Starting phenix.real_space_refine on Thu Jul 2 05:06:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6e7b_8997/07_2026/6e7b_8997.cif Found real_map, /net/cci-nas-00/data/ceres_data/6e7b_8997/07_2026/6e7b_8997.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6e7b_8997/07_2026/6e7b_8997.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6e7b_8997/07_2026/6e7b_8997.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6e7b_8997/07_2026/6e7b_8997.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6e7b_8997/07_2026/6e7b_8997.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6e7b_8997/07_2026/6e7b_8997.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6e7b_8997/07_2026/6e7b_8997.cif" } resolution = 3.5 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 ------------------------------------------------------------------------------- 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= 0.204 sd= 1.216 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 48 5.16 5 C 4259 2.51 5 N 1155 2.21 5 O 1304 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.00s 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: 6774 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 3350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3350 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 19, 'TRANS': 406} Chain: "A" Number of atoms: 3358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3358 Classifications: {'peptide': 428} Link IDs: {'PTRANS': 20, 'TRANS': 407} Chain breaks: 1 Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.43, per 1000 atoms: 0.21 Number of scatterers: 6774 At special positions: 0 Unit cell: (72, 70, 108, 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 48 16.00 P 6 15.00 Mg 2 11.99 O 1304 8.00 N 1155 7.00 C 4259 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: 0.53 Conformation dependent library (CDL) restraints added in 348.5 milliseconds 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1584 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 10 sheets defined 51.4% alpha, 10.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'B' and resid 9 through 28 removed outlier: 3.533A pdb=" N VAL B 23 " --> pdb=" O LYS B 19 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE B 24 " --> pdb=" O PHE B 20 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASP B 26 " --> pdb=" O GLU B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 46 removed outlier: 4.291A pdb=" N ARG B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 49 No H-bonds generated for 'chain 'B' and resid 47 through 49' Processing helix chain 'B' and resid 70 through 79 removed outlier: 3.526A pdb=" N SER B 75 " --> pdb=" O GLY B 71 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N SER B 78 " --> pdb=" O ASP B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 88 No H-bonds generated for 'chain 'B' and resid 86 through 88' Processing helix chain 'B' and resid 100 through 106 Processing helix chain 'B' and resid 106 through 127 removed outlier: 3.536A pdb=" N ALA B 110 " --> pdb=" O TYR B 106 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU B 112 " --> pdb=" O GLU B 108 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ASP B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N SER B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N VAL B 119 " --> pdb=" O SER B 115 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU B 125 " --> pdb=" O ARG B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 159 removed outlier: 3.852A pdb=" N GLY B 148 " --> pdb=" O GLY B 144 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N THR B 149 " --> pdb=" O SER B 145 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE B 152 " --> pdb=" O GLY B 148 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU B 157 " --> pdb=" O SER B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 193 removed outlier: 3.552A pdb=" N HIS B 190 " --> pdb=" O THR B 186 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLN B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 214 removed outlier: 3.651A pdb=" N TYR B 208 " --> pdb=" O ASN B 204 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG B 213 " --> pdb=" O ASP B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 242 removed outlier: 3.929A pdb=" N LEU B 228 " --> pdb=" O ASP B 224 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL B 229 " --> pdb=" O LEU B 225 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLY B 235 " --> pdb=" O ALA B 231 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N SER B 239 " --> pdb=" O GLY B 235 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N LEU B 240 " --> pdb=" O VAL B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 258 removed outlier: 4.109A pdb=" N ASN B 256 " --> pdb=" O LYS B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 294 Processing helix chain 'B' and resid 322 through 337 removed outlier: 3.597A pdb=" N VAL B 326 " --> pdb=" O SER B 322 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN B 329 " --> pdb=" O GLU B 325 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN B 334 " --> pdb=" O MET B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 391 removed outlier: 4.050A pdb=" N LEU B 377 " --> pdb=" O ALA B 373 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ARG B 391 " --> pdb=" O ALA B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 402 removed outlier: 3.898A pdb=" N GLU B 401 " --> pdb=" O TRP B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 426 removed outlier: 4.038A pdb=" N THR B 409 " --> pdb=" O GLU B 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 28 Processing helix chain 'A' and resid 47 through 51 Processing helix chain 'A' and resid 71 through 80 removed outlier: 4.161A pdb=" N ILE A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLU A 77 " --> pdb=" O THR A 73 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N VAL A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 110 through 113 Processing helix chain 'A' and resid 114 through 129 removed outlier: 3.517A pdb=" N VAL A 118 " --> pdb=" O ILE A 114 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASP A 120 " --> pdb=" O ASP A 116 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN A 128 " --> pdb=" O LYS A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 161 Processing helix chain 'A' and resid 182 through 197 removed outlier: 3.963A pdb=" N ILE A 188 " --> pdb=" O PRO A 184 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N HIS A 192 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N THR A 193 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR A 194 " --> pdb=" O THR A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 216 Processing helix chain 'A' and resid 223 through 244 removed outlier: 4.114A pdb=" N ARG A 229 " --> pdb=" O THR A 225 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU A 230 " --> pdb=" O ASN A 226 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N GLN A 233 " --> pdb=" O ARG A 229 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N LEU A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 260 Processing helix chain 'A' and resid 277 through 284 removed outlier: 3.752A pdb=" N TYR A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N HIS A 283 " --> pdb=" O GLU A 279 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU A 284 " --> pdb=" O LYS A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 296 removed outlier: 3.741A pdb=" N PHE A 296 " --> pdb=" O THR A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 338 removed outlier: 4.022A pdb=" N VAL A 328 " --> pdb=" O VAL A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 402 removed outlier: 4.109A pdb=" N ALA A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU A 391 " --> pdb=" O ALA A 387 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS A 401 " --> pdb=" O LEU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.976A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 437 removed outlier: 4.198A pdb=" N PHE A 418 " --> pdb=" O GLU A 414 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N SER A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR A 432 " --> pdb=" O LEU A 428 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 3 through 4 removed outlier: 7.242A pdb=" N GLU B 3 " --> pdb=" O GLN B 131 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 51 through 54 removed outlier: 3.513A pdb=" N VAL B 60 " --> pdb=" O ASN B 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 65 through 66 removed outlier: 6.683A pdb=" N LEU B 65 " --> pdb=" O ILE B 91 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 134 through 138 removed outlier: 7.176A pdb=" N LEU B 135 " --> pdb=" O PHE B 167 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N VAL B 169 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N HIS B 137 " --> pdb=" O VAL B 169 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 199 through 200 removed outlier: 6.811A pdb=" N THR B 199 " --> pdb=" O PHE B 266 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 349 through 352 removed outlier: 8.542A pdb=" N LYS B 350 " --> pdb=" O LEU B 311 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N VAL B 313 " --> pdb=" O LYS B 350 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N ALA B 352 " --> pdb=" O VAL B 313 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N THR B 315 " --> pdb=" O ALA B 352 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 65 through 68 removed outlier: 3.572A pdb=" N VAL A 66 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ILE A 5 " --> pdb=" O LEU A 136 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE A 135 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N CYS A 200 " --> pdb=" O LYS A 166 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLU A 168 " --> pdb=" O CYS A 200 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 53 through 56 Processing sheet with id=AA9, first strand: chain 'A' and resid 351 through 354 Processing sheet with id=AB1, first strand: chain 'A' and resid 351 through 354 removed outlier: 6.769A pdb=" N ASN A 380 " --> pdb=" O MET A 313 " (cutoff:3.500A) 282 hydrogen bonds defined for protein. 828 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: 0.75 Time building geometry restraints manager: 0.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2227 1.34 - 1.46: 1241 1.46 - 1.58: 3372 1.58 - 1.69: 10 1.69 - 1.81: 78 Bond restraints: 6928 Sorted by residual: bond pdb=" O3B G2P B 502 " pdb=" PG G2P B 502 " ideal model delta sigma weight residual 1.716 1.607 0.109 2.00e-02 2.50e+03 3.00e+01 bond pdb=" O1B G2P B 502 " pdb=" PB G2P B 502 " ideal model delta sigma weight residual 1.510 1.609 -0.099 2.00e-02 2.50e+03 2.45e+01 bond pdb=" O2A G2P B 502 " pdb=" PA G2P B 502 " ideal model delta sigma weight residual 1.513 1.608 -0.095 2.00e-02 2.50e+03 2.26e+01 bond pdb=" C5 GTP A 502 " pdb=" C6 GTP A 502 " ideal model delta sigma weight residual 1.390 1.473 -0.083 2.00e-02 2.50e+03 1.72e+01 bond pdb=" C4 G2P B 502 " pdb=" C5 G2P B 502 " ideal model delta sigma weight residual 1.384 1.465 -0.081 2.00e-02 2.50e+03 1.63e+01 ... (remaining 6923 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.55: 9258 2.55 - 5.10: 117 5.10 - 7.65: 23 7.65 - 10.19: 9 10.19 - 12.74: 2 Bond angle restraints: 9409 Sorted by residual: angle pdb=" PA G2P B 502 " pdb=" C3A G2P B 502 " pdb=" PB G2P B 502 " ideal model delta sigma weight residual 120.83 108.09 12.74 3.00e+00 1.11e-01 1.80e+01 angle pdb=" N TYR B 222 " pdb=" CA TYR B 222 " pdb=" C TYR B 222 " ideal model delta sigma weight residual 111.28 107.15 4.13 1.09e+00 8.42e-01 1.44e+01 angle pdb=" C3A G2P B 502 " pdb=" PA G2P B 502 " pdb=" O5' G2P B 502 " ideal model delta sigma weight residual 99.14 109.87 -10.73 3.00e+00 1.11e-01 1.28e+01 angle pdb=" O1B GTP A 502 " pdb=" PB GTP A 502 " pdb=" O2B GTP A 502 " ideal model delta sigma weight residual 109.50 119.65 -10.15 3.00e+00 1.11e-01 1.14e+01 angle pdb=" O1A GTP A 502 " pdb=" PA GTP A 502 " pdb=" O2A GTP A 502 " ideal model delta sigma weight residual 109.50 119.32 -9.82 3.00e+00 1.11e-01 1.07e+01 ... (remaining 9404 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.42: 4063 31.42 - 62.83: 38 62.83 - 94.24: 7 94.24 - 125.66: 1 125.66 - 157.07: 2 Dihedral angle restraints: 4111 sinusoidal: 1642 harmonic: 2469 Sorted by residual: dihedral pdb=" C5' GTP A 502 " pdb=" O5' GTP A 502 " pdb=" PA GTP A 502 " pdb=" O3A GTP A 502 " ideal model delta sinusoidal sigma weight residual 69.27 -133.66 -157.07 1 2.00e+01 2.50e-03 4.61e+01 dihedral pdb=" C8 GTP A 502 " pdb=" C1' GTP A 502 " pdb=" N9 GTP A 502 " pdb=" O4' GTP A 502 " ideal model delta sinusoidal sigma weight residual 104.59 -41.98 146.57 1 2.00e+01 2.50e-03 4.40e+01 dihedral pdb=" O3B GTP A 502 " pdb=" O3A GTP A 502 " pdb=" PB GTP A 502 " pdb=" PA GTP A 502 " ideal model delta sinusoidal sigma weight residual 291.08 171.08 120.00 1 2.00e+01 2.50e-03 3.60e+01 ... (remaining 4108 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 572 0.030 - 0.061: 302 0.061 - 0.091: 101 0.091 - 0.122: 43 0.122 - 0.152: 10 Chirality restraints: 1028 Sorted by residual: chirality pdb=" CA VAL A 363 " pdb=" N VAL A 363 " pdb=" C VAL A 363 " pdb=" CB VAL A 363 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.78e-01 chirality pdb=" CB ILE A 115 " pdb=" CA ILE A 115 " pdb=" CG1 ILE A 115 " pdb=" CG2 ILE A 115 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.77e-01 chirality pdb=" CA ILE B 368 " pdb=" N ILE B 368 " pdb=" C ILE B 368 " pdb=" CB ILE B 368 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.72e-01 ... (remaining 1025 not shown) Planarity restraints: 1221 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 79 " -0.172 9.50e-02 1.11e+02 7.73e-02 3.68e+00 pdb=" NE ARG A 79 " 0.011 2.00e-02 2.50e+03 pdb=" CZ ARG A 79 " -0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG A 79 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 79 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET B 267 " 0.030 5.00e-02 4.00e+02 4.59e-02 3.38e+00 pdb=" N PRO B 268 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO B 268 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 268 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 356 " 0.028 5.00e-02 4.00e+02 4.23e-02 2.87e+00 pdb=" N PRO B 357 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 357 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 357 " 0.024 5.00e-02 4.00e+02 ... (remaining 1218 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 99 2.59 - 3.17: 6292 3.17 - 3.74: 10676 3.74 - 4.32: 15716 4.32 - 4.90: 25100 Nonbonded interactions: 57883 Sorted by model distance: nonbonded pdb="MG MG B 501 " pdb=" O1G G2P B 502 " model vdw 2.009 2.170 nonbonded pdb="MG MG A 501 " pdb=" O3G GTP A 502 " model vdw 2.012 2.170 nonbonded pdb="MG MG B 501 " pdb=" O1B G2P B 502 " model vdw 2.049 2.170 nonbonded pdb="MG MG B 501 " pdb=" O3B G2P B 502 " model vdw 2.069 2.170 nonbonded pdb=" OE1 GLU A 71 " pdb="MG MG A 501 " model vdw 2.099 2.170 ... (remaining 57878 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 group one per residue 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: 11.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.050 Find NCS groups from input model: 0.040 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: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 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 : 0.006 0.109 6928 Z= 0.274 Angle : 0.828 12.742 9409 Z= 0.401 Chirality : 0.043 0.152 1028 Planarity : 0.004 0.077 1221 Dihedral : 11.475 157.073 2527 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 0.14 % Allowed : 3.84 % Favored : 96.02 % 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 are not related in a simple way. whole: -4.13 (0.25), residues: 848 helix: -2.97 (0.19), residues: 352 sheet: -3.95 (0.43), residues: 93 loop : -2.06 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 241 TYR 0.013 0.002 TYR B 208 PHE 0.019 0.002 PHE B 212 TRP 0.014 0.002 TRP A 21 HIS 0.008 0.001 HIS B 6 Details of bonding type rmsd/Z covalent geometry : bond 0.00600 / 0.27 ( 6928) covalent geometry : angle 0.82842 / 0.40 ( 9409) hydrogen bonds : bond 0.28612 / 19.13 ( 278) hydrogen bonds : angle 10.12227 / 6.93 ( 828) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 223 time to evaluate : 0.238 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 100 ASN cc_start: 0.7481 (t0) cc_final: 0.7193 (t0) REVERT: B 289 LEU cc_start: 0.8010 (mp) cc_final: 0.7744 (mp) REVERT: B 403 MET cc_start: 0.7705 (tpt) cc_final: 0.6434 (mmm) REVERT: A 50 ASN cc_start: 0.7276 (t0) cc_final: 0.7027 (t0) REVERT: A 203 MET cc_start: 0.7696 (mmm) cc_final: 0.7314 (mmm) outliers start: 1 outliers final: 1 residues processed: 224 average time/residue: 0.0957 time to fit residues: 27.1365 Evaluate side-chains 135 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 134 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 9.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 7.9990 chunk 74 optimal weight: 3.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 52 ASN B 291 GLN B 329 GLN A 11 GLN ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 ASN A 197 HIS A 206 ASN A 258 ASN A 300 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.129455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.111842 restraints weight = 9841.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.115692 restraints weight = 5342.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.118388 restraints weight = 3478.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.120266 restraints weight = 2514.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.121643 restraints weight = 1948.554| |-----------------------------------------------------------------------------| r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.3913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 6928 Z= 0.258 Angle : 0.746 7.121 9409 Z= 0.384 Chirality : 0.050 0.159 1028 Planarity : 0.005 0.057 1221 Dihedral : 9.995 161.902 948 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.74 % Allowed : 11.39 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -2.72 (0.26), residues: 848 helix: -1.44 (0.23), residues: 363 sheet: -3.35 (0.44), residues: 93 loop : -1.62 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 84 TYR 0.018 0.002 TYR B 36 PHE 0.027 0.003 PHE A 255 TRP 0.020 0.002 TRP A 21 HIS 0.008 0.001 HIS A 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00598 / 0.26 ( 6928) covalent geometry : angle 0.74613 / 0.38 ( 9409) hydrogen bonds : bond 0.05434 / 3.32 ( 278) hydrogen bonds : angle 5.82785 / 3.96 ( 828) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 150 time to evaluate : 0.238 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 86 ARG cc_start: 0.7068 (mmp-170) cc_final: 0.6425 (tpm170) REVERT: B 406 MET cc_start: 0.6878 (ptm) cc_final: 0.6553 (tpp) REVERT: A 103 TYR cc_start: 0.7004 (t80) cc_final: 0.6530 (t80) REVERT: A 108 TYR cc_start: 0.6255 (OUTLIER) cc_final: 0.5937 (t80) REVERT: A 147 SER cc_start: 0.8668 (m) cc_final: 0.8238 (p) outliers start: 20 outliers final: 11 residues processed: 165 average time/residue: 0.0756 time to fit residues: 16.6669 Evaluate side-chains 130 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 118 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 11 GLN Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 108 TYR Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 367 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 80 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 10 optimal weight: 8.9990 chunk 72 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 245 GLN B 298 ASN A 50 ASN ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.133328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.116047 restraints weight = 9554.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.120015 restraints weight = 5173.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.122739 restraints weight = 3332.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.124507 restraints weight = 2384.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.125957 restraints weight = 1856.641| |-----------------------------------------------------------------------------| r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.4448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6928 Z= 0.130 Angle : 0.610 7.946 9409 Z= 0.311 Chirality : 0.044 0.143 1028 Planarity : 0.004 0.036 1221 Dihedral : 9.658 172.719 946 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.88 % Allowed : 14.40 % Favored : 82.72 % 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 are not related in a simple way. whole: -2.03 (0.27), residues: 848 helix: -0.72 (0.25), residues: 373 sheet: -2.69 (0.48), residues: 103 loop : -1.46 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 2 TYR 0.012 0.001 TYR A 399 PHE 0.035 0.002 PHE B 20 TRP 0.013 0.001 TRP A 21 HIS 0.006 0.001 HIS B 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 ( 6928) covalent geometry : angle 0.61014 / 0.31 ( 9409) hydrogen bonds : bond 0.04447 / 2.75 ( 278) hydrogen bonds : angle 5.23458 / 3.57 ( 828) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 148 time to evaluate : 0.181 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 77 ARG cc_start: 0.8199 (mtt90) cc_final: 0.7995 (mtt-85) REVERT: B 86 ARG cc_start: 0.6929 (mmp-170) cc_final: 0.5222 (tpt170) REVERT: B 118 ASP cc_start: 0.7289 (m-30) cc_final: 0.7064 (m-30) REVERT: B 276 ARG cc_start: 0.7186 (OUTLIER) cc_final: 0.6849 (mmm160) REVERT: A 108 TYR cc_start: 0.6037 (OUTLIER) cc_final: 0.5786 (t80) REVERT: A 147 SER cc_start: 0.8472 (m) cc_final: 0.8034 (p) REVERT: A 225 THR cc_start: 0.8819 (p) cc_final: 0.8618 (t) REVERT: A 234 ILE cc_start: 0.8591 (OUTLIER) cc_final: 0.8193 (mt) REVERT: A 269 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8314 (pt) outliers start: 21 outliers final: 9 residues processed: 161 average time/residue: 0.0838 time to fit residues: 17.6526 Evaluate side-chains 129 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 116 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 276 ARG Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain A residue 108 TYR Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 192 HIS Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 269 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 27 optimal weight: 0.1980 chunk 51 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 46 optimal weight: 6.9990 chunk 13 optimal weight: 8.9990 chunk 10 optimal weight: 7.9990 chunk 78 optimal weight: 8.9990 chunk 65 optimal weight: 0.0970 chunk 42 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 298 ASN A 18 ASN A 50 ASN ** A 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.134159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.117458 restraints weight = 9658.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.121288 restraints weight = 5114.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.123965 restraints weight = 3261.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.125791 restraints weight = 2315.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.127051 restraints weight = 1773.127| |-----------------------------------------------------------------------------| r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.4822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6928 Z= 0.131 Angle : 0.602 8.899 9409 Z= 0.304 Chirality : 0.044 0.157 1028 Planarity : 0.004 0.036 1221 Dihedral : 9.534 179.670 946 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.57 % Allowed : 16.60 % Favored : 79.84 % 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 are not related in a simple way. whole: -1.66 (0.28), residues: 848 helix: -0.42 (0.25), residues: 374 sheet: -2.45 (0.47), residues: 110 loop : -1.24 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 359 TYR 0.013 0.001 TYR A 357 PHE 0.030 0.002 PHE B 20 TRP 0.014 0.001 TRP A 21 HIS 0.003 0.001 HIS B 307 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 ( 6928) covalent geometry : angle 0.60218 / 0.30 ( 9409) hydrogen bonds : bond 0.04085 / 2.52 ( 278) hydrogen bonds : angle 4.96619 / 3.39 ( 828) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 136 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 73 MET cc_start: 0.8462 (OUTLIER) cc_final: 0.8254 (mtt) REVERT: B 77 ARG cc_start: 0.8201 (mtt90) cc_final: 0.7990 (mtt-85) REVERT: B 245 GLN cc_start: 0.8428 (mt0) cc_final: 0.8123 (mt0) REVERT: B 276 ARG cc_start: 0.7126 (OUTLIER) cc_final: 0.6901 (mmm160) REVERT: B 406 MET cc_start: 0.7609 (tpp) cc_final: 0.7100 (ptm) REVERT: A 56 THR cc_start: 0.8269 (m) cc_final: 0.7829 (p) REVERT: A 103 TYR cc_start: 0.7133 (t80) cc_final: 0.6497 (t80) REVERT: A 108 TYR cc_start: 0.6078 (OUTLIER) cc_final: 0.5479 (t80) REVERT: A 147 SER cc_start: 0.8423 (m) cc_final: 0.7994 (p) REVERT: A 234 ILE cc_start: 0.8614 (OUTLIER) cc_final: 0.8229 (mt) REVERT: A 269 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8226 (pt) outliers start: 26 outliers final: 12 residues processed: 153 average time/residue: 0.0839 time to fit residues: 17.2305 Evaluate side-chains 136 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 119 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 276 ARG Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain A residue 108 TYR Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 192 HIS Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 378 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 26 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 4 optimal weight: 0.7980 chunk 39 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 38 optimal weight: 7.9990 chunk 16 optimal weight: 0.8980 chunk 67 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 70 optimal weight: 5.9990 chunk 61 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 298 ASN ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 226 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.133945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.116279 restraints weight = 9572.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.120215 restraints weight = 5127.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.122950 restraints weight = 3310.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.124775 restraints weight = 2383.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.126186 restraints weight = 1861.043| |-----------------------------------------------------------------------------| r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.5071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6928 Z= 0.118 Angle : 0.572 8.484 9409 Z= 0.289 Chirality : 0.043 0.142 1028 Planarity : 0.004 0.035 1221 Dihedral : 9.145 171.491 946 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.98 % Allowed : 16.60 % Favored : 79.42 % 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 are not related in a simple way. whole: -1.33 (0.28), residues: 848 helix: -0.16 (0.26), residues: 375 sheet: -2.20 (0.48), residues: 109 loop : -1.07 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 359 TYR 0.008 0.001 TYR A 399 PHE 0.020 0.001 PHE B 385 TRP 0.012 0.001 TRP A 21 HIS 0.007 0.001 HIS B 307 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 ( 6928) covalent geometry : angle 0.57233 / 0.29 ( 9409) hydrogen bonds : bond 0.03857 / 2.39 ( 278) hydrogen bonds : angle 4.81703 / 3.29 ( 828) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 136 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 213 ARG cc_start: 0.8059 (ptp-110) cc_final: 0.7790 (ptp-110) REVERT: B 276 ARG cc_start: 0.7111 (OUTLIER) cc_final: 0.6900 (mmm160) REVERT: B 406 MET cc_start: 0.7626 (tpp) cc_final: 0.7050 (ptm) REVERT: B 407 GLU cc_start: 0.7630 (tm-30) cc_final: 0.7370 (tm-30) REVERT: A 56 THR cc_start: 0.8249 (m) cc_final: 0.8002 (p) REVERT: A 108 TYR cc_start: 0.5975 (OUTLIER) cc_final: 0.5450 (t80) REVERT: A 147 SER cc_start: 0.8386 (m) cc_final: 0.7940 (p) REVERT: A 212 ILE cc_start: 0.8298 (OUTLIER) cc_final: 0.8058 (mt) REVERT: A 269 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8097 (pt) outliers start: 29 outliers final: 19 residues processed: 155 average time/residue: 0.0718 time to fit residues: 14.9912 Evaluate side-chains 143 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 120 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 276 ARG Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 108 TYR Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 161 TYR Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 192 HIS Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 361 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 19 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 38 optimal weight: 6.9990 chunk 32 optimal weight: 8.9990 chunk 20 optimal weight: 3.9990 chunk 17 optimal weight: 7.9990 chunk 39 optimal weight: 9.9990 chunk 7 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 298 ASN ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.126305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.108784 restraints weight = 9742.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.112516 restraints weight = 5261.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.115126 restraints weight = 3437.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.116932 restraints weight = 2505.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.118279 restraints weight = 1959.409| |-----------------------------------------------------------------------------| r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.5502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6928 Z= 0.189 Angle : 0.647 7.392 9409 Z= 0.325 Chirality : 0.046 0.168 1028 Planarity : 0.004 0.038 1221 Dihedral : 9.146 165.770 946 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 5.08 % Allowed : 17.83 % Favored : 77.09 % 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 are not related in a simple way. whole: -1.37 (0.28), residues: 848 helix: -0.19 (0.26), residues: 380 sheet: -2.31 (0.47), residues: 110 loop : -1.08 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 359 TYR 0.011 0.001 TYR B 310 PHE 0.021 0.002 PHE B 385 TRP 0.013 0.002 TRP A 388 HIS 0.003 0.001 HIS A 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.19 ( 6928) covalent geometry : angle 0.64652 / 0.33 ( 9409) hydrogen bonds : bond 0.04128 / 2.58 ( 278) hydrogen bonds : angle 5.01075 / 3.43 ( 828) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 128 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 57 HIS cc_start: 0.5918 (t-90) cc_final: 0.5689 (t-90) REVERT: B 213 ARG cc_start: 0.8095 (ptp-110) cc_final: 0.7827 (ptp-110) REVERT: B 276 ARG cc_start: 0.7256 (OUTLIER) cc_final: 0.7047 (mmm160) REVERT: B 406 MET cc_start: 0.7891 (tpp) cc_final: 0.7041 (tpp) REVERT: A 56 THR cc_start: 0.8237 (m) cc_final: 0.7757 (p) REVERT: A 103 TYR cc_start: 0.7273 (t80) cc_final: 0.6768 (t80) REVERT: A 108 TYR cc_start: 0.6148 (OUTLIER) cc_final: 0.5407 (t80) REVERT: A 147 SER cc_start: 0.8431 (m) cc_final: 0.8224 (p) REVERT: A 212 ILE cc_start: 0.8435 (OUTLIER) cc_final: 0.8173 (mt) REVERT: A 269 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8083 (pt) outliers start: 37 outliers final: 26 residues processed: 154 average time/residue: 0.0765 time to fit residues: 15.8530 Evaluate side-chains 146 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 116 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 83 HIS Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 276 ARG Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 354 CYS Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 108 TYR Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 161 TYR Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 361 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 60.1489 > 50: distance: 18 - 20: 9.912 distance: 20 - 21: 14.165 distance: 21 - 22: 11.021 distance: 21 - 24: 9.176 distance: 22 - 23: 26.946 distance: 22 - 28: 25.549 distance: 24 - 25: 8.410 distance: 24 - 26: 6.428 distance: 25 - 27: 12.731 distance: 28 - 29: 9.842 distance: 29 - 30: 16.555 distance: 29 - 32: 15.950 distance: 30 - 31: 3.443 distance: 30 - 37: 30.772 distance: 32 - 33: 15.827 distance: 34 - 35: 8.972 distance: 34 - 36: 7.047 distance: 37 - 38: 20.070 distance: 37 - 43: 10.518 distance: 38 - 39: 8.140 distance: 38 - 41: 8.853 distance: 39 - 40: 24.767 distance: 39 - 44: 7.885 distance: 41 - 42: 21.814 distance: 42 - 43: 37.337 distance: 44 - 45: 5.182 distance: 45 - 46: 7.922 distance: 45 - 48: 12.411 distance: 46 - 47: 26.067 distance: 46 - 52: 10.762 distance: 48 - 49: 25.025 distance: 49 - 51: 10.197 distance: 52 - 53: 19.343 distance: 53 - 54: 24.242 distance: 54 - 55: 17.065 distance: 54 - 56: 8.351 distance: 56 - 57: 30.772 distance: 57 - 58: 17.747 distance: 57 - 60: 16.807 distance: 58 - 59: 18.441 distance: 58 - 65: 28.332 distance: 60 - 61: 24.933 distance: 61 - 62: 20.165 distance: 62 - 63: 19.599 distance: 62 - 64: 21.097 distance: 65 - 66: 30.033 distance: 66 - 67: 21.479 distance: 66 - 69: 39.765 distance: 67 - 68: 13.038 distance: 67 - 73: 30.377 distance: 69 - 70: 11.710 distance: 70 - 71: 16.132 distance: 71 - 72: 11.328 distance: 73 - 74: 23.433 distance: 73 - 79: 25.865 distance: 74 - 75: 36.860 distance: 74 - 77: 15.872 distance: 75 - 76: 20.796 distance: 77 - 78: 29.669 distance: 78 - 79: 7.066 distance: 83 - 105: 3.982 distance: 91 - 111: 3.526