Starting phenix.real_space_refine on Fri Aug 22 14:20:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9edc_47944/08_2025/9edc_47944.cif Found real_map, /net/cci-nas-00/data/ceres_data/9edc_47944/08_2025/9edc_47944.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9edc_47944/08_2025/9edc_47944.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9edc_47944/08_2025/9edc_47944.map" model { file = "/net/cci-nas-00/data/ceres_data/9edc_47944/08_2025/9edc_47944.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9edc_47944/08_2025/9edc_47944.cif" } resolution = 4.18 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= 0.049 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 6 5.49 5 S 12 5.16 5 C 2596 2.51 5 N 690 2.21 5 O 758 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: 4062 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2777 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 338, 2761 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 13, 'TRANS': 324} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'GLU:plan': 4, 'TPO:plan-1': 1} Unresolved non-hydrogen planarities: 17 Conformer: "B" Number of residues, atoms: 338, 2762 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 13, 'TRANS': 324} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'GLU:plan': 4, 'TPO:plan-1': 1} Unresolved non-hydrogen planarities: 17 bond proxies already assigned to first conformer: 2816 Chain: "B" Number of atoms: 1254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1254 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 6, 'TRANS': 153} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.59, per 1000 atoms: 0.39 Number of scatterers: 4062 At special positions: 0 Unit cell: (73.632, 79.296, 85.904, 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 12 16.00 P 6 15.00 O 758 8.00 N 690 7.00 C 2596 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: 0.28 Conformation dependent library (CDL) restraints added in 200.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 934 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 6 sheets defined 42.4% alpha, 14.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'A' and resid 13 through 32 Processing helix chain 'A' and resid 39 through 41 No H-bonds generated for 'chain 'A' and resid 39 through 41' Processing helix chain 'A' and resid 76 through 82 Processing helix chain 'A' and resid 84 through 96 Processing helix chain 'A' and resid 127 through 136 Processing helix chain 'A' and resid 139 through 160 removed outlier: 3.835A pdb=" N TYR A 146 " --> pdb=" O HIS A 142 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLN A 149 " --> pdb=" O PHE A 145 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU A 160 " --> pdb=" O TYR A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 170 No H-bonds generated for 'chain 'A' and resid 168 through 170' Processing helix chain 'A' and resid 184 through 188 removed outlier: 4.643A pdb=" N PHE A 187 " --> pdb=" O ASP A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 211 Processing helix chain 'A' and resid 217 through 234 removed outlier: 4.020A pdb=" N TRP A 221 " --> pdb=" O LYS A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 253 removed outlier: 3.521A pdb=" N AGLY A 253 " --> pdb=" O LYS A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 273 Processing helix chain 'A' and resid 287 through 293 removed outlier: 4.207A pdb=" N ILE A 291 " --> pdb=" O GLY A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 300 removed outlier: 4.290A pdb=" N THR A 299 " --> pdb=" O TRP A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 307 Processing helix chain 'B' and resid 104 through 110 Processing helix chain 'B' and resid 119 through 130 Processing helix chain 'B' and resid 133 through 138 removed outlier: 4.463A pdb=" N HIS B 138 " --> pdb=" O VAL B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 151 Processing helix chain 'B' and resid 199 through 204 removed outlier: 3.500A pdb=" N ILE B 204 " --> pdb=" O LEU B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 242 Processing sheet with id=AA1, first strand: chain 'A' and resid 43 through 51 removed outlier: 5.588A pdb=" N ARG A 45 " --> pdb=" O LYS A 61 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LYS A 61 " --> pdb=" O ARG A 45 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS A 47 " --> pdb=" O LEU A 59 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL A 57 " --> pdb=" O LEU A 49 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N GLU A 121 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N LEU A 106 " --> pdb=" O GLU A 121 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 162 through 163 Processing sheet with id=AA3, first strand: chain 'A' and resid 172 through 174 Processing sheet with id=AA4, first strand: chain 'A' and resid 199 through 200 Processing sheet with id=AA5, first strand: chain 'B' and resid 152 through 156 removed outlier: 6.661A pdb=" N LYS B 220 " --> pdb=" O ASP B 176 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 161 through 163 removed outlier: 6.667A pdb=" N VAL B 213 " --> pdb=" O VAL B 162 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N VAL B 184 " --> pdb=" O TRP B 188 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N TRP B 188 " --> pdb=" O VAL B 184 " (cutoff:3.500A) 169 hydrogen bonds defined for protein. 471 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: 0.45 Time building geometry restraints manager: 0.37 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: 723 1.33 - 1.45: 1093 1.45 - 1.57: 2306 1.57 - 1.69: 16 1.69 - 1.81: 22 Bond restraints: 4160 Sorted by residual: bond pdb=" OG1 TPO A 197 " pdb=" P TPO A 197 " ideal model delta sigma weight residual 1.717 1.607 0.110 2.00e-02 2.50e+03 3.01e+01 bond pdb=" O3P TPO A 197 " pdb=" P TPO A 197 " ideal model delta sigma weight residual 1.528 1.609 -0.081 2.00e-02 2.50e+03 1.63e+01 bond pdb=" O2P TPO A 197 " pdb=" P TPO A 197 " ideal model delta sigma weight residual 1.528 1.608 -0.080 2.00e-02 2.50e+03 1.60e+01 bond pdb=" C PRO B 84 " pdb=" N PRO B 85 " ideal model delta sigma weight residual 1.334 1.393 -0.059 2.34e-02 1.83e+03 6.27e+00 bond pdb=" O1P TPO A 197 " pdb=" P TPO A 197 " ideal model delta sigma weight residual 1.525 1.479 0.046 2.00e-02 2.50e+03 5.35e+00 ... (remaining 4155 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.71: 5528 2.71 - 5.43: 87 5.43 - 8.14: 14 8.14 - 10.85: 2 10.85 - 13.57: 2 Bond angle restraints: 5633 Sorted by residual: angle pdb=" C PRO B 85 " pdb=" N ASN B 86 " pdb=" CA ASN B 86 " ideal model delta sigma weight residual 121.80 133.13 -11.33 2.44e+00 1.68e-01 2.16e+01 angle pdb=" C THR A 32 " pdb=" CA THR A 32 " pdb=" CB THR A 32 " ideal model delta sigma weight residual 110.17 115.24 -5.07 1.11e+00 8.12e-01 2.09e+01 angle pdb=" CB TPO A 197 " pdb=" OG1 TPO A 197 " pdb=" P TPO A 197 " ideal model delta sigma weight residual 119.31 105.74 13.57 3.00e+00 1.11e-01 2.05e+01 angle pdb=" N GLN A 96 " pdb=" CA GLN A 96 " pdb=" CB GLN A 96 " ideal model delta sigma weight residual 110.41 117.70 -7.29 1.68e+00 3.54e-01 1.88e+01 angle pdb=" C LEU A 95 " pdb=" N GLN A 96 " pdb=" CA GLN A 96 " ideal model delta sigma weight residual 121.58 114.02 7.56 1.95e+00 2.63e-01 1.50e+01 ... (remaining 5628 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 2264 17.88 - 35.76: 188 35.76 - 53.64: 29 53.64 - 71.52: 8 71.52 - 89.40: 4 Dihedral angle restraints: 2493 sinusoidal: 1038 harmonic: 1455 Sorted by residual: dihedral pdb=" CA LYS B 90 " pdb=" C LYS B 90 " pdb=" N GLY B 91 " pdb=" CA GLY B 91 " ideal model delta harmonic sigma weight residual -180.00 -149.29 -30.71 0 5.00e+00 4.00e-02 3.77e+01 dihedral pdb=" CA THR A 195 " pdb=" C THR A 195 " pdb=" N TRP A 196 " pdb=" CA TRP A 196 " ideal model delta harmonic sigma weight residual 180.00 -160.05 -19.95 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CA THR A 201 " pdb=" C THR A 201 " pdb=" N PRO A 202 " pdb=" CA PRO A 202 " ideal model delta harmonic sigma weight residual -180.00 -162.11 -17.89 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 2490 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 444 0.052 - 0.104: 118 0.104 - 0.156: 33 0.156 - 0.208: 2 0.208 - 0.260: 2 Chirality restraints: 599 Sorted by residual: chirality pdb=" CB THR A 32 " pdb=" CA THR A 32 " pdb=" OG1 THR A 32 " pdb=" CG2 THR A 32 " both_signs ideal model delta sigma weight residual False 2.55 2.29 0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CA ASN B 86 " pdb=" N ASN B 86 " pdb=" C ASN B 86 " pdb=" CB ASN B 86 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA THR A 32 " pdb=" N THR A 32 " pdb=" C THR A 32 " pdb=" CB THR A 32 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.18 2.00e-01 2.50e+01 7.81e-01 ... (remaining 596 not shown) Planarity restraints: 718 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 32 " 0.043 5.00e-02 4.00e+02 6.47e-02 6.70e+00 pdb=" N PRO A 33 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO A 33 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 33 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 168 " 0.026 5.00e-02 4.00e+02 3.99e-02 2.54e+00 pdb=" N PRO A 169 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 169 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 169 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 119 " 0.008 2.00e-02 2.50e+03 1.56e-02 2.45e+00 pdb=" C VAL A 119 " -0.027 2.00e-02 2.50e+03 pdb=" O VAL A 119 " 0.010 2.00e-02 2.50e+03 pdb=" N MET A 120 " 0.009 2.00e-02 2.50e+03 ... (remaining 715 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 959 2.79 - 3.32: 3520 3.32 - 3.85: 7147 3.85 - 4.37: 8165 4.37 - 4.90: 13864 Nonbonded interactions: 33655 Sorted by model distance: nonbonded pdb=" OH TYR A 229 " pdb=" O ARG A 256 " model vdw 2.263 3.040 nonbonded pdb=" OH TYR A 179 " pdb=" O VAL A 310 " model vdw 2.326 3.040 nonbonded pdb=" OG1 THR A 195 " pdb=" O2P TPO A 197 " model vdw 2.340 3.040 nonbonded pdb=" O PHE A 43 " pdb=" NH1 ARG A 45 " model vdw 2.409 3.120 nonbonded pdb=" NZ LYS A 111 " pdb=" O PHE A 347 " model vdw 2.410 3.120 ... (remaining 33650 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=0.00 max=1.00 mean=0.99 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: 0.310 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: 0.010 Process input model: 5.990 Find NCS groups from input model: 0.020 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5605 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 : 0.005 0.110 4160 Z= 0.245 Angle : 0.883 13.568 5633 Z= 0.482 Chirality : 0.051 0.260 599 Planarity : 0.006 0.065 718 Dihedral : 13.866 89.398 1559 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.47 % Favored : 97.32 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -1.43 (0.34), residues: 490 helix: -1.05 (0.33), residues: 192 sheet: -0.34 (0.59), residues: 66 loop : -0.91 (0.37), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 92 TYR 0.019 0.002 TYR B 229 PHE 0.020 0.002 PHE A 145 TRP 0.021 0.002 TRP A 30 HIS 0.005 0.001 HIS A 142 Details of bonding type rmsd covalent geometry : bond 0.00497 ( 4160) covalent geometry : angle 0.88266 ( 5633) hydrogen bonds : bond 0.16350 ( 169) hydrogen bonds : angle 6.50241 ( 471) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 980 Ramachandran restraints generated. 490 Oldfield, 0 Emsley, 490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.100 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: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.6897 (mt) cc_final: 0.6545 (mt) REVERT: A 102 PHE cc_start: 0.9345 (m-80) cc_final: 0.8887 (m-80) REVERT: A 155 GLU cc_start: 0.9257 (tt0) cc_final: 0.8988 (tt0) REVERT: A 179 TYR cc_start: 0.1788 (m-80) cc_final: 0.1450 (m-80) REVERT: A 182 VAL cc_start: 0.9223 (t) cc_final: 0.8916 (p) REVERT: A 221 TRP cc_start: 0.9055 (m100) cc_final: 0.8368 (m100) REVERT: A 222 TRP cc_start: 0.9095 (t-100) cc_final: 0.8763 (t-100) REVERT: A 231 MET cc_start: 0.9110 (mtm) cc_final: 0.8721 (mmm) REVERT: A 236 PRO cc_start: 0.8786 (Cg_endo) cc_final: 0.7453 (Cg_exo) REVERT: A 301 ASP cc_start: 0.7956 (t0) cc_final: 0.7566 (p0) REVERT: A 308 ARG cc_start: 0.8436 (mtp85) cc_final: 0.7859 (mtt90) outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 0.0976 time to fit residues: 17.3661 Evaluate side-chains 89 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.174 ------------------------------------------------------------------------------- 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: 70.3844 > 50: distance: 31 - 48: 20.324 distance: 31 - 54: 10.867 distance: 43 - 48: 22.257 distance: 43 - 54: 7.166 distance: 48 - 49: 19.512 distance: 49 - 50: 34.712 distance: 49 - 52: 33.048 distance: 50 - 60: 22.961 distance: 52 - 53: 40.995 distance: 54 - 55: 9.115 distance: 55 - 58: 7.770 distance: 56 - 57: 19.510 distance: 56 - 64: 7.273 distance: 58 - 59: 22.391 distance: 60 - 61: 18.241 distance: 61 - 62: 34.907 distance: 62 - 63: 20.600 distance: 62 - 68: 15.264 distance: 64 - 65: 16.146 distance: 65 - 66: 16.678 distance: 66 - 67: 11.087 distance: 66 - 73: 6.424 distance: 68 - 69: 20.819 distance: 69 - 70: 16.149 distance: 69 - 72: 25.498 distance: 70 - 71: 16.767 distance: 70 - 79: 19.440 distance: 73 - 74: 5.675 distance: 74 - 75: 20.724 distance: 74 - 77: 21.112 distance: 75 - 76: 8.337 distance: 75 - 79: 28.543 distance: 77 - 78: 48.896 distance: 79 - 80: 5.710 distance: 80 - 81: 7.767 distance: 80 - 83: 28.671 distance: 81 - 82: 4.496 distance: 81 - 86: 21.970 distance: 83 - 84: 40.106 distance: 83 - 85: 23.927 distance: 86 - 87: 24.560 distance: 87 - 88: 35.178 distance: 87 - 90: 9.341 distance: 88 - 89: 28.916 distance: 88 - 97: 17.345 distance: 90 - 91: 37.634 distance: 91 - 92: 21.745 distance: 92 - 93: 25.037 distance: 93 - 94: 15.398 distance: 94 - 95: 6.789 distance: 94 - 96: 10.556 distance: 97 - 98: 22.591 distance: 98 - 99: 36.239 distance: 98 - 101: 30.262 distance: 99 - 100: 8.895 distance: 99 - 108: 19.380 distance: 101 - 102: 11.814 distance: 102 - 103: 5.092 distance: 102 - 104: 12.029 distance: 103 - 105: 19.652 distance: 104 - 106: 7.348 distance: 105 - 107: 15.080 distance: 106 - 107: 23.514 distance: 108 - 109: 32.106 distance: 108 - 114: 40.786 distance: 109 - 110: 23.197 distance: 109 - 112: 19.251 distance: 110 - 111: 20.383 distance: 110 - 115: 16.104 distance: 112 - 113: 38.793 distance: 113 - 114: 40.147 distance: 115 - 116: 24.382 distance: 116 - 117: 15.203 distance: 116 - 119: 15.283 distance: 117 - 118: 14.476 distance: 117 - 121: 15.032 distance: 119 - 120: 4.797 distance: 121 - 122: 8.012 distance: 122 - 123: 7.042 distance: 122 - 125: 11.238 distance: 123 - 124: 7.937 distance: 123 - 131: 22.749 distance: 125 - 126: 9.390 distance: 126 - 127: 13.713 distance: 126 - 128: 25.627 distance: 127 - 129: 16.812 distance: 129 - 130: 26.220 distance: 131 - 132: 11.608 distance: 132 - 133: 15.838 distance: 132 - 135: 7.270 distance: 133 - 134: 16.029 distance: 133 - 142: 18.767 distance: 135 - 136: 13.478 distance: 136 - 137: 8.941 distance: 136 - 138: 26.706 distance: 137 - 139: 5.826 distance: 138 - 140: 9.361 distance: 139 - 141: 23.539 distance: 140 - 141: 18.582