Starting phenix.real_space_refine on Fri Aug 22 19:44:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gi9_40063/08_2025/8gi9_40063.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gi9_40063/08_2025/8gi9_40063.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gi9_40063/08_2025/8gi9_40063.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gi9_40063/08_2025/8gi9_40063.map" model { file = "/net/cci-nas-00/data/ceres_data/8gi9_40063/08_2025/8gi9_40063.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gi9_40063/08_2025/8gi9_40063.cif" } resolution = 2.84 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= 0.222 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 6 5.49 5 S 39 5.16 5 Na 9 4.78 5 C 4842 2.51 5 N 894 2.21 5 O 1062 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: 6852 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1948 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 12, 'TRANS': 227} Chain: "A" Number of atoms: 336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 336 Unusual residues: {' NA': 3, 'CLR': 7, 'PEE': 2, 'RET': 1} Classifications: {'undetermined': 13, 'water': 15} Link IDs: {None: 27} 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: 1.22, per 1000 atoms: 0.18 Number of scatterers: 6852 At special positions: 0 Unit cell: (79.31, 78.28, 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 39 16.00 P 6 15.00 Na 9 11.00 O 1062 8.00 N 894 7.00 C 4842 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.60 Conformation dependent library (CDL) restraints added in 233.5 milliseconds Enol-peptide restraints added in 476.8 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: 1326 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 0 sheets defined 79.6% 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 removed outlier: 3.562A pdb=" N ASP A 48 " --> pdb=" O LEU A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 67 removed outlier: 3.523A pdb=" N ASN A 67 " --> pdb=" O PRO A 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 64 through 67' Processing helix chain 'A' and resid 68 through 90 removed outlier: 3.570A pdb=" N CYS A 74 " --> pdb=" O SER A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.576A pdb=" N VAL A 107 " --> pdb=" O TYR A 103 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N PHE A 108 " --> pdb=" O LEU A 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 103 through 108' Processing helix chain 'A' and resid 109 through 122 Processing helix chain 'A' and resid 125 through 146 Processing helix chain 'A' and resid 150 through 177 Proline residue: A 164 - end of helix Processing helix chain 'A' and resid 181 through 199 removed outlier: 3.904A pdb=" N LEU A 187 " --> pdb=" O LYS A 183 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TRP A 190 " --> pdb=" O LYS A 186 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TRP A 199 " --> pdb=" O PHE A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 209 removed outlier: 3.755A 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 Processing helix chain 'B' and resid 21 through 48 removed outlier: 3.562A pdb=" N ASP B 48 " --> pdb=" O LEU B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 67 removed outlier: 3.523A pdb=" N ASN B 67 " --> pdb=" O PRO B 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 64 through 67' Processing helix chain 'B' and resid 68 through 90 removed outlier: 3.570A pdb=" N CYS B 74 " --> pdb=" O SER B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 108 removed outlier: 3.576A pdb=" N VAL B 107 " --> pdb=" O TYR B 103 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N PHE B 108 " --> pdb=" O LEU B 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 103 through 108' Processing helix chain 'B' and resid 109 through 122 Processing helix chain 'B' and resid 125 through 146 Processing helix chain 'B' and resid 150 through 177 Proline residue: B 164 - end of helix Processing helix chain 'B' and resid 181 through 199 removed outlier: 3.904A pdb=" N LEU B 187 " --> pdb=" O LYS B 183 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TRP B 190 " --> pdb=" O LYS B 186 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TRP B 199 " --> pdb=" O PHE B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 209 removed outlier: 3.755A 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 Processing helix chain 'C' and resid 21 through 48 removed outlier: 3.562A pdb=" N ASP C 48 " --> pdb=" O LEU C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 67 removed outlier: 3.522A pdb=" N ASN C 67 " --> pdb=" O PRO C 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 64 through 67' Processing helix chain 'C' and resid 68 through 90 removed outlier: 3.570A pdb=" N CYS C 74 " --> pdb=" O SER C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 108 removed outlier: 3.576A pdb=" N VAL C 107 " --> pdb=" O TYR C 103 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N PHE C 108 " --> pdb=" O LEU C 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 103 through 108' Processing helix chain 'C' and resid 109 through 122 Processing helix chain 'C' and resid 125 through 146 Processing helix chain 'C' and resid 150 through 177 Proline residue: C 164 - end of helix Processing helix chain 'C' and resid 181 through 199 removed outlier: 3.904A pdb=" N LEU C 187 " --> pdb=" O LYS C 183 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TRP C 190 " --> pdb=" O LYS C 186 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TRP C 199 " --> pdb=" O PHE C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 209 removed outlier: 3.755A 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 252 408 hydrogen bonds defined for protein. 1224 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: 0.91 Time building geometry restraints manager: 0.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1518 1.33 - 1.45: 1521 1.45 - 1.57: 3876 1.57 - 1.69: 114 1.69 - 1.81: 57 Bond restraints: 7086 Sorted by residual: bond pdb=" O4P PEE A 312 " pdb=" P PEE A 312 " ideal model delta sigma weight residual 1.653 1.786 -0.133 2.00e-02 2.50e+03 4.41e+01 bond pdb=" O4P PEE B 312 " pdb=" P PEE B 312 " ideal model delta sigma weight residual 1.653 1.786 -0.133 2.00e-02 2.50e+03 4.39e+01 bond pdb=" O4P PEE C 312 " pdb=" P PEE C 312 " ideal model delta sigma weight residual 1.653 1.785 -0.132 2.00e-02 2.50e+03 4.39e+01 bond pdb=" O4P PEE B 313 " pdb=" P PEE B 313 " ideal model delta sigma weight residual 1.653 1.778 -0.125 2.00e-02 2.50e+03 3.91e+01 bond pdb=" O4P PEE A 313 " pdb=" P PEE A 313 " ideal model delta sigma weight residual 1.653 1.778 -0.125 2.00e-02 2.50e+03 3.90e+01 ... (remaining 7081 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.72: 9300 2.72 - 5.44: 318 5.44 - 8.15: 78 8.15 - 10.87: 3 10.87 - 13.59: 6 Bond angle restraints: 9705 Sorted by residual: angle pdb=" O1P PEE B 312 " pdb=" P PEE B 312 " pdb=" O2P PEE B 312 " ideal model delta sigma weight residual 119.43 133.02 -13.59 3.00e+00 1.11e-01 2.05e+01 angle pdb=" O1P PEE A 312 " pdb=" P PEE A 312 " pdb=" O2P PEE A 312 " ideal model delta sigma weight residual 119.43 133.01 -13.58 3.00e+00 1.11e-01 2.05e+01 angle pdb=" O1P PEE C 312 " pdb=" P PEE C 312 " pdb=" O2P PEE C 312 " ideal model delta sigma weight residual 119.43 133.01 -13.58 3.00e+00 1.11e-01 2.05e+01 angle pdb=" O1P PEE B 313 " pdb=" P PEE B 313 " pdb=" O2P PEE B 313 " ideal model delta sigma weight residual 119.43 133.01 -13.58 3.00e+00 1.11e-01 2.05e+01 angle pdb=" O1P PEE A 313 " pdb=" P PEE A 313 " pdb=" O2P PEE A 313 " ideal model delta sigma weight residual 119.43 133.00 -13.57 3.00e+00 1.11e-01 2.05e+01 ... (remaining 9700 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.20: 4794 29.20 - 58.39: 168 58.39 - 87.59: 21 87.59 - 116.78: 12 116.78 - 145.98: 9 Dihedral angle restraints: 5004 sinusoidal: 2922 harmonic: 2082 Sorted by residual: dihedral pdb=" C32 PEE A 312 " pdb=" C30 PEE A 312 " pdb=" C31 PEE A 312 " pdb=" O3 PEE A 312 " ideal model delta sinusoidal sigma weight residual 161.16 -52.86 -145.98 1 3.00e+01 1.11e-03 1.95e+01 dihedral pdb=" C32 PEE C 312 " pdb=" C30 PEE C 312 " pdb=" C31 PEE C 312 " pdb=" O3 PEE C 312 " ideal model delta sinusoidal sigma weight residual 161.16 -52.87 -145.97 1 3.00e+01 1.11e-03 1.95e+01 dihedral pdb=" C32 PEE B 312 " pdb=" C30 PEE B 312 " pdb=" C31 PEE B 312 " pdb=" O3 PEE B 312 " ideal model delta sinusoidal sigma weight residual 161.16 -52.89 -145.95 1 3.00e+01 1.11e-03 1.95e+01 ... (remaining 5001 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 892 0.078 - 0.157: 74 0.157 - 0.235: 3 0.235 - 0.313: 54 0.313 - 0.391: 33 Chirality restraints: 1056 Sorted by residual: chirality pdb=" C2 PEE A 312 " pdb=" C1 PEE A 312 " pdb=" C3 PEE A 312 " pdb=" O2 PEE A 312 " both_signs ideal model delta sigma weight residual False -2.33 -2.72 0.39 2.00e-01 2.50e+01 3.83e+00 chirality pdb=" C2 PEE C 312 " pdb=" C1 PEE C 312 " pdb=" C3 PEE C 312 " pdb=" O2 PEE C 312 " both_signs ideal model delta sigma weight residual False -2.33 -2.72 0.39 2.00e-01 2.50e+01 3.80e+00 chirality pdb=" C17 CLR A 305 " pdb=" C13 CLR A 305 " pdb=" C16 CLR A 305 " pdb=" C20 CLR A 305 " both_signs ideal model delta sigma weight residual False 2.55 2.94 -0.39 2.00e-01 2.50e+01 3.79e+00 ... (remaining 1053 not shown) Planarity restraints: 1035 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 94 " 0.015 5.00e-02 4.00e+02 2.27e-02 8.24e-01 pdb=" N PRO A 95 " -0.039 5.00e-02 4.00e+02 pdb=" CA PRO A 95 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO A 95 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 94 " 0.015 5.00e-02 4.00e+02 2.26e-02 8.18e-01 pdb=" N PRO C 95 " -0.039 5.00e-02 4.00e+02 pdb=" CA PRO C 95 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO C 95 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 94 " 0.015 5.00e-02 4.00e+02 2.25e-02 8.12e-01 pdb=" N PRO B 95 " -0.039 5.00e-02 4.00e+02 pdb=" CA PRO B 95 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO B 95 " 0.013 5.00e-02 4.00e+02 ... (remaining 1032 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 39 2.48 - 3.09: 4814 3.09 - 3.69: 9987 3.69 - 4.30: 16770 4.30 - 4.90: 27808 Nonbonded interactions: 59418 Sorted by model distance: nonbonded pdb=" OH TYR B 62 " pdb=" OE1 GLN C 175 " model vdw 1.878 3.040 nonbonded pdb=" OH TYR A 62 " pdb=" OE1 GLN B 175 " model vdw 1.878 3.040 nonbonded pdb=" OE1 GLN A 175 " pdb=" OH TYR C 62 " model vdw 1.878 3.040 nonbonded pdb=" O ALA A 132 " pdb=" OG1 THR A 136 " model vdw 2.243 3.040 nonbonded pdb=" O ALA B 132 " pdb=" OG1 THR B 136 " model vdw 2.243 3.040 ... (remaining 59413 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: 0.02 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: 0.830 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: 0.060 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.260 Find NCS groups from input model: 0.040 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:5.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 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 : 0.009 0.133 7089 Z= 0.458 Angle : 1.113 13.589 9705 Z= 0.394 Chirality : 0.100 0.391 1056 Planarity : 0.003 0.023 1035 Dihedral : 15.912 145.981 3678 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % 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: 1.20 (0.33), residues: 714 helix: 1.73 (0.24), residues: 504 sheet: None (None), residues: 0 loop : -1.58 (0.42), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 176 TYR 0.006 0.001 TYR C 177 PHE 0.005 0.001 PHE B 221 TRP 0.005 0.001 TRP C 190 HIS 0.002 0.001 HIS A 225 Details of bonding type rmsd covalent geometry : bond 0.00920 ( 7086) covalent geometry : angle 1.11301 ( 9705) hydrogen bonds : bond 0.21610 ( 408) hydrogen bonds : angle 7.85021 ( 1224) Misc. bond : bond 0.00129 ( 3) *********************** 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 76 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.138 Fit side-chains revert: symmetry clash REVERT: A 116 ASP cc_start: 0.8221 (t0) cc_final: 0.7865 (t0) REVERT: A 186 LYS cc_start: 0.7719 (mptt) cc_final: 0.7415 (ttmm) REVERT: B 144 PHE cc_start: 0.7667 (t80) cc_final: 0.7043 (t80) REVERT: B 186 LYS cc_start: 0.7894 (mptt) cc_final: 0.7558 (ttmm) REVERT: C 144 PHE cc_start: 0.7330 (t80) cc_final: 0.7103 (t80) REVERT: C 186 LYS cc_start: 0.7595 (mptt) cc_final: 0.7142 (ttmm) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.5173 time to fit residues: 41.3459 Evaluate side-chains 68 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.201 ------------------------------------------------------------------------------- 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: 50.2778 > 50: distance: 38 - 48: 3.098 distance: 44 - 52: 3.045 distance: 51 - 62: 3.094 distance: 80 - 85: 6.644 distance: 85 - 86: 9.137 distance: 86 - 87: 24.673 distance: 86 - 89: 25.868 distance: 87 - 88: 16.850 distance: 87 - 90: 14.533 distance: 90 - 91: 8.006 distance: 91 - 92: 12.085 distance: 91 - 94: 5.947 distance: 92 - 93: 11.265 distance: 92 - 98: 15.697 distance: 94 - 95: 8.478 distance: 95 - 96: 9.711 distance: 95 - 97: 13.395 distance: 98 - 99: 13.702 distance: 99 - 100: 5.736 distance: 99 - 102: 7.793 distance: 100 - 104: 12.540 distance: 101 - 126: 20.893 distance: 102 - 103: 3.932 distance: 104 - 105: 10.316 distance: 105 - 106: 14.006 distance: 105 - 108: 26.751 distance: 106 - 107: 9.415 distance: 106 - 115: 8.235 distance: 107 - 134: 4.396 distance: 108 - 109: 12.919 distance: 109 - 110: 3.472 distance: 109 - 111: 6.105 distance: 110 - 112: 14.457 distance: 111 - 113: 5.924 distance: 112 - 114: 8.361 distance: 113 - 114: 6.005 distance: 115 - 116: 12.615 distance: 116 - 117: 21.005 distance: 116 - 119: 9.546 distance: 117 - 118: 17.148 distance: 117 - 121: 37.367 distance: 119 - 120: 8.167 distance: 121 - 122: 18.514 distance: 122 - 123: 15.243 distance: 122 - 125: 4.278 distance: 123 - 124: 26.073 distance: 123 - 126: 21.988 distance: 124 - 146: 33.103 distance: 126 - 127: 10.426 distance: 127 - 128: 12.833 distance: 127 - 130: 15.237 distance: 128 - 129: 10.154 distance: 128 - 134: 5.687 distance: 129 - 154: 10.816 distance: 130 - 131: 12.617 distance: 131 - 132: 7.759 distance: 131 - 133: 4.702 distance: 134 - 135: 3.531 distance: 135 - 136: 5.279 distance: 135 - 138: 8.987 distance: 136 - 140: 4.081 distance: 137 - 161: 7.864 distance: 138 - 139: 34.041 distance: 140 - 141: 3.013 distance: 141 - 142: 9.539 distance: 141 - 144: 13.107 distance: 142 - 143: 20.274 distance: 142 - 146: 14.618 distance: 143 - 167: 21.387 distance: 144 - 145: 20.740 distance: 146 - 147: 13.837 distance: 147 - 148: 12.824 distance: 147 - 150: 23.575 distance: 148 - 149: 13.139 distance: 148 - 154: 8.257 distance: 149 - 171: 13.214 distance: 150 - 151: 8.834 distance: 151 - 152: 19.568 distance: 151 - 153: 14.884 distance: 178 - 189: 3.060 distance: 184 - 200: 3.033