Starting phenix.real_space_refine on Fri Aug 22 17:11:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wrd_37774/08_2025/8wrd_37774.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wrd_37774/08_2025/8wrd_37774.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8wrd_37774/08_2025/8wrd_37774.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wrd_37774/08_2025/8wrd_37774.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wrd_37774/08_2025/8wrd_37774.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wrd_37774/08_2025/8wrd_37774.map" } resolution = 3.05 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= 1.000 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: 4 Type Number sf(0) Gaussians S 42 5.16 5 C 4078 2.51 5 N 1017 2.21 5 O 1189 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6326 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 2957 Classifications: {'peptide': 393} Link IDs: {'PTRANS': 23, 'TRANS': 369} Chain breaks: 1 Chain: "L" Number of atoms: 1667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1667 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 202} Chain: "H" Number of atoms: 1702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1702 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 12, 'TRANS': 211} Time building chain proxies: 1.75, per 1000 atoms: 0.28 Number of scatterers: 6326 At special positions: 0 Unit cell: (84.48, 84.48, 132, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 42 16.00 O 1189 8.00 N 1017 7.00 C 4078 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 151 " - pdb=" SG CYS H 206 " distance=2.04 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: 0.59 Conformation dependent library (CDL) restraints added in 384.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1528 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 11 sheets defined 46.9% alpha, 25.8% 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 7 through 14 removed outlier: 3.733A pdb=" N TRP A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 41 removed outlier: 3.807A pdb=" N VAL A 40 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N VAL A 41 " --> pdb=" O LEU A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 157 removed outlier: 3.815A pdb=" N GLY A 132 " --> pdb=" O ASN A 128 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N LYS A 138 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N ALA A 139 " --> pdb=" O PHE A 135 " (cutoff:3.500A) Proline residue: A 147 - end of helix removed outlier: 3.707A pdb=" N ASN A 154 " --> pdb=" O GLY A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 177 Processing helix chain 'A' and resid 181 through 211 removed outlier: 3.731A pdb=" N ARG A 189 " --> pdb=" O LEU A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 246 removed outlier: 3.549A pdb=" N GLY A 226 " --> pdb=" O GLY A 222 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLY A 227 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LEU A 228 " --> pdb=" O ALA A 224 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA A 229 " --> pdb=" O LEU A 225 " (cutoff:3.500A) Proline residue: A 236 - end of helix removed outlier: 3.714A pdb=" N LEU A 242 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLU A 244 " --> pdb=" O SER A 240 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE A 245 " --> pdb=" O VAL A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 270 removed outlier: 4.295A pdb=" N ALA A 257 " --> pdb=" O LEU A 253 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU A 258 " --> pdb=" O VAL A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 290 Processing helix chain 'A' and resid 291 through 324 removed outlier: 3.860A pdb=" N ALA A 297 " --> pdb=" O TYR A 293 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE A 301 " --> pdb=" O ALA A 297 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLY A 307 " --> pdb=" O PHE A 303 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ILE A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) Proline residue: A 313 - end of helix Proline residue: A 316 - end of helix Processing helix chain 'A' and resid 326 through 334 removed outlier: 3.777A pdb=" N LEU A 330 " --> pdb=" O ARG A 326 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLY A 331 " --> pdb=" O LYS A 327 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL A 332 " --> pdb=" O TRP A 328 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N PHE A 334 " --> pdb=" O LEU A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 352 removed outlier: 3.610A pdb=" N SER A 338 " --> pdb=" O PHE A 334 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TYR A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN A 346 " --> pdb=" O LEU A 342 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY A 349 " --> pdb=" O THR A 345 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ILE A 350 " --> pdb=" O ASN A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 375 Processing helix chain 'A' and resid 376 through 378 No H-bonds generated for 'chain 'A' and resid 376 through 378' Processing helix chain 'A' and resid 380 through 414 removed outlier: 4.518A pdb=" N ALA A 386 " --> pdb=" O TYR A 382 " (cutoff:3.500A) Proline residue: A 387 - end of helix Proline residue: A 404 - end of helix removed outlier: 4.924A pdb=" N GLY A 407 " --> pdb=" O MET A 403 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N VAL A 410 " --> pdb=" O MET A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 447 removed outlier: 3.939A pdb=" N ILE A 424 " --> pdb=" O SER A 420 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA A 425 " --> pdb=" O VAL A 421 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLY A 432 " --> pdb=" O ALA A 428 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N TYR A 433 " --> pdb=" O PHE A 429 " (cutoff:3.500A) Proline residue: A 437 - end of helix removed outlier: 3.975A pdb=" N GLY A 441 " --> pdb=" O PRO A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 464 removed outlier: 3.522A pdb=" N ALA A 464 " --> pdb=" O ASP A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 471 removed outlier: 3.548A pdb=" N PHE A 469 " --> pdb=" O LEU A 466 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.847A pdb=" N LEU L 83 " --> pdb=" O SER L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 127 Processing helix chain 'L' and resid 183 through 189 removed outlier: 3.767A pdb=" N HIS L 189 " --> pdb=" O GLU L 185 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.514A pdb=" N SER H 31 " --> pdb=" O THR H 28 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'H' and resid 62 through 65 removed outlier: 3.676A pdb=" N LYS H 65 " --> pdb=" O GLU H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 62 through 65' Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.583A pdb=" N SER H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 167 through 169 No H-bonds generated for 'chain 'H' and resid 167 through 169' Processing helix chain 'H' and resid 197 through 202 removed outlier: 3.589A pdb=" N SER H 201 " --> pdb=" O SER H 197 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 10 through 13 Processing sheet with id=AA2, first strand: chain 'L' and resid 19 through 24 removed outlier: 3.508A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.589A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N TYR L 49 " --> pdb=" O VAL L 33 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N VAL L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 115 through 118 removed outlier: 3.862A pdb=" N ASN L 138 " --> pdb=" O TYR L 173 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 145 through 150 Processing sheet with id=AA6, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA7, first strand: chain 'H' and resid 9 through 12 removed outlier: 6.593A pdb=" N ILE H 34 " --> pdb=" O ASN H 50 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ASN H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER H 57 " --> pdb=" O TYR H 52 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 9 through 12 removed outlier: 6.693A pdb=" N CYS H 96 " --> pdb=" O TRP H 114 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N TRP H 114 " --> pdb=" O CYS H 96 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ARG H 98 " --> pdb=" O ASP H 112 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ALA H 110 " --> pdb=" O ASP H 100 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 131 through 135 removed outlier: 6.101A pdb=" N TYR H 186 " --> pdb=" O GLY H 155 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 131 through 135 removed outlier: 6.101A pdb=" N TYR H 186 " --> pdb=" O GLY H 155 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 162 through 165 removed outlier: 3.627A pdb=" N THR H 215 " --> pdb=" O HIS H 210 " (cutoff:3.500A) 369 hydrogen bonds defined for protein. 1041 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: 1.07 Time building geometry restraints manager: 0.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1957 1.34 - 1.46: 1540 1.46 - 1.58: 2914 1.58 - 1.70: 0 1.70 - 1.82: 67 Bond restraints: 6478 Sorted by residual: bond pdb=" CA LYS H 126 " pdb=" CB LYS H 126 " ideal model delta sigma weight residual 1.533 1.546 -0.013 1.37e-02 5.33e+03 8.60e-01 bond pdb=" C ILE A 375 " pdb=" N PRO A 376 " ideal model delta sigma weight residual 1.334 1.355 -0.021 2.34e-02 1.83e+03 8.31e-01 bond pdb=" CB ASP H 103 " pdb=" CG ASP H 103 " ideal model delta sigma weight residual 1.516 1.537 -0.021 2.50e-02 1.60e+03 7.12e-01 bond pdb=" CB LYS H 126 " pdb=" CG LYS H 126 " ideal model delta sigma weight residual 1.520 1.545 -0.025 3.00e-02 1.11e+03 6.86e-01 bond pdb=" CB VAL L 146 " pdb=" CG2 VAL L 146 " ideal model delta sigma weight residual 1.521 1.494 0.027 3.30e-02 9.18e+02 6.53e-01 ... (remaining 6473 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 8657 1.61 - 3.23: 121 3.23 - 4.84: 28 4.84 - 6.45: 9 6.45 - 8.06: 1 Bond angle restraints: 8816 Sorted by residual: angle pdb=" CA LYS H 126 " pdb=" CB LYS H 126 " pdb=" CG LYS H 126 " ideal model delta sigma weight residual 114.10 122.16 -8.06 2.00e+00 2.50e-01 1.63e+01 angle pdb=" N TYR A 158 " pdb=" CA TYR A 158 " pdb=" C TYR A 158 " ideal model delta sigma weight residual 109.81 115.40 -5.59 2.21e+00 2.05e-01 6.41e+00 angle pdb=" N GLY A 436 " pdb=" CA GLY A 436 " pdb=" C GLY A 436 " ideal model delta sigma weight residual 112.34 117.07 -4.73 2.04e+00 2.40e-01 5.39e+00 angle pdb=" N PRO A 236 " pdb=" CA PRO A 236 " pdb=" C PRO A 236 " ideal model delta sigma weight residual 110.70 113.28 -2.58 1.22e+00 6.72e-01 4.48e+00 angle pdb=" N GLY H 49 " pdb=" CA GLY H 49 " pdb=" C GLY H 49 " ideal model delta sigma weight residual 110.42 113.57 -3.15 1.49e+00 4.50e-01 4.47e+00 ... (remaining 8811 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.15: 3344 17.15 - 34.30: 374 34.30 - 51.45: 98 51.45 - 68.61: 18 68.61 - 85.76: 6 Dihedral angle restraints: 3840 sinusoidal: 1451 harmonic: 2389 Sorted by residual: dihedral pdb=" CA LYS H 126 " pdb=" C LYS H 126 " pdb=" N THR H 127 " pdb=" CA THR H 127 " ideal model delta harmonic sigma weight residual 180.00 156.27 23.73 0 5.00e+00 4.00e-02 2.25e+01 dihedral pdb=" CA LEU L 136 " pdb=" C LEU L 136 " pdb=" N ASN L 137 " pdb=" CA ASN L 137 " ideal model delta harmonic sigma weight residual -180.00 -157.43 -22.57 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" CB CYS H 151 " pdb=" SG CYS H 151 " pdb=" SG CYS H 206 " pdb=" CB CYS H 206 " ideal model delta sinusoidal sigma weight residual 93.00 58.97 34.03 1 1.00e+01 1.00e-02 1.64e+01 ... (remaining 3837 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 604 0.029 - 0.058: 260 0.058 - 0.087: 87 0.087 - 0.116: 59 0.116 - 0.145: 8 Chirality restraints: 1018 Sorted by residual: chirality pdb=" CA VAL H 37 " pdb=" N VAL H 37 " pdb=" C VAL H 37 " pdb=" CB VAL H 37 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.27e-01 chirality pdb=" CA ILE L 48 " pdb=" N ILE L 48 " pdb=" C ILE L 48 " pdb=" CB ILE L 48 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.24e-01 chirality pdb=" CA ILE L 144 " pdb=" N ILE L 144 " pdb=" C ILE L 144 " pdb=" CB ILE L 144 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.16e-01 ... (remaining 1015 not shown) Planarity restraints: 1103 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS H 126 " -0.010 2.00e-02 2.50e+03 2.02e-02 4.10e+00 pdb=" C LYS H 126 " 0.035 2.00e-02 2.50e+03 pdb=" O LYS H 126 " -0.014 2.00e-02 2.50e+03 pdb=" N THR H 127 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 160 " 0.029 5.00e-02 4.00e+02 4.43e-02 3.14e+00 pdb=" N PRO A 161 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 161 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 161 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 386 " -0.027 5.00e-02 4.00e+02 4.11e-02 2.71e+00 pdb=" N PRO A 387 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 387 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 387 " -0.023 5.00e-02 4.00e+02 ... (remaining 1100 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 265 2.72 - 3.27: 6059 3.27 - 3.81: 10078 3.81 - 4.36: 12165 4.36 - 4.90: 22210 Nonbonded interactions: 50777 Sorted by model distance: nonbonded pdb=" O ASN L 137 " pdb=" OG SER L 174 " model vdw 2.177 3.040 nonbonded pdb=" OG1 THR H 195 " pdb=" OG1 THR H 198 " model vdw 2.280 3.040 nonbonded pdb=" OD2 ASP A 291 " pdb=" NE2 HIS A 414 " model vdw 2.287 3.120 nonbonded pdb=" OD1 ASP A 291 " pdb=" NH1 ARG A 413 " model vdw 2.310 3.120 nonbonded pdb=" O GLU L 123 " pdb=" OG1 THR L 126 " model vdw 2.316 3.040 ... (remaining 50772 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: 2.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.150 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 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 : 0.004 0.033 6482 Z= 0.146 Angle : 0.552 8.063 8824 Z= 0.285 Chirality : 0.042 0.145 1018 Planarity : 0.004 0.044 1103 Dihedral : 15.710 85.756 2300 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.14 % Allowed : 22.33 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.84 (0.30), residues: 822 helix: 1.34 (0.30), residues: 329 sheet: 1.38 (0.36), residues: 221 loop : -1.13 (0.37), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 155 TYR 0.012 0.001 TYR A 422 PHE 0.012 0.001 PHE L 87 TRP 0.008 0.001 TRP H 114 HIS 0.001 0.000 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 6478) covalent geometry : angle 0.55189 ( 8816) SS BOND : bond 0.00397 ( 4) SS BOND : angle 0.87427 ( 8) hydrogen bonds : bond 0.14359 ( 347) hydrogen bonds : angle 6.89795 ( 1041) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 62 time to evaluate : 0.249 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 63 average time/residue: 0.1027 time to fit residues: 8.4556 Evaluate side-chains 61 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 0.0570 chunk 45 optimal weight: 4.9990 chunk 74 optimal weight: 8.9990 overall best weight: 1.1302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 GLN L 210 ASN H 59 ASN H 182 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.126824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.093338 restraints weight = 8189.394| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 2.19 r_work: 0.2979 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.0538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 6482 Z= 0.187 Angle : 0.592 6.093 8824 Z= 0.309 Chirality : 0.043 0.135 1018 Planarity : 0.005 0.045 1103 Dihedral : 4.615 23.803 884 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.13 % Allowed : 20.91 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.73 (0.30), residues: 822 helix: 1.14 (0.29), residues: 334 sheet: 1.25 (0.36), residues: 217 loop : -0.95 (0.37), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 16 TYR 0.011 0.001 TYR L 140 PHE 0.013 0.001 PHE L 87 TRP 0.010 0.001 TRP H 114 HIS 0.002 0.000 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00468 ( 6478) covalent geometry : angle 0.59157 ( 8816) SS BOND : bond 0.00445 ( 4) SS BOND : angle 0.99101 ( 8) hydrogen bonds : bond 0.04732 ( 347) hydrogen bonds : angle 5.36366 ( 1041) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 63 time to evaluate : 0.247 Fit side-chains outliers start: 15 outliers final: 9 residues processed: 76 average time/residue: 0.0953 time to fit residues: 9.6892 Evaluate side-chains 70 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 164 THR Chi-restraints excluded: chain L residue 193 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 195 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 66 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 16 optimal weight: 0.0980 chunk 50 optimal weight: 0.9980 chunk 58 optimal weight: 7.9990 chunk 8 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.128332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.095195 restraints weight = 8160.564| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 2.14 r_work: 0.3014 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.0661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6482 Z= 0.132 Angle : 0.542 6.277 8824 Z= 0.281 Chirality : 0.041 0.137 1018 Planarity : 0.004 0.044 1103 Dihedral : 4.493 24.504 884 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.99 % Allowed : 21.19 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.85 (0.30), residues: 822 helix: 1.33 (0.30), residues: 334 sheet: 1.21 (0.35), residues: 222 loop : -0.98 (0.38), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG L 155 TYR 0.009 0.001 TYR L 140 PHE 0.011 0.001 PHE L 87 TRP 0.009 0.001 TRP H 114 HIS 0.001 0.000 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 6478) covalent geometry : angle 0.54113 ( 8816) SS BOND : bond 0.00405 ( 4) SS BOND : angle 1.23697 ( 8) hydrogen bonds : bond 0.03921 ( 347) hydrogen bonds : angle 4.99020 ( 1041) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 65 time to evaluate : 0.236 Fit side-chains REVERT: L 6 GLN cc_start: 0.8569 (OUTLIER) cc_final: 0.8274 (tt0) REVERT: H 89 ASP cc_start: 0.8584 (t0) cc_final: 0.8243 (t0) outliers start: 21 outliers final: 12 residues processed: 85 average time/residue: 0.0828 time to fit residues: 9.5686 Evaluate side-chains 76 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 164 THR Chi-restraints excluded: chain L residue 176 SER Chi-restraints excluded: chain L residue 193 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 208 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 16 optimal weight: 0.0870 chunk 38 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 74 optimal weight: 7.9990 chunk 69 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 7 optimal weight: 0.2980 chunk 42 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 overall best weight: 0.5760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 5 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.129520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.096009 restraints weight = 8168.098| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 2.18 r_work: 0.3022 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.0797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6482 Z= 0.124 Angle : 0.533 6.442 8824 Z= 0.274 Chirality : 0.041 0.138 1018 Planarity : 0.004 0.044 1103 Dihedral : 4.403 24.281 884 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 4.27 % Allowed : 20.77 % Favored : 74.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.88 (0.30), residues: 822 helix: 1.41 (0.30), residues: 332 sheet: 1.20 (0.35), residues: 222 loop : -1.00 (0.38), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 16 TYR 0.009 0.001 TYR L 49 PHE 0.011 0.001 PHE L 87 TRP 0.009 0.001 TRP H 114 HIS 0.001 0.000 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 6478) covalent geometry : angle 0.53244 ( 8816) SS BOND : bond 0.00486 ( 4) SS BOND : angle 1.11434 ( 8) hydrogen bonds : bond 0.03698 ( 347) hydrogen bonds : angle 4.79324 ( 1041) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 67 time to evaluate : 0.263 Fit side-chains REVERT: L 6 GLN cc_start: 0.8538 (OUTLIER) cc_final: 0.8234 (tt0) REVERT: H 89 ASP cc_start: 0.8585 (t0) cc_final: 0.8259 (t0) outliers start: 30 outliers final: 20 residues processed: 96 average time/residue: 0.0777 time to fit residues: 10.3038 Evaluate side-chains 87 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 66 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 164 THR Chi-restraints excluded: chain L residue 176 SER Chi-restraints excluded: chain L residue 193 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain H residue 188 LEU Chi-restraints excluded: chain H residue 195 THR Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 217 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.8958 > 50: distance: 68 - 72: 3.064 distance: 72 - 73: 11.291 distance: 73 - 74: 19.036 distance: 73 - 76: 23.713 distance: 74 - 75: 24.134 distance: 74 - 80: 16.915 distance: 76 - 77: 9.504 distance: 77 - 78: 26.325 distance: 77 - 79: 7.664 distance: 80 - 81: 20.038 distance: 81 - 82: 33.567 distance: 81 - 84: 10.871 distance: 82 - 83: 40.566 distance: 82 - 86: 31.569 distance: 84 - 85: 39.279 distance: 86 - 87: 28.590 distance: 87 - 88: 13.988 distance: 87 - 90: 58.709 distance: 88 - 92: 36.254 distance: 90 - 91: 13.771 distance: 92 - 93: 39.003 distance: 93 - 94: 41.150 distance: 94 - 96: 28.164 distance: 96 - 97: 21.035 distance: 97 - 98: 30.086 distance: 97 - 100: 33.197 distance: 98 - 99: 18.386 distance: 98 - 103: 20.387 distance: 100 - 101: 56.848 distance: 100 - 102: 42.287 distance: 103 - 104: 35.787 distance: 103 - 179: 20.637 distance: 104 - 105: 49.282 distance: 104 - 107: 28.206 distance: 105 - 106: 25.140 distance: 105 - 113: 18.628 distance: 106 - 176: 31.613 distance: 107 - 108: 26.346 distance: 108 - 109: 18.769 distance: 108 - 110: 28.356 distance: 109 - 111: 28.994 distance: 110 - 112: 21.870 distance: 111 - 112: 27.905 distance: 113 - 114: 19.316 distance: 114 - 115: 42.491 distance: 114 - 117: 28.581 distance: 115 - 116: 35.737 distance: 115 - 120: 42.045 distance: 117 - 118: 24.384 distance: 117 - 119: 17.714 distance: 120 - 121: 21.489 distance: 121 - 122: 4.071 distance: 121 - 124: 29.762 distance: 122 - 123: 22.637 distance: 122 - 131: 17.099 distance: 124 - 125: 22.012 distance: 125 - 126: 31.848 distance: 125 - 127: 7.942 distance: 126 - 128: 19.152 distance: 127 - 129: 47.671 distance: 128 - 130: 35.955 distance: 129 - 130: 16.752 distance: 131 - 132: 27.055 distance: 131 - 137: 39.380 distance: 132 - 133: 30.741 distance: 132 - 135: 7.164 distance: 133 - 134: 23.795 distance: 133 - 138: 19.694 distance: 135 - 136: 49.267 distance: 136 - 137: 5.533 distance: 138 - 139: 7.157 distance: 139 - 140: 10.823 distance: 139 - 142: 15.423 distance: 140 - 141: 28.613 distance: 140 - 143: 6.154