Starting phenix.real_space_refine on Fri Aug 22 19:59:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gi8_40062/08_2025/8gi8_40062.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gi8_40062/08_2025/8gi8_40062.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gi8_40062/08_2025/8gi8_40062.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gi8_40062/08_2025/8gi8_40062.map" model { file = "/net/cci-nas-00/data/ceres_data/8gi8_40062/08_2025/8gi8_40062.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gi8_40062/08_2025/8gi8_40062.cif" } resolution = 2.88 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= 0.179 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 15 5.49 5 S 60 5.16 5 Na 3 4.78 5 C 4884 2.51 5 N 906 2.21 5 O 1122 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 6990 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1955 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 12, 'TRANS': 227} Chain: "A" Number of atoms: 375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 375 Unusual residues: {' NA': 1, 'CLR': 3, 'PEE': 5, 'RET': 1} Classifications: {'undetermined': 10, 'water': 15} Link IDs: {None: 24} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "C" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Restraints were copied for chains: B, C Time building chain proxies: 1.13, per 1000 atoms: 0.16 Number of scatterers: 6990 At special positions: 0 Unit cell: (79.31, 77.25, 76.22, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 60 16.00 P 15 15.00 Na 3 11.00 O 1122 8.00 N 906 7.00 C 4884 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=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.45 Conformation dependent library (CDL) restraints added in 276.2 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1332 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 0 sheets defined 77.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'A' and resid 21 through 48 Processing helix chain 'A' and resid 68 through 91 removed outlier: 3.608A pdb=" N CYS A 74 " --> pdb=" O SER A 70 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY A 91 " --> pdb=" O ASP A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 108 Processing helix chain 'A' and resid 109 through 121 Processing helix chain 'A' and resid 125 through 145 Processing helix chain 'A' and resid 150 through 178 Proline residue: A 164 - end of helix removed outlier: 3.576A pdb=" N LEU A 178 " --> pdb=" O LYS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 199 removed outlier: 4.577A pdb=" N TRP A 187 " --> pdb=" O LYS A 183 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU A 188 " --> pdb=" O CYS A 184 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TRP A 190 " --> pdb=" O ARG A 186 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TRP A 199 " --> pdb=" O PHE A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 209 removed outlier: 3.619A pdb=" N ILE A 204 " --> pdb=" O PRO A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 233 Processing helix chain 'A' and resid 233 through 252 removed outlier: 3.538A pdb=" N THR A 251 " --> pdb=" O LEU A 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 48 Processing helix chain 'B' and resid 68 through 91 removed outlier: 3.608A pdb=" N CYS B 74 " --> pdb=" O SER B 70 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY B 91 " --> pdb=" O ASP B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 108 Processing helix chain 'B' and resid 109 through 121 Processing helix chain 'B' and resid 125 through 145 Processing helix chain 'B' and resid 150 through 178 Proline residue: B 164 - end of helix removed outlier: 3.576A pdb=" N LEU B 178 " --> pdb=" O LYS B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 199 removed outlier: 4.577A pdb=" N TRP B 187 " --> pdb=" O LYS B 183 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU B 188 " --> pdb=" O CYS B 184 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TRP B 190 " --> pdb=" O ARG B 186 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TRP B 199 " --> pdb=" O PHE B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 209 removed outlier: 3.619A pdb=" N ILE B 204 " --> pdb=" O PRO B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 233 Processing helix chain 'B' and resid 233 through 252 removed outlier: 3.538A pdb=" N THR B 251 " --> pdb=" O LEU B 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 48 Processing helix chain 'C' and resid 68 through 91 removed outlier: 3.608A pdb=" N CYS C 74 " --> pdb=" O SER C 70 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY C 91 " --> pdb=" O ASP C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 108 Processing helix chain 'C' and resid 109 through 121 Processing helix chain 'C' and resid 125 through 145 Processing helix chain 'C' and resid 150 through 178 Proline residue: C 164 - end of helix removed outlier: 3.576A pdb=" N LEU C 178 " --> pdb=" O LYS C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 199 removed outlier: 4.577A pdb=" N TRP C 187 " --> pdb=" O LYS C 183 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU C 188 " --> pdb=" O CYS C 184 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TRP C 190 " --> pdb=" O ARG C 186 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TRP C 199 " --> pdb=" O PHE C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 209 removed outlier: 3.619A pdb=" N ILE C 204 " --> pdb=" O PRO C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 233 Processing helix chain 'C' and resid 233 through 252 removed outlier: 3.538A pdb=" N THR C 251 " --> pdb=" O LEU C 247 " (cutoff:3.500A) 405 hydrogen bonds defined for protein. 1197 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: 0.78 Time building geometry restraints manager: 0.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1188 1.33 - 1.45: 1847 1.45 - 1.57: 3988 1.57 - 1.69: 60 1.69 - 1.81: 96 Bond restraints: 7179 Sorted by residual: bond pdb=" O4P PEE B 307 " pdb=" P PEE B 307 " ideal model delta sigma weight residual 1.653 1.778 -0.125 2.00e-02 2.50e+03 3.90e+01 bond pdb=" O4P PEE A 307 " pdb=" P PEE A 307 " ideal model delta sigma weight residual 1.653 1.777 -0.124 2.00e-02 2.50e+03 3.85e+01 bond pdb=" O4P PEE C 307 " pdb=" P PEE C 307 " ideal model delta sigma weight residual 1.653 1.777 -0.124 2.00e-02 2.50e+03 3.82e+01 bond pdb=" O4P PEE C 306 " pdb=" P PEE C 306 " ideal model delta sigma weight residual 1.653 1.776 -0.123 2.00e-02 2.50e+03 3.79e+01 bond pdb=" O4P PEE A 306 " pdb=" P PEE A 306 " ideal model delta sigma weight residual 1.653 1.775 -0.122 2.00e-02 2.50e+03 3.75e+01 ... (remaining 7174 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.79: 9275 2.79 - 5.59: 251 5.59 - 8.38: 92 8.38 - 11.17: 0 11.17 - 13.96: 15 Bond angle restraints: 9633 Sorted by residual: angle pdb=" O1P PEE B 308 " pdb=" P PEE B 308 " pdb=" O2P PEE B 308 " ideal model delta sigma weight residual 119.43 133.39 -13.96 3.00e+00 1.11e-01 2.17e+01 angle pdb=" O1P PEE C 308 " pdb=" P PEE C 308 " pdb=" O2P PEE C 308 " ideal model delta sigma weight residual 119.43 133.37 -13.94 3.00e+00 1.11e-01 2.16e+01 angle pdb=" O1P PEE A 308 " pdb=" P PEE A 308 " pdb=" O2P PEE A 308 " ideal model delta sigma weight residual 119.43 133.37 -13.94 3.00e+00 1.11e-01 2.16e+01 angle pdb=" O1P PEE B 307 " pdb=" P PEE B 307 " pdb=" O2P PEE B 307 " ideal model delta sigma weight residual 119.43 133.35 -13.92 3.00e+00 1.11e-01 2.15e+01 angle pdb=" O1P PEE A 307 " pdb=" P PEE A 307 " pdb=" O2P PEE A 307 " ideal model delta sigma weight residual 119.43 133.31 -13.88 3.00e+00 1.11e-01 2.14e+01 ... (remaining 9628 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.37: 4377 34.37 - 68.74: 219 68.74 - 103.11: 30 103.11 - 137.48: 27 137.48 - 171.85: 33 Dihedral angle restraints: 4686 sinusoidal: 2592 harmonic: 2094 Sorted by residual: dihedral pdb=" N PEE C 306 " pdb=" C4 PEE C 306 " pdb=" C5 PEE C 306 " pdb=" O4P PEE C 306 " ideal model delta sinusoidal sigma weight residual -56.97 114.88 -171.85 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" N PEE A 306 " pdb=" C4 PEE A 306 " pdb=" C5 PEE A 306 " pdb=" O4P PEE A 306 " ideal model delta sinusoidal sigma weight residual -56.97 114.86 -171.83 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" N PEE B 306 " pdb=" C4 PEE B 306 " pdb=" C5 PEE B 306 " pdb=" O4P PEE B 306 " ideal model delta sinusoidal sigma weight residual -56.97 114.83 -171.80 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 4683 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 859 0.085 - 0.170: 50 0.170 - 0.256: 9 0.256 - 0.341: 18 0.341 - 0.426: 24 Chirality restraints: 960 Sorted by residual: chirality pdb=" C2 PEE C 307 " pdb=" C1 PEE C 307 " pdb=" C3 PEE C 307 " pdb=" O2 PEE C 307 " both_signs ideal model delta sigma weight residual False -2.33 -2.75 0.43 2.00e-01 2.50e+01 4.54e+00 chirality pdb=" C2 PEE B 307 " pdb=" C1 PEE B 307 " pdb=" C3 PEE B 307 " pdb=" O2 PEE B 307 " both_signs ideal model delta sigma weight residual False -2.33 -2.75 0.43 2.00e-01 2.50e+01 4.52e+00 chirality pdb=" C2 PEE A 307 " pdb=" C1 PEE A 307 " pdb=" C3 PEE A 307 " pdb=" O2 PEE A 307 " both_signs ideal model delta sigma weight residual False -2.33 -2.75 0.42 2.00e-01 2.50e+01 4.51e+00 ... (remaining 957 not shown) Planarity restraints: 1050 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 94 " 0.016 5.00e-02 4.00e+02 2.40e-02 9.24e-01 pdb=" N PRO C 95 " -0.042 5.00e-02 4.00e+02 pdb=" CA PRO C 95 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO C 95 " 0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 94 " 0.016 5.00e-02 4.00e+02 2.40e-02 9.23e-01 pdb=" N PRO A 95 " -0.042 5.00e-02 4.00e+02 pdb=" CA PRO A 95 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 95 " 0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 94 " 0.016 5.00e-02 4.00e+02 2.39e-02 9.17e-01 pdb=" N PRO B 95 " -0.041 5.00e-02 4.00e+02 pdb=" CA PRO B 95 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO B 95 " 0.014 5.00e-02 4.00e+02 ... (remaining 1047 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 60 2.53 - 3.12: 5155 3.12 - 3.71: 10808 3.71 - 4.31: 16937 4.31 - 4.90: 28257 Nonbonded interactions: 61217 Sorted by model distance: nonbonded pdb=" OE2 GLU B 65 " pdb=" N LYS C 126 " model vdw 1.935 3.120 nonbonded pdb=" OE2 GLU A 65 " pdb=" N LYS B 126 " model vdw 1.935 3.120 nonbonded pdb=" N LYS A 126 " pdb=" OE2 GLU C 65 " model vdw 1.935 3.120 nonbonded pdb=" OH TYR A 150 " pdb=" O5 PEE A 308 " model vdw 2.223 3.040 nonbonded pdb=" OH TYR B 150 " pdb=" O5 PEE B 308 " model vdw 2.223 3.040 ... (remaining 61212 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.120 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.150 Find NCS groups from input model: 0.030 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:5.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 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 : 0.012 0.362 7185 Z= 0.890 Angle : 1.162 13.963 9633 Z= 0.413 Chirality : 0.088 0.426 960 Planarity : 0.003 0.024 1050 Dihedral : 26.084 171.850 3354 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % 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: 1.50 (0.34), residues: 714 helix: 1.77 (0.24), residues: 519 sheet: None (None), residues: 0 loop : -1.14 (0.50), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 244 TYR 0.008 0.001 TYR A 81 PHE 0.007 0.001 PHE A 152 TRP 0.006 0.001 TRP A 42 HIS 0.002 0.001 HIS A 225 Details of bonding type rmsd covalent geometry : bond 0.00995 ( 7179) covalent geometry : angle 1.16208 ( 9633) hydrogen bonds : bond 0.22031 ( 405) hydrogen bonds : angle 7.17232 ( 1197) Misc. bond : bond 0.25634 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.138 Fit side-chains REVERT: A 21 ASP cc_start: 0.7632 (t70) cc_final: 0.6608 (t70) REVERT: A 81 TYR cc_start: 0.8374 (m-80) cc_final: 0.8137 (m-80) REVERT: A 108 PHE cc_start: 0.8215 (m-80) cc_final: 0.7763 (m-80) REVERT: A 174 LYS cc_start: 0.8304 (mtmm) cc_final: 0.8057 (mtmt) REVERT: A 185 GLN cc_start: 0.8137 (tt0) cc_final: 0.7898 (tt0) REVERT: B 21 ASP cc_start: 0.7347 (t70) cc_final: 0.6580 (t70) REVERT: B 81 TYR cc_start: 0.8411 (m-80) cc_final: 0.8178 (m-80) REVERT: B 106 TYR cc_start: 0.8162 (m-80) cc_final: 0.7787 (m-80) REVERT: B 108 PHE cc_start: 0.8300 (m-80) cc_final: 0.7966 (m-80) REVERT: B 185 GLN cc_start: 0.8117 (tt0) cc_final: 0.7858 (tt0) REVERT: C 21 ASP cc_start: 0.7741 (t70) cc_final: 0.6728 (t70) REVERT: C 106 TYR cc_start: 0.8130 (m-80) cc_final: 0.7734 (m-80) REVERT: C 186 ARG cc_start: 0.7109 (ttt90) cc_final: 0.6858 (ttt90) outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.3647 time to fit residues: 48.2352 Evaluate side-chains 113 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 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-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: 72.511 > 50: distance: 11 - 18: 3.031 distance: 37 - 46: 3.096 distance: 58 - 80: 31.573 distance: 62 - 85: 29.284 distance: 66 - 93: 28.512 distance: 70 - 80: 28.278 distance: 71 - 97: 26.365 distance: 80 - 81: 45.882 distance: 81 - 82: 30.983 distance: 81 - 84: 4.159 distance: 82 - 83: 9.137 distance: 82 - 85: 14.406 distance: 83 - 103: 59.271 distance: 85 - 86: 21.934 distance: 86 - 87: 27.407 distance: 86 - 89: 6.760 distance: 87 - 88: 3.181 distance: 87 - 93: 35.738 distance: 88 - 109: 41.431 distance: 89 - 90: 40.847 distance: 90 - 91: 58.469 distance: 90 - 92: 17.684 distance: 93 - 94: 16.152 distance: 94 - 95: 7.222 distance: 95 - 96: 24.816 distance: 95 - 97: 3.954 distance: 96 - 123: 33.646 distance: 97 - 98: 32.014 distance: 98 - 99: 40.776 distance: 98 - 101: 33.438 distance: 99 - 100: 48.816 distance: 99 - 103: 10.329 distance: 100 - 134: 57.177 distance: 101 - 102: 37.146 distance: 103 - 104: 47.764 distance: 104 - 105: 26.901 distance: 104 - 107: 46.996 distance: 107 - 108: 69.675 distance: 109 - 110: 4.320 distance: 110 - 111: 44.660 distance: 110 - 113: 29.416 distance: 111 - 112: 25.954 distance: 111 - 123: 41.542 distance: 113 - 114: 51.669 distance: 114 - 115: 48.388 distance: 115 - 117: 39.478 distance: 116 - 119: 38.778 distance: 117 - 118: 19.150 distance: 119 - 121: 41.045 distance: 123 - 124: 38.937 distance: 124 - 125: 9.802 distance: 125 - 126: 29.642 distance: 125 - 134: 9.154 distance: 128 - 129: 56.074 distance: 129 - 131: 3.749 distance: 131 - 133: 39.568 distance: 132 - 133: 40.702 distance: 134 - 135: 56.362 distance: 135 - 136: 40.412 distance: 135 - 138: 57.345 distance: 136 - 141: 39.775 distance: 137 - 164: 34.489 distance: 138 - 140: 40.976 distance: 141 - 142: 37.065 distance: 141 - 147: 56.584 distance: 142 - 143: 3.871 distance: 142 - 145: 39.958 distance: 143 - 144: 56.150 distance: 144 - 171: 37.419 distance: 145 - 146: 70.299 distance: 146 - 147: 41.236 distance: 148 - 149: 56.196 distance: 149 - 150: 8.710 distance: 149 - 152: 35.843 distance: 150 - 151: 7.525 distance: 150 - 159: 31.184 distance: 151 - 176: 37.140 distance: 152 - 153: 10.215 distance: 153 - 154: 37.554 distance: 153 - 155: 34.710 distance: 154 - 156: 38.066 distance: 155 - 157: 12.695 distance: 156 - 158: 40.746