Starting phenix.real_space_refine on Tue Feb 3 14:31:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lwo_63452/02_2026/9lwo_63452_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lwo_63452/02_2026/9lwo_63452.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9lwo_63452/02_2026/9lwo_63452_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lwo_63452/02_2026/9lwo_63452_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lwo_63452/02_2026/9lwo_63452.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lwo_63452/02_2026/9lwo_63452.map" } resolution = 4.77 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= 0.020 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 22 5.16 5 C 2396 2.51 5 N 634 2.21 5 O 632 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-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3684 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1565 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 2, 'TRANS': 180} Chain: "B" Number of atoms: 1468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1468 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 3, 'TRANS': 175} Chain: "C" Number of atoms: 651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 651 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Time building chain proxies: 0.86, per 1000 atoms: 0.23 Number of scatterers: 3684 At special positions: 0 Unit cell: (78.264, 89.134, 93.482, 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 22 16.00 O 632 8.00 N 634 7.00 C 2396 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: 0.27 Conformation dependent library (CDL) restraints added in 126.1 milliseconds 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 842 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 0 sheets defined 70.7% 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 8 through 12 removed outlier: 3.635A pdb=" N LEU A 12 " --> pdb=" O LEU A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 37 removed outlier: 3.639A pdb=" N ASP A 37 " --> pdb=" O PHE A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 57 Processing helix chain 'A' and resid 60 through 71 Processing helix chain 'A' and resid 80 through 95 removed outlier: 4.032A pdb=" N PHE A 84 " --> pdb=" O GLY A 80 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N GLN A 95 " --> pdb=" O LEU A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 103 Processing helix chain 'A' and resid 106 through 115 Processing helix chain 'A' and resid 123 through 128 removed outlier: 3.954A pdb=" N PHE A 127 " --> pdb=" O GLY A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 148 Processing helix chain 'A' and resid 157 through 168 Processing helix chain 'A' and resid 170 through 182 removed outlier: 4.328A pdb=" N ARG A 182 " --> pdb=" O ARG A 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 73 Processing helix chain 'B' and resid 78 through 97 removed outlier: 4.495A pdb=" N ARG B 82 " --> pdb=" O SER B 78 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY B 97 " --> pdb=" O SER B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 104 removed outlier: 3.544A pdb=" N ALA B 101 " --> pdb=" O GLY B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 115 removed outlier: 4.348A pdb=" N VAL B 111 " --> pdb=" O TYR B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 138 removed outlier: 3.783A pdb=" N LYS B 126 " --> pdb=" O SER B 122 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N TYR B 138 " --> pdb=" O ALA B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 147 Processing helix chain 'B' and resid 152 through 161 removed outlier: 3.866A pdb=" N GLU B 161 " --> pdb=" O ILE B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 188 removed outlier: 3.753A pdb=" N ARG B 176 " --> pdb=" O ILE B 172 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N VAL B 188 " --> pdb=" O TYR B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 203 removed outlier: 3.964A pdb=" N GLU B 199 " --> pdb=" O ALA B 195 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TYR B 203 " --> pdb=" O GLU B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 216 Processing helix chain 'B' and resid 224 through 234 removed outlier: 3.672A pdb=" N VAL B 228 " --> pdb=" O ASN B 224 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLY B 234 " --> pdb=" O TYR B 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 121 No H-bonds generated for 'chain 'C' and resid 119 through 121' Processing helix chain 'C' and resid 122 through 133 removed outlier: 3.843A pdb=" N HIS C 126 " --> pdb=" O LEU C 122 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N THR C 128 " --> pdb=" O LYS C 124 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR C 129 " --> pdb=" O PRO C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 164 Processing helix chain 'C' and resid 169 through 187 removed outlier: 3.548A pdb=" N LYS C 187 " --> pdb=" O LYS C 183 " (cutoff:3.500A) 184 hydrogen bonds defined for protein. 549 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: 0.42 Time building geometry restraints manager: 0.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 655 1.33 - 1.45: 1013 1.45 - 1.57: 2069 1.57 - 1.69: 0 1.69 - 1.81: 35 Bond restraints: 3772 Sorted by residual: bond pdb=" CG1 ILE B 89 " pdb=" CD1 ILE B 89 " ideal model delta sigma weight residual 1.513 1.397 0.116 3.90e-02 6.57e+02 8.88e+00 bond pdb=" C LYS C 124 " pdb=" N PRO C 125 " ideal model delta sigma weight residual 1.334 1.388 -0.054 2.34e-02 1.83e+03 5.38e+00 bond pdb=" CG LEU B 129 " pdb=" CD2 LEU B 129 " ideal model delta sigma weight residual 1.521 1.453 0.068 3.30e-02 9.18e+02 4.30e+00 bond pdb=" C ILE B 153 " pdb=" N PRO B 154 " ideal model delta sigma weight residual 1.336 1.360 -0.024 1.23e-02 6.61e+03 3.85e+00 bond pdb=" CD GLU B 67 " pdb=" OE1 GLU B 67 " ideal model delta sigma weight residual 1.249 1.213 0.036 1.90e-02 2.77e+03 3.69e+00 ... (remaining 3767 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.28: 4902 4.28 - 8.57: 140 8.57 - 12.85: 32 12.85 - 17.14: 4 17.14 - 21.42: 2 Bond angle restraints: 5080 Sorted by residual: angle pdb=" N GLU B 67 " pdb=" CA GLU B 67 " pdb=" CB GLU B 67 " ideal model delta sigma weight residual 110.30 120.50 -10.20 1.54e+00 4.22e-01 4.38e+01 angle pdb=" C TRP C 123 " pdb=" N LYS C 124 " pdb=" CA LYS C 124 " ideal model delta sigma weight residual 120.09 127.85 -7.76 1.25e+00 6.40e-01 3.85e+01 angle pdb=" CA LEU C 137 " pdb=" CB LEU C 137 " pdb=" CG LEU C 137 " ideal model delta sigma weight residual 116.30 137.72 -21.42 3.50e+00 8.16e-02 3.75e+01 angle pdb=" C PHE A 134 " pdb=" N ASN A 135 " pdb=" CA ASN A 135 " ideal model delta sigma weight residual 121.54 132.37 -10.83 1.91e+00 2.74e-01 3.22e+01 angle pdb=" C PHE A 68 " pdb=" N ASP A 69 " pdb=" CA ASP A 69 " ideal model delta sigma weight residual 122.26 112.57 9.69 1.73e+00 3.34e-01 3.14e+01 ... (remaining 5075 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.36: 1830 13.36 - 26.73: 286 26.73 - 40.09: 111 40.09 - 53.45: 14 53.45 - 66.82: 3 Dihedral angle restraints: 2244 sinusoidal: 949 harmonic: 1295 Sorted by residual: dihedral pdb=" CA SER B 163 " pdb=" C SER B 163 " pdb=" N PHE B 164 " pdb=" CA PHE B 164 " ideal model delta harmonic sigma weight residual 180.00 148.31 31.69 0 5.00e+00 4.00e-02 4.02e+01 dihedral pdb=" CA LYS B 169 " pdb=" C LYS B 169 " pdb=" N THR B 170 " pdb=" CA THR B 170 " ideal model delta harmonic sigma weight residual 180.00 152.06 27.94 0 5.00e+00 4.00e-02 3.12e+01 dihedral pdb=" CA MET C 170 " pdb=" C MET C 170 " pdb=" N THR C 171 " pdb=" CA THR C 171 " ideal model delta harmonic sigma weight residual 180.00 155.49 24.51 0 5.00e+00 4.00e-02 2.40e+01 ... (remaining 2241 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 439 0.097 - 0.193: 96 0.193 - 0.290: 12 0.290 - 0.386: 4 0.386 - 0.483: 1 Chirality restraints: 552 Sorted by residual: chirality pdb=" CB ILE B 153 " pdb=" CA ILE B 153 " pdb=" CG1 ILE B 153 " pdb=" CG2 ILE B 153 " both_signs ideal model delta sigma weight residual False 2.64 2.16 0.48 2.00e-01 2.50e+01 5.82e+00 chirality pdb=" CB VAL B 188 " pdb=" CA VAL B 188 " pdb=" CG1 VAL B 188 " pdb=" CG2 VAL B 188 " both_signs ideal model delta sigma weight residual False -2.63 -2.25 -0.37 2.00e-01 2.50e+01 3.50e+00 chirality pdb=" CB ILE B 172 " pdb=" CA ILE B 172 " pdb=" CG1 ILE B 172 " pdb=" CG2 ILE B 172 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.24e+00 ... (remaining 549 not shown) Planarity restraints: 633 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 130 " -0.039 2.00e-02 2.50e+03 3.30e-02 2.72e+01 pdb=" CG TRP C 130 " 0.089 2.00e-02 2.50e+03 pdb=" CD1 TRP C 130 " -0.037 2.00e-02 2.50e+03 pdb=" CD2 TRP C 130 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP C 130 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP C 130 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 130 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 130 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 130 " -0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP C 130 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 190 " 0.024 2.00e-02 2.50e+03 2.33e-02 1.09e+01 pdb=" CG TYR C 190 " -0.058 2.00e-02 2.50e+03 pdb=" CD1 TYR C 190 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR C 190 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR C 190 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR C 190 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR C 190 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 190 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 175 " -0.225 9.50e-02 1.11e+02 1.02e-01 7.89e+00 pdb=" NE ARG A 175 " 0.021 2.00e-02 2.50e+03 pdb=" CZ ARG A 175 " -0.020 2.00e-02 2.50e+03 pdb=" NH1 ARG A 175 " 0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG A 175 " -0.001 2.00e-02 2.50e+03 ... (remaining 630 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 1149 2.84 - 3.35: 3676 3.35 - 3.87: 6487 3.87 - 4.38: 7184 4.38 - 4.90: 11120 Nonbonded interactions: 29616 Sorted by model distance: nonbonded pdb=" OG SER B 163 " pdb=" O SER B 167 " model vdw 2.321 3.040 nonbonded pdb=" O LEU A 53 " pdb=" OG1 THR A 57 " model vdw 2.328 3.040 nonbonded pdb=" OG1 THR A 43 " pdb=" O ILE A 79 " model vdw 2.330 3.040 nonbonded pdb=" OG1 THR A 151 " pdb=" O LEU A 155 " model vdw 2.335 3.040 nonbonded pdb=" O THR C 159 " pdb=" OG1 THR C 163 " model vdw 2.335 3.040 ... (remaining 29611 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.600 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: 0.050 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 4.760 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 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 : 0.007 0.116 3772 Z= 0.325 Angle : 1.747 21.424 5080 Z= 0.853 Chirality : 0.083 0.483 552 Planarity : 0.010 0.102 633 Dihedral : 14.705 66.817 1402 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.50 % Favored : 93.27 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Cbeta Deviations : 0.48 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.25 (0.33), residues: 431 helix: -2.85 (0.23), residues: 277 sheet: None (None), residues: 0 loop : -2.41 (0.47), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG A 175 TYR 0.058 0.004 TYR C 190 PHE 0.036 0.004 PHE C 120 TRP 0.089 0.005 TRP C 130 HIS 0.013 0.003 HIS A 101 Details of bonding type rmsd covalent geometry : bond 0.00666 ( 3772) covalent geometry : angle 1.74740 ( 5080) hydrogen bonds : bond 0.13116 ( 184) hydrogen bonds : angle 8.53387 ( 549) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.086 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 CYS cc_start: 0.8871 (m) cc_final: 0.8343 (m) REVERT: A 55 HIS cc_start: 0.9417 (t-90) cc_final: 0.9085 (t-90) REVERT: A 101 HIS cc_start: 0.8742 (t-170) cc_final: 0.8333 (t-170) REVERT: A 104 TYR cc_start: 0.9390 (t80) cc_final: 0.9051 (t80) REVERT: A 159 LYS cc_start: 0.9584 (pptt) cc_final: 0.9336 (pptt) REVERT: B 64 LYS cc_start: 0.9481 (ptpp) cc_final: 0.9134 (pttm) REVERT: B 65 ILE cc_start: 0.9611 (pt) cc_final: 0.9301 (pt) REVERT: B 103 PHE cc_start: 0.8807 (t80) cc_final: 0.8593 (t80) REVERT: C 148 GLU cc_start: 0.9353 (pm20) cc_final: 0.9138 (pm20) REVERT: C 151 ASP cc_start: 0.9372 (m-30) cc_final: 0.9141 (m-30) REVERT: C 175 GLN cc_start: 0.9227 (tm-30) cc_final: 0.8998 (tm-30) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.0491 time to fit residues: 9.5396 Evaluate side-chains 132 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.085 ------------------------------------------------------------------------------- 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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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: 71.0781 > 50: distance: 46 - 68: 34.818 distance: 50 - 76: 34.142 distance: 61 - 84: 33.214 distance: 64 - 68: 32.640 distance: 65 - 92: 32.248 distance: 68 - 69: 54.239 distance: 69 - 70: 56.889 distance: 69 - 72: 39.770 distance: 70 - 71: 69.020 distance: 70 - 76: 39.787 distance: 71 - 100: 40.921 distance: 72 - 73: 40.058 distance: 72 - 74: 36.947 distance: 73 - 75: 32.982 distance: 76 - 77: 41.003 distance: 77 - 80: 5.410 distance: 78 - 79: 56.766 distance: 79 - 109: 56.589 distance: 80 - 81: 23.959 distance: 81 - 82: 43.169 distance: 81 - 83: 23.241 distance: 85 - 86: 56.259 distance: 85 - 88: 51.191 distance: 86 - 87: 40.004 distance: 86 - 92: 40.618 distance: 87 - 115: 42.044 distance: 88 - 89: 41.175 distance: 89 - 90: 56.382 distance: 89 - 91: 57.201 distance: 92 - 93: 38.823 distance: 93 - 94: 57.213 distance: 93 - 96: 56.706 distance: 94 - 95: 39.106 distance: 95 - 122: 54.973 distance: 96 - 97: 57.034 distance: 97 - 98: 39.879 distance: 97 - 99: 39.857 distance: 100 - 101: 39.712 distance: 101 - 102: 40.254 distance: 101 - 104: 51.379 distance: 102 - 103: 40.990 distance: 102 - 109: 18.016 distance: 103 - 127: 45.462 distance: 104 - 105: 39.171 distance: 105 - 106: 38.638 distance: 110 - 111: 59.774 distance: 110 - 113: 17.196 distance: 112 - 133: 54.045 distance: 113 - 114: 57.224 distance: 115 - 116: 50.040 distance: 116 - 117: 57.531 distance: 116 - 119: 40.309 distance: 117 - 118: 70.176 distance: 117 - 122: 66.385 distance: 118 - 147: 31.726 distance: 119 - 120: 40.561 distance: 119 - 121: 40.011 distance: 122 - 123: 52.391 distance: 123 - 126: 39.706 distance: 124 - 125: 57.293 distance: 124 - 127: 45.517 distance: 127 - 128: 14.476 distance: 128 - 129: 40.067 distance: 128 - 131: 57.033 distance: 129 - 130: 50.415 distance: 129 - 133: 57.135 distance: 131 - 132: 41.157 distance: 134 - 137: 39.843 distance: 135 - 136: 57.246 distance: 135 - 147: 34.646 distance: 138 - 139: 40.537 distance: 138 - 140: 39.379 distance: 139 - 141: 39.338 distance: 140 - 142: 39.799 distance: 140 - 143: 20.124 distance: 141 - 142: 57.885 distance: 142 - 144: 56.479 distance: 143 - 145: 20.224 distance: 145 - 146: 56.449