Starting phenix.real_space_refine on Thu Jul 2 12:46:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yjo_33876/07_2026/7yjo_33876.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yjo_33876/07_2026/7yjo_33876.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7yjo_33876/07_2026/7yjo_33876.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yjo_33876/07_2026/7yjo_33876.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7yjo_33876/07_2026/7yjo_33876.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yjo_33876/07_2026/7yjo_33876.map" } resolution = 2.8 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 Anisotropic ADP refinement not supported. Converting 22 atoms to isotropic. 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 49 5.16 5 C 5651 2.51 5 N 1482 2.21 5 O 1586 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 82 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8769 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3226 Classifications: {'peptide': 418} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 400} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 3643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3643 Classifications: {'peptide': 467} Link IDs: {'PTRANS': 20, 'TRANS': 446} Chain breaks: 1 Chain: "D" Number of atoms: 1201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1201 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 7, 'TRANS': 138} Chain: "E" Number of atoms: 195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 195 Classifications: {'peptide': 27} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 24} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "C" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 436 Classifications: {'peptide': 48} Link IDs: {'TRANS': 47} Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'peptide': 1} Chain: "D" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'Z1T': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.41, per 1000 atoms: 0.16 Number of scatterers: 8769 At special positions: 0 Unit cell: (88.56, 82.08, 118.8, 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 49 16.00 P 1 15.00 O 1586 8.00 N 1482 7.00 C 5651 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: 0.47 Conformation dependent library (CDL) restraints added in 373.5 milliseconds 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2048 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 7 sheets defined 50.6% alpha, 8.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 65 through 76 removed outlier: 3.673A pdb=" N ASP A 70 " --> pdb=" O GLU A 66 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU A 71 " --> pdb=" O GLN A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 140 removed outlier: 3.732A pdb=" N SER A 134 " --> pdb=" O GLU A 130 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA A 135 " --> pdb=" O SER A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 168 removed outlier: 3.840A pdb=" N LEU A 157 " --> pdb=" O ILE A 153 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR A 161 " --> pdb=" O LEU A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 184 removed outlier: 4.109A pdb=" N PHE A 183 " --> pdb=" O LEU A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 190 Processing helix chain 'A' and resid 203 through 213 Processing helix chain 'A' and resid 224 through 239 Processing helix chain 'A' and resid 263 through 275 removed outlier: 3.704A pdb=" N LYS A 269 " --> pdb=" O ASP A 265 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS A 273 " --> pdb=" O LYS A 269 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR A 274 " --> pdb=" O LEU A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 307 Processing helix chain 'A' and resid 328 through 336 Processing helix chain 'A' and resid 349 through 366 removed outlier: 3.527A pdb=" N ALA A 355 " --> pdb=" O TYR A 351 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE A 357 " --> pdb=" O ALA A 353 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N THR A 358 " --> pdb=" O SER A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 383 removed outlier: 3.769A pdb=" N LYS A 374 " --> pdb=" O LEU A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 431 removed outlier: 3.693A pdb=" N LEU A 417 " --> pdb=" O LYS A 413 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU A 418 " --> pdb=" O ASP A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 473 removed outlier: 3.801A pdb=" N LEU A 471 " --> pdb=" O ALA A 467 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG A 473 " --> pdb=" O GLU A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 479 Processing helix chain 'B' and resid 6 through 31 removed outlier: 3.677A pdb=" N PHE B 29 " --> pdb=" O LEU B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 59 Processing helix chain 'B' and resid 119 through 132 removed outlier: 3.871A pdb=" N ARG B 123 " --> pdb=" O TYR B 119 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU B 126 " --> pdb=" O PRO B 122 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS B 130 " --> pdb=" O GLU B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 160 removed outlier: 3.592A pdb=" N GLU B 152 " --> pdb=" O HIS B 148 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU B 153 " --> pdb=" O ALA B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 176 removed outlier: 3.893A pdb=" N ASN B 174 " --> pdb=" O GLY B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 182 removed outlier: 3.591A pdb=" N LEU B 181 " --> pdb=" O ILE B 177 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE B 182 " --> pdb=" O ILE B 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 177 through 182' Processing helix chain 'B' and resid 195 through 205 removed outlier: 3.579A pdb=" N SER B 205 " --> pdb=" O GLY B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 231 removed outlier: 3.567A pdb=" N GLU B 221 " --> pdb=" O PRO B 217 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG B 222 " --> pdb=" O SER B 218 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU B 230 " --> pdb=" O GLU B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 270 Processing helix chain 'B' and resid 290 through 296 Processing helix chain 'B' and resid 298 through 302 removed outlier: 3.837A pdb=" N VAL B 302 " --> pdb=" O THR B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 334 removed outlier: 3.618A pdb=" N HIS B 332 " --> pdb=" O GLN B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 340 removed outlier: 3.522A pdb=" N ALA B 340 " --> pdb=" O ALA B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 360 removed outlier: 3.637A pdb=" N GLN B 350 " --> pdb=" O PRO B 346 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ILE B 351 " --> pdb=" O SER B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 387 removed outlier: 3.689A pdb=" N LEU B 371 " --> pdb=" O GLY B 367 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG B 375 " --> pdb=" O LEU B 371 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER B 378 " --> pdb=" O ILE B 374 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN B 379 " --> pdb=" O ARG B 375 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LYS B 387 " --> pdb=" O ALA B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 421 removed outlier: 3.760A pdb=" N ALA B 413 " --> pdb=" O ALA B 409 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLN B 421 " --> pdb=" O GLU B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 468 removed outlier: 4.101A pdb=" N ARG B 455 " --> pdb=" O GLU B 451 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS B 462 " --> pdb=" O LYS B 458 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 23 removed outlier: 3.725A pdb=" N MET D 22 " --> pdb=" O GLU D 19 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TYR D 23 " --> pdb=" O TRP D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 45 removed outlier: 3.529A pdb=" N LEU D 34 " --> pdb=" O TYR D 30 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER D 45 " --> pdb=" O VAL D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 70 removed outlier: 3.587A pdb=" N VAL D 55 " --> pdb=" O MET D 51 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE D 61 " --> pdb=" O ASN D 57 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL D 62 " --> pdb=" O LEU D 58 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL D 63 " --> pdb=" O ALA D 59 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR D 64 " --> pdb=" O HIS D 60 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TRP D 70 " --> pdb=" O HIS D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 92 Processing helix chain 'D' and resid 93 through 96 Processing helix chain 'D' and resid 99 through 119 Proline residue: D 109 - end of helix Processing helix chain 'D' and resid 123 through 140 removed outlier: 3.512A pdb=" N PHE D 128 " --> pdb=" O HIS D 124 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N LEU D 129 " --> pdb=" O PRO D 125 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL D 134 " --> pdb=" O ASN D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 146 removed outlier: 6.219A pdb=" N ASN D 144 " --> pdb=" O LYS D 141 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N HIS D 146 " --> pdb=" O PRO D 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 38 through 52 removed outlier: 3.907A pdb=" N GLY E 42 " --> pdb=" O PHE E 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 15 removed outlier: 3.515A pdb=" N TYR C 9 " --> pdb=" O GLN C 5 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 20 removed outlier: 3.550A pdb=" N MET C 19 " --> pdb=" O GLY C 16 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU C 20 " --> pdb=" O LEU C 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 16 through 20' Processing helix chain 'C' and resid 21 through 42 removed outlier: 3.556A pdb=" N PHE C 28 " --> pdb=" O GLU C 24 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LEU C 31 " --> pdb=" O LEU C 27 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE C 38 " --> pdb=" O VAL C 34 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 96 through 97 removed outlier: 3.771A pdb=" N THR A 105 " --> pdb=" O GLU A 97 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR A 104 " --> pdb=" O VAL A 111 " (cutoff:3.500A) removed outlier: 8.521A pdb=" N LEU A 433 " --> pdb=" O ASP A 110 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N VAL A 112 " --> pdb=" O LEU A 433 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 171 through 175 removed outlier: 3.692A pdb=" N ASP A 171 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY A 327 " --> pdb=" O ASP A 171 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP A 281 " --> pdb=" O ALA A 251 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL A 195 " --> pdb=" O TYR A 248 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N VAL A 250 " --> pdb=" O VAL A 195 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N VAL A 197 " --> pdb=" O VAL A 250 " (cutoff:3.500A) removed outlier: 8.686A pdb=" N GLU A 252 " --> pdb=" O VAL A 197 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 390 through 392 Processing sheet with id=AA4, first strand: chain 'B' and resid 78 through 81 removed outlier: 7.984A pdb=" N ALA B 424 " --> pdb=" O ARG B 101 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LEU B 103 " --> pdb=" O ALA B 424 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 163 through 167 removed outlier: 6.505A pdb=" N VAL B 273 " --> pdb=" O VAL B 304 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N MET B 306 " --> pdb=" O VAL B 273 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LEU B 275 " --> pdb=" O MET B 306 " (cutoff:3.500A) removed outlier: 8.530A pdb=" N THR B 308 " --> pdb=" O LEU B 275 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N GLU B 247 " --> pdb=" O ASP B 191 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N ILE B 188 " --> pdb=" O ARG B 210 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N PHE B 212 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N SER B 190 " --> pdb=" O PHE B 212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 249 through 250 Processing sheet with id=AA7, first strand: chain 'B' and resid 403 through 404 removed outlier: 3.921A pdb=" N VAL B 426 " --> pdb=" O ARG B 441 " (cutoff:3.500A) 380 hydrogen bonds defined for protein. 1086 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: 1.08 Time building geometry restraints manager: 0.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1670 1.32 - 1.45: 2208 1.45 - 1.57: 5017 1.57 - 1.69: 1 1.69 - 1.81: 76 Bond restraints: 8972 Sorted by residual: bond pdb=" C14 Z1T D 201 " pdb=" C15 Z1T D 201 " ideal model delta sigma weight residual 1.329 1.523 -0.194 2.00e-02 2.50e+03 9.36e+01 bond pdb=" C HIS B 236 " pdb=" N ARG B 237 " ideal model delta sigma weight residual 1.330 1.201 0.129 1.47e-02 4.63e+03 7.75e+01 bond pdb=" O4P PLS B 601 " pdb=" P PLS B 601 " ideal model delta sigma weight residual 1.712 1.610 0.102 2.00e-02 2.50e+03 2.58e+01 bond pdb=" C CYS D 47 " pdb=" N SER D 48 " ideal model delta sigma weight residual 1.327 1.252 0.075 1.71e-02 3.42e+03 1.93e+01 bond pdb=" C4 PLS B 601 " pdb=" C5 PLS B 601 " ideal model delta sigma weight residual 1.399 1.483 -0.084 2.00e-02 2.50e+03 1.76e+01 ... (remaining 8967 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.78: 11876 2.78 - 5.55: 236 5.55 - 8.33: 19 8.33 - 11.11: 9 11.11 - 13.88: 1 Bond angle restraints: 12141 Sorted by residual: angle pdb=" N PHE B 430 " pdb=" CA PHE B 430 " pdb=" C PHE B 430 " ideal model delta sigma weight residual 109.81 123.69 -13.88 2.21e+00 2.05e-01 3.95e+01 angle pdb=" N HIS D 124 " pdb=" CA HIS D 124 " pdb=" C HIS D 124 " ideal model delta sigma weight residual 109.81 120.75 -10.94 2.21e+00 2.05e-01 2.45e+01 angle pdb=" C HIS D 124 " pdb=" N PRO D 125 " pdb=" CA PRO D 125 " ideal model delta sigma weight residual 119.32 114.33 4.99 1.14e+00 7.69e-01 1.92e+01 angle pdb=" N TYR B 85 " pdb=" CA TYR B 85 " pdb=" C TYR B 85 " ideal model delta sigma weight residual 111.71 117.32 -5.61 1.34e+00 5.57e-01 1.75e+01 angle pdb=" N LEU B 437 " pdb=" CA LEU B 437 " pdb=" C LEU B 437 " ideal model delta sigma weight residual 110.44 115.40 -4.96 1.20e+00 6.94e-01 1.71e+01 ... (remaining 12136 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 4844 17.98 - 35.96: 399 35.96 - 53.94: 77 53.94 - 71.92: 11 71.92 - 89.91: 10 Dihedral angle restraints: 5341 sinusoidal: 2146 harmonic: 3195 Sorted by residual: dihedral pdb=" CA ASP D 79 " pdb=" C ASP D 79 " pdb=" N GLN D 80 " pdb=" CA GLN D 80 " ideal model delta harmonic sigma weight residual 180.00 -152.86 -27.14 0 5.00e+00 4.00e-02 2.95e+01 dihedral pdb=" N PHE B 430 " pdb=" C PHE B 430 " pdb=" CA PHE B 430 " pdb=" CB PHE B 430 " ideal model delta harmonic sigma weight residual 122.80 135.22 -12.42 0 2.50e+00 1.60e-01 2.47e+01 dihedral pdb=" CA VAL A 288 " pdb=" C VAL A 288 " pdb=" N LEU A 289 " pdb=" CA LEU A 289 " ideal model delta harmonic sigma weight residual -180.00 -155.64 -24.36 0 5.00e+00 4.00e-02 2.37e+01 ... (remaining 5338 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.117: 1285 0.117 - 0.233: 66 0.233 - 0.350: 1 0.350 - 0.466: 1 0.466 - 0.583: 1 Chirality restraints: 1354 Sorted by residual: chirality pdb=" CA PHE B 430 " pdb=" N PHE B 430 " pdb=" C PHE B 430 " pdb=" CB PHE B 430 " both_signs ideal model delta sigma weight residual False 2.51 1.93 0.58 2.00e-01 2.50e+01 8.50e+00 chirality pdb=" CA HIS D 124 " pdb=" N HIS D 124 " pdb=" C HIS D 124 " pdb=" CB HIS D 124 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.74e+00 chirality pdb=" CA PHE B 79 " pdb=" N PHE B 79 " pdb=" C PHE B 79 " pdb=" CB PHE B 79 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.82e+00 ... (remaining 1351 not shown) Planarity restraints: 1522 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 380 " -0.017 2.00e-02 2.50e+03 3.57e-02 1.27e+01 pdb=" C LEU A 380 " 0.062 2.00e-02 2.50e+03 pdb=" O LEU A 380 " -0.023 2.00e-02 2.50e+03 pdb=" N TRP A 381 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP D 20 " -0.012 2.00e-02 2.50e+03 2.38e-02 5.66e+00 pdb=" C TRP D 20 " 0.041 2.00e-02 2.50e+03 pdb=" O TRP D 20 " -0.015 2.00e-02 2.50e+03 pdb=" N PHE D 21 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR B 406 " -0.010 2.00e-02 2.50e+03 2.10e-02 4.39e+00 pdb=" C TYR B 406 " 0.036 2.00e-02 2.50e+03 pdb=" O TYR B 406 " -0.013 2.00e-02 2.50e+03 pdb=" N ASN B 407 " -0.012 2.00e-02 2.50e+03 ... (remaining 1519 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 336 2.71 - 3.26: 8228 3.26 - 3.80: 13002 3.80 - 4.35: 17194 4.35 - 4.90: 29964 Nonbonded interactions: 68724 Sorted by model distance: nonbonded pdb=" O SER B 132 " pdb=" OG SER B 132 " model vdw 2.161 3.040 nonbonded pdb=" O PHE B 430 " pdb=" O THR B 433 " model vdw 2.207 3.040 nonbonded pdb=" OG1 THR B 287 " pdb=" OE2 GLU B 293 " model vdw 2.262 3.040 nonbonded pdb=" OE2 GLU A 66 " pdb=" NH2 ARG B 225 " model vdw 2.297 3.120 nonbonded pdb=" NH1 ARG B 373 " pdb=" O ALA B 446 " model vdw 2.310 3.120 ... (remaining 68719 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: 1.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 7.310 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 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: 0.010 Load rotamer database and sin/cos tables:8.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8860 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 : 0.011 0.194 8972 Z= 0.465 Angle : 1.010 13.884 12141 Z= 0.578 Chirality : 0.063 0.583 1354 Planarity : 0.006 0.045 1522 Dihedral : 14.171 89.905 3293 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.03 % Favored : 93.88 % Rotamer: Outliers : 0.74 % Allowed : 0.84 % Favored : 98.42 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.89 (0.24), residues: 1094 helix: -1.18 (0.21), residues: 526 sheet: -0.60 (0.46), residues: 121 loop : -1.34 (0.28), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 277 TYR 0.024 0.003 TYR A 177 PHE 0.025 0.003 PHE A 220 TRP 0.019 0.003 TRP B 239 HIS 0.007 0.002 HIS A 299 Details of bonding type rmsd/Z covalent geometry : bond 0.01084 / 0.47 ( 8972) covalent geometry : angle 1.01019 / 0.58 (12141) hydrogen bonds : bond 0.25165 / 17.17 ( 380) hydrogen bonds : angle 7.60436 / 5.19 ( 1086) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 104 time to evaluate : 0.299 Fit side-chains REVERT: B 31 ARG cc_start: 0.7749 (ttp-170) cc_final: 0.7019 (ttt90) REVERT: B 475 GLU cc_start: 0.5859 (OUTLIER) cc_final: 0.5659 (pp20) REVERT: C 2 ASN cc_start: 0.7983 (p0) cc_final: 0.7778 (p0) outliers start: 7 outliers final: 2 residues processed: 110 average time/residue: 0.7041 time to fit residues: 81.2265 Evaluate side-chains 91 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 88 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 GLU Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 475 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.2935 > 50: distance: 2 - 12: 3.037 distance: 72 - 78: 6.171 distance: 78 - 79: 6.212 distance: 79 - 80: 9.206 distance: 79 - 82: 10.663 distance: 80 - 81: 4.880 distance: 80 - 86: 3.089 distance: 82 - 83: 12.259 distance: 83 - 84: 10.767 distance: 83 - 85: 9.600 distance: 86 - 87: 6.256 distance: 87 - 90: 5.615 distance: 88 - 89: 15.578 distance: 88 - 94: 4.109 distance: 90 - 91: 16.455 distance: 91 - 92: 6.978 distance: 91 - 93: 10.299 distance: 94 - 95: 10.169 distance: 95 - 96: 17.084 distance: 95 - 98: 7.719 distance: 96 - 97: 12.933 distance: 96 - 102: 9.461 distance: 98 - 99: 7.401 distance: 99 - 100: 8.119 distance: 99 - 101: 11.206 distance: 102 - 103: 3.173 distance: 103 - 104: 4.748 distance: 103 - 106: 6.637 distance: 104 - 105: 11.877 distance: 104 - 111: 4.541 distance: 106 - 107: 8.408 distance: 107 - 108: 5.684 distance: 108 - 109: 15.279 distance: 109 - 110: 27.041 distance: 111 - 112: 12.969 distance: 112 - 113: 10.287 distance: 112 - 115: 13.617 distance: 113 - 114: 4.229 distance: 113 - 118: 9.751 distance: 115 - 116: 9.664 distance: 115 - 117: 21.455 distance: 118 - 119: 13.909 distance: 119 - 120: 11.485 distance: 119 - 122: 12.464 distance: 120 - 121: 6.932 distance: 120 - 126: 11.886 distance: 122 - 123: 4.481 distance: 123 - 124: 4.593 distance: 123 - 125: 6.519 distance: 126 - 127: 5.881 distance: 127 - 128: 17.437 distance: 127 - 130: 9.305 distance: 128 - 129: 9.864 distance: 128 - 135: 4.581 distance: 130 - 131: 4.269 distance: 131 - 132: 8.211 distance: 132 - 133: 19.298 distance: 133 - 134: 10.015 distance: 135 - 136: 4.548 distance: 136 - 137: 4.725 distance: 136 - 139: 6.748 distance: 137 - 138: 8.116 distance: 137 - 146: 14.488 distance: 139 - 140: 7.291 distance: 140 - 141: 8.629 distance: 141 - 142: 6.798 distance: 142 - 143: 13.810 distance: 143 - 144: 11.760 distance: 143 - 145: 12.617 distance: 146 - 147: 36.650 distance: 147 - 148: 32.855 distance: 147 - 150: 24.213 distance: 148 - 153: 20.533 distance: 150 - 151: 21.846 distance: 150 - 152: 18.524 distance: 153 - 154: 31.783 distance: 154 - 155: 20.806 distance: 154 - 157: 30.553 distance: 155 - 156: 6.956 distance: 155 - 160: 15.824 distance: 157 - 158: 31.024