Starting phenix.real_space_refine on Thu Jul 2 00:49:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vmd_65185/07_2026/9vmd_65185.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vmd_65185/07_2026/9vmd_65185.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9vmd_65185/07_2026/9vmd_65185.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vmd_65185/07_2026/9vmd_65185.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vmd_65185/07_2026/9vmd_65185.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vmd_65185/07_2026/9vmd_65185.map" } resolution = 4.38 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 75 5.49 5 S 15 5.16 5 C 2692 2.51 5 N 816 2.21 5 O 1145 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 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: 4743 Number of models: 1 Model: "" Number of chains: 4 Chain: "O" Number of atoms: 1391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1391 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 5, 'TRANS': 174} Chain: "P" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 973 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 2, 'TRANS': 124} Chain: "Q" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 792 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "R" Number of atoms: 1587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1587 Classifications: {'RNA': 75} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 5, 'rna3p_pur': 30, 'rna3p_pyr': 36} Link IDs: {'rna2p': 8, 'rna3p': 66} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 0.98, per 1000 atoms: 0.21 Number of scatterers: 4743 At special positions: 0 Unit cell: (76.8, 87.36, 96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 15 16.00 P 75 15.00 O 1145 8.00 N 816 7.00 C 2692 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: 0.40 Conformation dependent library (CDL) restraints added in 78.9 milliseconds 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 734 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 8 sheets defined 8.9% alpha, 44.2% beta 26 base pairs and 46 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'O' and resid 3 through 14 Processing helix chain 'O' and resid 38 through 42 Processing helix chain 'O' and resid 86 through 90 removed outlier: 3.881A pdb=" N ILE O 90 " --> pdb=" O ARG O 87 " (cutoff:3.500A) Processing helix chain 'P' and resid 89 through 93 removed outlier: 3.791A pdb=" N THR P 93 " --> pdb=" O ALA P 90 " (cutoff:3.500A) Processing helix chain 'Q' and resid 26 through 30 removed outlier: 3.837A pdb=" N ASP Q 29 " --> pdb=" O LYS Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 78 through 82 removed outlier: 4.019A pdb=" N GLU Q 82 " --> pdb=" O ALA Q 79 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'O' and resid 15 through 20 removed outlier: 6.956A pdb=" N VAL O 34 " --> pdb=" O ILE O 30 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE O 68 " --> pdb=" O ASP O 64 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU O 70 " --> pdb=" O LEU O 62 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N LEU O 62 " --> pdb=" O LEU O 70 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N LEU O 72 " --> pdb=" O TYR O 60 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N TYR O 60 " --> pdb=" O LEU O 72 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N VAL O 74 " --> pdb=" O ASP O 58 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ASP O 58 " --> pdb=" O VAL O 74 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N THR O 76 " --> pdb=" O VAL O 56 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N VAL O 56 " --> pdb=" O THR O 76 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'O' and resid 119 through 120 removed outlier: 3.747A pdb=" N THR O 119 " --> pdb=" O ARG O 136 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N ALA O 171 " --> pdb=" O HIS O 160 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N HIS O 160 " --> pdb=" O ALA O 171 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N ILE O 156 " --> pdb=" O ALA O 152 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ALA O 152 " --> pdb=" O ILE O 156 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLY O 158 " --> pdb=" O LEU O 150 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N SER O 105 " --> pdb=" O THR O 109 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N THR O 109 " --> pdb=" O SER O 105 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'O' and resid 123 through 126 removed outlier: 3.752A pdb=" N ILE O 124 " --> pdb=" O THR O 131 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR O 131 " --> pdb=" O ILE O 124 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'P' and resid 5 through 10 Processing sheet with id=AA5, first strand: chain 'P' and resid 12 through 14 removed outlier: 3.660A pdb=" N GLY P 12 " --> pdb=" O THR P 123 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR P 125 " --> pdb=" O GLY P 12 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N MET P 36 " --> pdb=" O VAL P 52 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N VAL P 52 " --> pdb=" O MET P 36 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N TRP P 38 " --> pdb=" O VAL P 50 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'Q' and resid 4 through 5 Processing sheet with id=AA7, first strand: chain 'Q' and resid 9 through 11 removed outlier: 3.682A pdb=" N THR Q 104 " --> pdb=" O VAL Q 10 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR Q 31 " --> pdb=" O TRP Q 90 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N TRP Q 34 " --> pdb=" O VAL Q 46 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'Q' and resid 9 through 11 removed outlier: 3.682A pdb=" N THR Q 104 " --> pdb=" O VAL Q 10 " (cutoff:3.500A) 122 hydrogen bonds defined for protein. 297 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 67 hydrogen bonds 122 hydrogen bond angles 0 basepair planarities 26 basepair parallelities 46 stacking parallelities Total time for adding SS restraints: 0.48 Time building geometry restraints manager: 0.50 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: 1237 1.34 - 1.46: 1540 1.46 - 1.58: 2040 1.58 - 1.70: 148 1.70 - 1.82: 22 Bond restraints: 4987 Sorted by residual: bond pdb=" C VAL Q 3 " pdb=" O VAL Q 3 " ideal model delta sigma weight residual 1.236 1.275 -0.039 1.04e-02 9.25e+03 1.41e+01 bond pdb=" CA PRO Q 7 " pdb=" C PRO Q 7 " ideal model delta sigma weight residual 1.514 1.495 0.020 5.50e-03 3.31e+04 1.29e+01 bond pdb=" C TYR Q 2 " pdb=" O TYR Q 2 " ideal model delta sigma weight residual 1.234 1.278 -0.044 1.27e-02 6.20e+03 1.19e+01 bond pdb=" CA SER Q 11 " pdb=" CB SER Q 11 " ideal model delta sigma weight residual 1.534 1.482 0.052 1.76e-02 3.23e+03 8.62e+00 bond pdb=" N GLN P 8 " pdb=" CA GLN P 8 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.18e-02 7.18e+03 8.31e+00 ... (remaining 4982 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 6563 2.08 - 4.16: 426 4.16 - 6.24: 109 6.24 - 8.32: 6 8.32 - 10.40: 2 Bond angle restraints: 7106 Sorted by residual: angle pdb=" N TYR P 97 " pdb=" CA TYR P 97 " pdb=" C TYR P 97 " ideal model delta sigma weight residual 110.42 116.35 -5.93 1.55e+00 4.16e-01 1.46e+01 angle pdb=" O3' A R 45 " pdb=" P G R 46 " pdb=" O5' G R 46 " ideal model delta sigma weight residual 104.00 109.32 -5.32 1.50e+00 4.44e-01 1.26e+01 angle pdb=" N TYR P 96 " pdb=" CA TYR P 96 " pdb=" C TYR P 96 " ideal model delta sigma weight residual 108.90 114.59 -5.69 1.63e+00 3.76e-01 1.22e+01 angle pdb=" CB MET Q 80 " pdb=" CG MET Q 80 " pdb=" SD MET Q 80 " ideal model delta sigma weight residual 112.70 123.10 -10.40 3.00e+00 1.11e-01 1.20e+01 angle pdb=" N TYR P 97 " pdb=" CA TYR P 97 " pdb=" CB TYR P 97 " ideal model delta sigma weight residual 110.56 105.25 5.31 1.56e+00 4.11e-01 1.16e+01 ... (remaining 7101 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 2431 17.96 - 35.91: 352 35.91 - 53.87: 142 53.87 - 71.82: 117 71.82 - 89.78: 29 Dihedral angle restraints: 3071 sinusoidal: 1907 harmonic: 1164 Sorted by residual: dihedral pdb=" C3' U R 38 " pdb=" C4' U R 38 " pdb=" O4' U R 38 " pdb=" C1' U R 38 " ideal model delta sinusoidal sigma weight residual -2.00 -26.68 24.68 1 8.00e+00 1.56e-02 1.37e+01 dihedral pdb=" C4' U R 38 " pdb=" O4' U R 38 " pdb=" C1' U R 38 " pdb=" C2' U R 38 " ideal model delta sinusoidal sigma weight residual -21.00 2.95 -23.95 1 8.00e+00 1.56e-02 1.29e+01 dihedral pdb=" C4' C R 7 " pdb=" O4' C R 7 " pdb=" C1' C R 7 " pdb=" C2' C R 7 " ideal model delta sinusoidal sigma weight residual 3.00 -20.91 23.91 1 8.00e+00 1.56e-02 1.29e+01 ... (remaining 3068 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.116: 676 0.116 - 0.231: 135 0.231 - 0.346: 4 0.346 - 0.462: 29 0.462 - 0.577: 16 Chirality restraints: 860 Sorted by residual: chirality pdb=" P C R 25 " pdb=" OP1 C R 25 " pdb=" OP2 C R 25 " pdb=" O5' C R 25 " both_signs ideal model delta sigma weight residual True 2.41 -2.99 -0.58 2.00e-01 2.50e+01 8.34e+00 chirality pdb=" P G R 1 " pdb=" OP1 G R 1 " pdb=" OP2 G R 1 " pdb=" O5' G R 1 " both_signs ideal model delta sigma weight residual True 2.41 -2.98 -0.57 2.00e-01 2.50e+01 8.16e+00 chirality pdb=" P U R 42 " pdb=" OP1 U R 42 " pdb=" OP2 U R 42 " pdb=" O5' U R 42 " both_signs ideal model delta sigma weight residual True 2.41 -2.94 -0.53 2.00e-01 2.50e+01 6.91e+00 ... (remaining 857 not shown) Planarity restraints: 635 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE O 37 " -0.034 5.00e-02 4.00e+02 5.20e-02 4.32e+00 pdb=" N PRO O 38 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO O 38 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO O 38 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG O 79 " -0.161 9.50e-02 1.11e+02 7.21e-02 3.19e+00 pdb=" NE ARG O 79 " 0.010 2.00e-02 2.50e+03 pdb=" CZ ARG O 79 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG O 79 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG O 79 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU P 7 " -0.008 2.00e-02 2.50e+03 1.52e-02 2.32e+00 pdb=" C LEU P 7 " 0.026 2.00e-02 2.50e+03 pdb=" O LEU P 7 " -0.010 2.00e-02 2.50e+03 pdb=" N GLN P 8 " -0.009 2.00e-02 2.50e+03 ... (remaining 632 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 31 2.54 - 3.13: 3425 3.13 - 3.72: 8029 3.72 - 4.31: 10879 4.31 - 4.90: 16137 Nonbonded interactions: 38501 Sorted by model distance: nonbonded pdb=" OD1 ASP O 64 " pdb=" CD PRO O 65 " model vdw 1.946 3.440 nonbonded pdb=" O ASP O 93 " pdb=" OD1 ASP O 93 " model vdw 2.202 3.040 nonbonded pdb=" OG1 THR O 26 " pdb=" OG SER O 105 " model vdw 2.241 3.040 nonbonded pdb=" OG SER P 19 " pdb=" OE1 GLN P 84 " model vdw 2.249 3.040 nonbonded pdb=" OD2 ASP P 75 " pdb=" NZ LYS P 78 " model vdw 2.257 3.120 ... (remaining 38496 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.290 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: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.410 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4018 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 : 0.008 0.052 4987 Z= 0.499 Angle : 1.163 10.396 7106 Z= 0.663 Chirality : 0.133 0.577 860 Planarity : 0.005 0.072 635 Dihedral : 22.707 89.776 2337 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 0.00 % Allowed : 25.22 % Favored : 74.78 % 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: -0.35 (0.44), residues: 408 helix: 0.39 (1.52), residues: 12 sheet: 0.04 (0.42), residues: 171 loop : -0.40 (0.43), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG O 84 TYR 0.022 0.002 TYR O 60 PHE 0.008 0.001 PHE O 178 TRP 0.009 0.002 TRP Q 90 HIS 0.006 0.001 HIS O 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00797 / 0.50 ( 4987) covalent geometry : angle 1.16269 / 0.66 ( 7106) hydrogen bonds : bond 0.16790 / 10.59 ( 186) hydrogen bonds : angle 8.42412 / 6.57 ( 419) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 110 ASN cc_start: 0.7303 (m110) cc_final: 0.6339 (m-40) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.0887 time to fit residues: 6.8684 Evaluate side-chains 27 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.3272 > 50: distance: 5 - 9: 28.566 distance: 9 - 10: 13.582 distance: 9 - 120: 31.184 distance: 10 - 11: 27.178 distance: 10 - 13: 21.785 distance: 11 - 12: 10.808 distance: 11 - 16: 33.933 distance: 13 - 14: 56.173 distance: 13 - 15: 26.831 distance: 16 - 17: 21.866 distance: 17 - 18: 48.443 distance: 17 - 20: 32.613 distance: 18 - 19: 21.017 distance: 18 - 22: 41.746 distance: 20 - 21: 7.245 distance: 22 - 23: 7.257 distance: 23 - 26: 33.086 distance: 24 - 25: 28.196 distance: 24 - 29: 46.330 distance: 29 - 30: 10.564 distance: 30 - 31: 42.408 distance: 30 - 33: 7.425 distance: 31 - 32: 36.886 distance: 31 - 35: 47.609 distance: 33 - 34: 31.649 distance: 35 - 36: 36.920 distance: 35 - 41: 8.430 distance: 36 - 37: 23.674 distance: 36 - 39: 38.782 distance: 37 - 42: 13.238 distance: 39 - 40: 42.501 distance: 40 - 41: 46.258 distance: 42 - 43: 11.284 distance: 43 - 44: 20.601 distance: 44 - 45: 5.516 distance: 44 - 46: 40.411 distance: 47 - 48: 38.878 distance: 47 - 50: 14.270 distance: 48 - 49: 36.812 distance: 50 - 51: 35.304 distance: 51 - 52: 40.708 distance: 52 - 53: 37.114 distance: 52 - 54: 12.953 distance: 56 - 59: 47.825 distance: 57 - 62: 41.612 distance: 59 - 60: 22.385 distance: 59 - 61: 31.285 distance: 62 - 63: 39.630 distance: 62 - 99: 32.166 distance: 63 - 64: 9.992 distance: 63 - 66: 39.174 distance: 64 - 65: 18.938 distance: 64 - 67: 7.239 distance: 65 - 96: 31.016 distance: 68 - 69: 12.462 distance: 69 - 73: 25.683 distance: 71 - 72: 36.636 distance: 73 - 88: 3.083