Starting phenix.real_space_refine on Fri Aug 22 14:04:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9f6p_50237/08_2025/9f6p_50237.cif Found real_map, /net/cci-nas-00/data/ceres_data/9f6p_50237/08_2025/9f6p_50237.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9f6p_50237/08_2025/9f6p_50237.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9f6p_50237/08_2025/9f6p_50237.map" model { file = "/net/cci-nas-00/data/ceres_data/9f6p_50237/08_2025/9f6p_50237.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9f6p_50237/08_2025/9f6p_50237.cif" } resolution = 3.7 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= 0.001 sd= 0.030 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Mn 1 7.51 5 S 22 5.16 5 C 2460 2.51 5 N 606 2.21 5 O 631 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.00s 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: 3720 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3719 Classifications: {'peptide': 482} Link IDs: {'PTRANS': 19, 'TRANS': 462} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.13, per 1000 atoms: 0.30 Number of scatterers: 3720 At special positions: 0 Unit cell: (83.328, 69.006, 79.422, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Mn 1 24.99 S 22 16.00 O 631 8.00 N 606 7.00 C 2460 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 233 " - pdb=" SG CYS A 236 " distance=2.03 Simple disulfide: pdb=" SG CYS A 322 " - pdb=" SG CYS A 354 " distance=2.03 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: 0.33 Conformation dependent library (CDL) restraints added in 151.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 886 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 0 sheets defined 84.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing helix chain 'A' and resid 65 through 73 removed outlier: 3.913A pdb=" N SER A 69 " --> pdb=" O GLY A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 88 removed outlier: 3.918A pdb=" N ASP A 81 " --> pdb=" O ASN A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 118 Processing helix chain 'A' and resid 120 through 128 Processing helix chain 'A' and resid 130 through 164 removed outlier: 3.566A pdb=" N SER A 164 " --> pdb=" O PHE A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 188 removed outlier: 3.849A pdb=" N GLY A 173 " --> pdb=" O PRO A 169 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL A 174 " --> pdb=" O LEU A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 218 removed outlier: 3.627A pdb=" N ARG A 218 " --> pdb=" O TYR A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 230 Processing helix chain 'A' and resid 237 through 252 removed outlier: 4.224A pdb=" N ILE A 252 " --> pdb=" O VAL A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 266 removed outlier: 4.035A pdb=" N ILE A 257 " --> pdb=" O MET A 253 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N TYR A 258 " --> pdb=" O PRO A 254 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER A 266 " --> pdb=" O ALA A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 311 removed outlier: 4.347A pdb=" N ILE A 277 " --> pdb=" O ARG A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 325 Processing helix chain 'A' and resid 328 through 333 Processing helix chain 'A' and resid 344 through 357 Processing helix chain 'A' and resid 357 through 391 removed outlier: 4.293A pdb=" N LEU A 361 " --> pdb=" O GLY A 357 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N TYR A 362 " --> pdb=" O PRO A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 419 Proline residue: A 411 - end of helix Processing helix chain 'A' and resid 420 through 439 Processing helix chain 'A' and resid 439 through 451 Proline residue: A 445 - end of helix Processing helix chain 'A' and resid 462 through 488 Processing helix chain 'A' and resid 497 through 523 Processing helix chain 'A' and resid 533 through 538 removed outlier: 3.721A pdb=" N TYR A 537 " --> pdb=" O HIS A 533 " (cutoff:3.500A) 302 hydrogen bonds defined for protein. 906 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: 0.50 Time building geometry restraints manager: 0.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1151 1.34 - 1.46: 954 1.46 - 1.58: 1675 1.58 - 1.70: 0 1.70 - 1.82: 34 Bond restraints: 3814 Sorted by residual: bond pdb=" N MET A 253 " pdb=" CA MET A 253 " ideal model delta sigma weight residual 1.454 1.477 -0.023 1.30e-02 5.92e+03 3.21e+00 bond pdb=" N LEU A 437 " pdb=" CA LEU A 437 " ideal model delta sigma weight residual 1.459 1.479 -0.020 1.28e-02 6.10e+03 2.45e+00 bond pdb=" CA ARG A 218 " pdb=" CB ARG A 218 " ideal model delta sigma weight residual 1.522 1.532 -0.010 7.00e-03 2.04e+04 1.86e+00 bond pdb=" CB GLU A 268 " pdb=" CG GLU A 268 " ideal model delta sigma weight residual 1.520 1.556 -0.036 3.00e-02 1.11e+03 1.47e+00 bond pdb=" CB ARG A 193 " pdb=" CG ARG A 193 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.23e+00 ... (remaining 3809 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 5013 2.10 - 4.19: 143 4.19 - 6.29: 31 6.29 - 8.39: 9 8.39 - 10.48: 6 Bond angle restraints: 5202 Sorted by residual: angle pdb=" N LEU A 437 " pdb=" CA LEU A 437 " pdb=" CB LEU A 437 " ideal model delta sigma weight residual 110.28 104.86 5.42 1.55e+00 4.16e-01 1.22e+01 angle pdb=" CB MET A 68 " pdb=" CG MET A 68 " pdb=" SD MET A 68 " ideal model delta sigma weight residual 112.70 123.09 -10.39 3.00e+00 1.11e-01 1.20e+01 angle pdb=" CA GLN A 312 " pdb=" CB GLN A 312 " pdb=" CG GLN A 312 " ideal model delta sigma weight residual 114.10 120.97 -6.87 2.00e+00 2.50e-01 1.18e+01 angle pdb=" CA LYS A 91 " pdb=" CB LYS A 91 " pdb=" CG LYS A 91 " ideal model delta sigma weight residual 114.10 120.30 -6.20 2.00e+00 2.50e-01 9.60e+00 angle pdb=" CA LEU A 391 " pdb=" CB LEU A 391 " pdb=" CG LEU A 391 " ideal model delta sigma weight residual 116.30 126.78 -10.48 3.50e+00 8.16e-02 8.97e+00 ... (remaining 5197 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.84: 1790 15.84 - 31.68: 291 31.68 - 47.52: 90 47.52 - 63.36: 29 63.36 - 79.20: 4 Dihedral angle restraints: 2204 sinusoidal: 819 harmonic: 1385 Sorted by residual: dihedral pdb=" CB CYS A 322 " pdb=" SG CYS A 322 " pdb=" SG CYS A 354 " pdb=" CB CYS A 354 " ideal model delta sinusoidal sigma weight residual -86.00 -156.87 70.87 1 1.00e+01 1.00e-02 6.45e+01 dihedral pdb=" CA ALA A 342 " pdb=" C ALA A 342 " pdb=" N VAL A 343 " pdb=" CA VAL A 343 " ideal model delta harmonic sigma weight residual 180.00 -160.89 -19.11 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA TYR A 311 " pdb=" C TYR A 311 " pdb=" N GLN A 312 " pdb=" CA GLN A 312 " ideal model delta harmonic sigma weight residual -180.00 -161.61 -18.39 0 5.00e+00 4.00e-02 1.35e+01 ... (remaining 2201 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 509 0.062 - 0.124: 96 0.124 - 0.186: 8 0.186 - 0.247: 2 0.247 - 0.309: 1 Chirality restraints: 616 Sorted by residual: chirality pdb=" CG LEU A 102 " pdb=" CB LEU A 102 " pdb=" CD1 LEU A 102 " pdb=" CD2 LEU A 102 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.31 2.00e-01 2.50e+01 2.39e+00 chirality pdb=" CB VAL A 174 " pdb=" CA VAL A 174 " pdb=" CG1 VAL A 174 " pdb=" CG2 VAL A 174 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CB THR A 177 " pdb=" CA THR A 177 " pdb=" OG1 THR A 177 " pdb=" CG2 THR A 177 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 9.09e-01 ... (remaining 613 not shown) Planarity restraints: 643 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 311 " -0.016 2.00e-02 2.50e+03 1.31e-02 3.43e+00 pdb=" CG TYR A 311 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 TYR A 311 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR A 311 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR A 311 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR A 311 " -0.009 2.00e-02 2.50e+03 pdb=" CZ TYR A 311 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 311 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 270 " -0.008 2.00e-02 2.50e+03 1.65e-02 2.72e+00 pdb=" CG ASP A 270 " 0.029 2.00e-02 2.50e+03 pdb=" OD1 ASP A 270 " -0.010 2.00e-02 2.50e+03 pdb=" OD2 ASP A 270 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 230 " -0.026 5.00e-02 4.00e+02 3.98e-02 2.53e+00 pdb=" N PRO A 231 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 231 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 231 " -0.022 5.00e-02 4.00e+02 ... (remaining 640 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 46 2.65 - 3.21: 3781 3.21 - 3.78: 6236 3.78 - 4.34: 7513 4.34 - 4.90: 12437 Nonbonded interactions: 30013 Sorted by model distance: nonbonded pdb=" OD1 ASN A 77 " pdb="MN MN A 701 " model vdw 2.090 2.320 nonbonded pdb=" O SER A 374 " pdb=" OG1 THR A 378 " model vdw 2.263 3.040 nonbonded pdb=" O LYS A 131 " pdb=" OG1 THR A 135 " model vdw 2.332 3.040 nonbonded pdb=" O CYS A 518 " pdb=" ND1 HIS A 522 " model vdw 2.341 3.120 nonbonded pdb=" OG SER A 451 " pdb=" OD1 ASN A 461 " model vdw 2.351 3.040 ... (remaining 30008 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 0.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.050 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 5.840 Find NCS groups from input model: 0.010 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:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6919 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 0.038 3816 Z= 0.186 Angle : 0.931 10.484 5206 Z= 0.455 Chirality : 0.048 0.309 616 Planarity : 0.005 0.040 643 Dihedral : 18.008 79.197 1312 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 19.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.05 % Allowed : 44.10 % Favored : 53.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.39 (0.38), residues: 480 helix: 1.66 (0.26), residues: 377 sheet: None (None), residues: 0 loop : -1.89 (0.59), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 400 TYR 0.029 0.002 TYR A 311 PHE 0.024 0.002 PHE A 184 TRP 0.020 0.002 TRP A 138 HIS 0.003 0.001 HIS A 522 Details of bonding type rmsd covalent geometry : bond 0.00404 ( 3814) covalent geometry : angle 0.92868 ( 5202) SS BOND : bond 0.00168 ( 2) SS BOND : angle 2.48456 ( 4) hydrogen bonds : bond 0.09532 ( 302) hydrogen bonds : angle 5.50313 ( 906) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 149 time to evaluate : 0.083 Fit side-chains revert: symmetry clash REVERT: A 58 LEU cc_start: 0.2433 (OUTLIER) cc_final: 0.2194 (tp) REVERT: A 68 MET cc_start: 0.6634 (tpp) cc_final: 0.5464 (tpt) REVERT: A 135 THR cc_start: 0.9084 (m) cc_final: 0.8877 (t) REVERT: A 178 ILE cc_start: 0.8263 (tp) cc_final: 0.7995 (pt) REVERT: A 214 TYR cc_start: 0.7164 (t80) cc_final: 0.6904 (t80) REVERT: A 228 LEU cc_start: 0.8310 (tp) cc_final: 0.7999 (tt) REVERT: A 278 ARG cc_start: 0.7002 (tmt170) cc_final: 0.6615 (mtm-85) REVERT: A 287 GLU cc_start: 0.8032 (tt0) cc_final: 0.7327 (tm-30) REVERT: A 393 LEU cc_start: 0.8120 (tt) cc_final: 0.7906 (mt) REVERT: A 475 LEU cc_start: 0.8984 (tp) cc_final: 0.8659 (pp) REVERT: A 537 TYR cc_start: 0.8050 (m-10) cc_final: 0.7696 (m-10) outliers start: 8 outliers final: 4 residues processed: 153 average time/residue: 0.0523 time to fit residues: 10.1478 Evaluate side-chains 116 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 111 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 183 PHE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 487 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 62.6333 > 50: distance: 5 - 24: 4.695 distance: 11 - 29: 9.495 distance: 14 - 19: 11.994 distance: 15 - 40: 11.513 distance: 19 - 20: 8.053 distance: 20 - 21: 11.648 distance: 20 - 23: 14.670 distance: 21 - 22: 13.280 distance: 21 - 24: 15.083 distance: 22 - 48: 6.764 distance: 24 - 25: 3.992 distance: 25 - 26: 10.521 distance: 25 - 28: 10.532 distance: 26 - 27: 9.256 distance: 26 - 29: 9.902 distance: 27 - 56: 8.282 distance: 29 - 30: 10.808 distance: 30 - 31: 15.647 distance: 30 - 33: 10.908 distance: 31 - 32: 14.198 distance: 31 - 40: 5.157 distance: 32 - 62: 9.317 distance: 33 - 34: 6.647 distance: 34 - 36: 15.162 distance: 35 - 37: 6.214 distance: 36 - 38: 7.396 distance: 37 - 39: 15.445 distance: 40 - 41: 16.793 distance: 41 - 42: 10.430 distance: 41 - 44: 12.843 distance: 42 - 43: 6.414 distance: 42 - 48: 8.519 distance: 43 - 67: 11.537 distance: 44 - 45: 22.089 distance: 45 - 46: 15.135 distance: 45 - 47: 16.216 distance: 48 - 49: 11.213 distance: 49 - 50: 11.031 distance: 49 - 52: 11.810 distance: 50 - 51: 18.484 distance: 50 - 56: 7.442 distance: 51 - 75: 26.899 distance: 52 - 53: 20.530 distance: 52 - 54: 15.381 distance: 53 - 55: 19.674 distance: 56 - 57: 9.926 distance: 57 - 58: 5.278 distance: 57 - 60: 10.941 distance: 58 - 59: 13.769 distance: 58 - 62: 6.116 distance: 60 - 61: 31.685 distance: 61 - 128: 18.556 distance: 62 - 63: 8.365 distance: 63 - 64: 4.420 distance: 63 - 66: 11.108 distance: 64 - 65: 19.277 distance: 64 - 67: 10.501 distance: 67 - 68: 4.489 distance: 68 - 69: 16.627 distance: 68 - 71: 24.759 distance: 69 - 70: 25.178 distance: 69 - 75: 7.394 distance: 71 - 72: 17.988 distance: 72 - 73: 14.619 distance: 72 - 74: 18.203 distance: 75 - 76: 30.932 distance: 76 - 77: 21.659 distance: 76 - 79: 31.537 distance: 77 - 78: 9.762 distance: 77 - 81: 31.951 distance: 79 - 80: 37.385 distance: 81 - 82: 12.631 distance: 82 - 83: 17.884 distance: 82 - 85: 19.026 distance: 83 - 84: 23.535 distance: 83 - 87: 20.443 distance: 85 - 86: 10.944