc_start: 0.9067 (OUTLIER) cc_final: 0.8666 (mt) REVERT: D 167 LEU cc_start: 0.8899 (tp) cc_final: 0.8593 (tp) REVERT: D 207 ASP cc_start: 0.8205 (t0) cc_final: 0.7875 (t0) REVERT: D 240 MET cc_start: 0.8802 (mmm) cc_final: 0.8428 (mmm) REVERT: D 277 ASP cc_start: 0.7641 (t0) cc_final: 0.7269 (t0) outliers start: 10 outliers final: 6 residues processed: 118 average time/residue: 0.1091 time to fit residues: 16.8002 Evaluate side-chains 111 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 104 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 360 SER Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 233 GLU Chi-restraints excluded: chain D residue 475 VAL Chi-restraints excluded: chain D residue 487 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 15 optimal weight: 1.9990 chunk 6 optimal weight: 0.3980 chunk 1 optimal weight: 0.0870 chunk 111 optimal weight: 0.6980 chunk 113 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 94 optimal weight: 0.0670 chunk 16 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 306 GLN D 542 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.116036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.093833 restraints weight = 11155.083| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 1.51 r_work: 0.2879 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9269 Z= 0.116 Angle : 0.489 6.958 12604 Z= 0.247 Chirality : 0.038 0.147 1461 Planarity : 0.003 0.043 1604 Dihedral : 6.528 62.820 1329 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.59 % Allowed : 9.23 % Favored : 89.18 % 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: 1.71 (0.25), residues: 1157 helix: 1.94 (0.19), residues: 723 sheet: 0.25 (0.67), residues: 58 loop : -0.26 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 139 TYR 0.016 0.001 TYR D 88 PHE 0.012 0.001 PHE D 467 TRP 0.018 0.001 TRP D 81 HIS 0.003 0.001 HIS D 542 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 9269) covalent geometry : angle 0.48882 (12604) hydrogen bonds : bond 0.04634 ( 569) hydrogen bonds : angle 4.00518 ( 1677) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 113 time to evaluate : 0.242 Fit side-chains REVERT: C 183 ARG cc_start: 0.7991 (ttm110) cc_final: 0.7717 (ttm170) REVERT: C 515 GLU cc_start: 0.7889 (tm-30) cc_final: 0.7449 (tm-30) REVERT: D 1 MET cc_start: 0.5668 (ptt) cc_final: 0.5261 (tpt) REVERT: D 11 ARG cc_start: 0.8220 (OUTLIER) cc_final: 0.7806 (ttt180) REVERT: D 15 GLN cc_start: 0.8464 (mt0) cc_final: 0.7950 (tp-100) REVERT: D 108 GLN cc_start: 0.8171 (tt0) cc_final: 0.7954 (mt0) REVERT: D 148 VAL cc_start: 0.9056 (p) cc_final: 0.8806 (m) REVERT: D 216 ARG cc_start: 0.8438 (ttp-170) cc_final: 0.8218 (ptt90) REVERT: D 240 MET cc_start: 0.8807 (mmm) cc_final: 0.8412 (mmm) outliers start: 15 outliers final: 11 residues processed: 124 average time/residue: 0.0967 time to fit residues: 15.7229 Evaluate side-chains 118 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 106 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 360 SER Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain D residue 11 ARG Chi-restraints excluded: chain D residue 202 SER Chi-restraints excluded: chain D residue 212 MET Chi-restraints excluded: chain D residue 233 GLU Chi-restraints excluded: chain D residue 351 GLU Chi-restraints excluded: chain D residue 475 VAL Chi-restraints excluded: chain D residue 487 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 81 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 chunk 53 optimal weight: 0.0670 chunk 58 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 306 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.115419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.093128 restraints weight = 11080.579| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 1.51 r_work: 0.2856 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9269 Z= 0.128 Angle : 0.496 6.322 12604 Z= 0.251 Chirality : 0.039 0.148 1461 Planarity : 0.004 0.042 1604 Dihedral : 6.278 63.474 1329 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.48 % Allowed : 9.97 % Favored : 88.55 % 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: 1.85 (0.25), residues: 1157 helix: 2.07 (0.19), residues: 723 sheet: 0.18 (0.67), residues: 58 loop : -0.24 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 522 TYR 0.017 0.001 TYR D 88 PHE 0.013 0.001 PHE D 467 TRP 0.017 0.001 TRP D 81 HIS 0.003 0.001 HIS C 85 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 9269) covalent geometry : angle 0.49572 (12604) hydrogen bonds : bond 0.04668 ( 569) hydrogen bonds : angle 3.94407 ( 1677) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 106 time to evaluate : 0.340 Fit side-chains REVERT: C 183 ARG cc_start: 0.7977 (ttm110) cc_final: 0.7691 (ttm170) REVERT: C 515 GLU cc_start: 0.7871 (tm-30) cc_final: 0.7450 (tm-30) REVERT: D 1 MET cc_start: 0.5542 (ptt) cc_final: 0.5199 (tpt) REVERT: D 11 ARG cc_start: 0.8156 (OUTLIER) cc_final: 0.7756 (ttt180) REVERT: D 15 GLN cc_start: 0.8461 (mt0) cc_final: 0.7946 (tp-100) REVERT: D 108 GLN cc_start: 0.8188 (tt0) cc_final: 0.7953 (mt0) REVERT: D 216 ARG cc_start: 0.8447 (ttp-170) cc_final: 0.8192 (ptt90) REVERT: D 240 MET cc_start: 0.8837 (mmm) cc_final: 0.8440 (mmm) REVERT: D 526 GLU cc_start: 0.8331 (tt0) cc_final: 0.7912 (mt-10) outliers start: 14 outliers final: 11 residues processed: 114 average time/residue: 0.1080 time to fit residues: 16.0299 Evaluate side-chains 114 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 360 SER Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain D residue 11 ARG Chi-restraints excluded: chain D residue 202 SER Chi-restraints excluded: chain D residue 212 MET Chi-restraints excluded: chain D residue 351 GLU Chi-restraints excluded: chain D residue 475 VAL Chi-restraints excluded: chain D residue 487 SER Chi-restraints excluded: chain D residue 581 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 19 optimal weight: 1.9990 chunk 38 optimal weight: 0.0770 chunk 90 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 96 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 306 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.115129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.092810 restraints weight = 11065.712| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 1.50 r_work: 0.2845 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9269 Z= 0.129 Angle : 0.492 6.716 12604 Z= 0.249 Chirality : 0.039 0.150 1461 Planarity : 0.004 0.042 1604 Dihedral : 6.155 63.830 1329 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.70 % Allowed : 10.29 % Favored : 88.02 % 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: 1.94 (0.25), residues: 1157 helix: 2.16 (0.19), residues: 723 sheet: 0.15 (0.65), residues: 59 loop : -0.23 (0.33), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 522 TYR 0.018 0.001 TYR D 88 PHE 0.013 0.001 PHE D 467 TRP 0.020 0.001 TRP D 427 HIS 0.003 0.001 HIS C 85 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 9269) covalent geometry : angle 0.49165 (12604) hydrogen bonds : bond 0.04622 ( 569) hydrogen bonds : angle 3.91476 ( 1677) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 104 time to evaluate : 0.252 Fit side-chains REVERT: C 183 ARG cc_start: 0.7989 (ttm110) cc_final: 0.7697 (ttm170) REVERT: C 515 GLU cc_start: 0.7924 (tm-30) cc_final: 0.7466 (tm-30) REVERT: D 1 MET cc_start: 0.5555 (ptt) cc_final: 0.5200 (tpt) REVERT: D 11 ARG cc_start: 0.8178 (OUTLIER) cc_final: 0.7775 (ttt180) REVERT: D 15 GLN cc_start: 0.8475 (mt0) cc_final: 0.7966 (tp-100) REVERT: D 216 ARG cc_start: 0.8457 (ttp-170) cc_final: 0.8188 (ptt90) REVERT: D 526 GLU cc_start: 0.8293 (tt0) cc_final: 0.7922 (mt-10) outliers start: 16 outliers final: 12 residues processed: 114 average time/residue: 0.1028 time to fit residues: 15.2818 Evaluate side-chains 115 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 102 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 360 SER Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain D residue 11 ARG Chi-restraints excluded: chain D residue 202 SER Chi-restraints excluded: chain D residue 212 MET Chi-restraints excluded: chain D residue 233 GLU Chi-restraints excluded: chain D residue 351 GLU Chi-restraints excluded: chain D residue 475 VAL Chi-restraints excluded: chain D residue 487 SER Chi-restraints excluded: chain D residue 546 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 4 optimal weight: 0.8980 chunk 48 optimal weight: 0.5980 chunk 54 optimal weight: 4.9990 chunk 67 optimal weight: 0.9980 chunk 111 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 306 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.114854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.092410 restraints weight = 11174.205| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 1.51 r_work: 0.2835 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2696 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9269 Z= 0.140 Angle : 0.502 6.572 12604 Z= 0.255 Chirality : 0.039 0.149 1461 Planarity : 0.004 0.042 1604 Dihedral : 6.126 64.133 1329 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.70 % Allowed : 10.71 % Favored : 87.59 % 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: 1.97 (0.25), residues: 1157 helix: 2.19 (0.19), residues: 723 sheet: 0.14 (0.64), residues: 59 loop : -0.23 (0.33), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 522 TYR 0.018 0.001 TYR D 88 PHE 0.014 0.001 PHE D 467 TRP 0.016 0.001 TRP D 81 HIS 0.003 0.001 HIS C 85 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 9269) covalent geometry : angle 0.50242 (12604) hydrogen bonds : bond 0.04684 ( 569) hydrogen bonds : angle 3.92062 ( 1677) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 102 time to evaluate : 0.282 Fit side-chains REVERT: C 183 ARG cc_start: 0.7994 (ttm110) cc_final: 0.7701 (ttm170) REVERT: D 15 GLN cc_start: 0.8493 (mt0) cc_final: 0.7973 (tp-100) REVERT: D 216 ARG cc_start: 0.8483 (ttp-170) cc_final: 0.8196 (ptt90) REVERT: D 526 GLU cc_start: 0.8288 (tt0) cc_final: 0.7901 (mt-10) outliers start: 16 outliers final: 15 residues processed: 113 average time/residue: 0.1000 time to fit residues: 14.8026 Evaluate side-chains 116 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 101 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 360 SER Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 521 MET Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 202 SER Chi-restraints excluded: chain D residue 212 MET Chi-restraints excluded: chain D residue 233 GLU Chi-restraints excluded: chain D residue 351 GLU Chi-restraints excluded: chain D residue 475 VAL Chi-restraints excluded: chain D residue 487 SER Chi-restraints excluded: chain D residue 546 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- 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: 63.0336 > 50: distance: 32 - 36: 4.058 distance: 36 - 37: 12.226 distance: 37 - 38: 18.061 distance: 37 - 40: 6.496 distance: 38 - 39: 27.380 distance: 38 - 45: 28.216 distance: 40 - 41: 12.046 distance: 41 - 42: 3.914 distance: 42 - 43: 4.952 distance: 42 - 44: 6.060 distance: 45 - 46: 5.257 distance: 46 - 47: 26.621 distance: 46 - 49: 9.542 distance: 47 - 48: 24.140 distance: 47 - 54: 14.104 distance: 49 - 50: 41.948 distance: 50 - 51: 15.848 distance: 51 - 52: 19.347 distance: 52 - 53: 28.716 distance: 54 - 55: 13.938 distance: 54 - 60: 24.967 distance: 55 - 56: 24.651 distance: 55 - 58: 30.152 distance: 56 - 57: 13.624 distance: 56 - 61: 33.431 distance: 58 - 59: 12.930 distance: 59 - 60: 15.105 distance: 61 - 62: 17.933 distance: 62 - 63: 9.953 distance: 62 - 65: 4.981 distance: 63 - 64: 19.083 distance: 63 - 70: 12.201 distance: 65 - 66: 19.546 distance: 66 - 67: 12.514 distance: 67 - 68: 23.909 distance: 67 - 69: 30.823 distance: 70 - 71: 9.081 distance: 71 - 74: 16.087 distance: 72 - 73: 29.173 distance: 72 - 77: 12.669 distance: 74 - 75: 27.355 distance: 74 - 76: 63.034 distance: 77 - 78: 22.816 distance: 78 - 79: 24.579 distance: 78 - 81: 21.588 distance: 79 - 80: 5.642 distance: 79 - 84: 17.841 distance: 81 - 82: 5.386 distance: 81 - 83: 10.506 distance: 84 - 85: 8.153 distance: 85 - 86: 12.761 distance: 85 - 88: 7.536 distance: 86 - 87: 23.953 distance: 86 - 95: 6.255 distance: 88 - 89: 8.204 distance: 89 - 90: 7.522 distance: 89 - 91: 7.804 distance: 90 - 92: 10.363 distance: 91 - 93: 7.443 distance: 92 - 94: 7.325 distance: 93 - 94: 9.760 distance: 95 - 96: 6.237 distance: 95 - 101: 7.091 distance: 96 - 97: 10.110 distance: 96 - 99: 9.937 distance: 97 - 98: 8.469 distance: 97 - 102: 12.830 distance: 99 - 100: 14.723 distance: 100 - 101: 12.260 distance: 102 - 103: 4.629 distance: 103 - 104: 10.774 distance: 103 - 106: 8.188 distance: 104 - 105: 7.826 distance: 104 - 110: 22.467 distance: 106 - 107: 6.516 distance: 107 - 108: 5.239 distance: 107 - 109: 7.725 distance: 110 - 111: 9.460 distance: 111 - 112: 11.833 distance: 112 - 113: 11.592 distance: 112 - 117: 10.501 distance: 114 - 115: 9.799 distance: 114 - 116: 18.486