Starting phenix.real_space_refine on Fri Aug 22 19:37:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h87_34531/08_2025/8h87_34531.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h87_34531/08_2025/8h87_34531.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8h87_34531/08_2025/8h87_34531.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h87_34531/08_2025/8h87_34531.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8h87_34531/08_2025/8h87_34531.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h87_34531/08_2025/8h87_34531.map" } resolution = 2.53 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= 0.009 sd= 0.430 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 3 5.49 5 S 48 5.16 5 C 4830 2.51 5 N 978 2.21 5 O 1224 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s 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: 7083 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2097 Classifications: {'peptide': 259} Link IDs: {'PTRANS': 16, 'TRANS': 242} Chain: "A" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 264 Unusual residues: {'PLM': 9, 'PSC': 6, 'RET': 1} Classifications: {'undetermined': 16, 'water': 49} Link IDs: {None: 64} Unresolved non-hydrogen bonds: 280 Unresolved non-hydrogen angles: 331 Unresolved non-hydrogen dihedrals: 250 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'RET:plan-5': 1, 'PSC:plan-1': 4, 'PSC:plan-2': 4, 'PSC:plan-3': 4, 'PSC:plan-4': 4, 'PLM:plan-1': 8} Unresolved non-hydrogen planarities: 84 Chain: "B" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 49 Classifications: {'water': 49} Link IDs: {None: 48} Chain: "C" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 49 Classifications: {'water': 49} Link IDs: {None: 48} Restraints were copied for chains: B, C Time building chain proxies: 1.53, per 1000 atoms: 0.22 Number of scatterers: 7083 At special positions: 0 Unit cell: (78.02, 77.19, 84.66, 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 48 16.00 P 3 15.00 O 1224 8.00 N 978 7.00 C 4830 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: 0.69 Conformation dependent library (CDL) restraints added in 333.9 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1440 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 0 sheets defined 72.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 21 through 48 Processing helix chain 'A' and resid 64 through 67 Processing helix chain 'A' and resid 68 through 90 Processing helix chain 'A' and resid 105 through 122 removed outlier: 4.182A pdb=" N THR A 109 " --> pdb=" O ASP A 105 " (cutoff:3.500A) Proline residue: A 111 - end of helix Processing helix chain 'A' and resid 125 through 146 Processing helix chain 'A' and resid 149 through 177 removed outlier: 3.878A pdb=" N ALA A 153 " --> pdb=" O ALA A 149 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TRP A 161 " --> pdb=" O LEU A 157 " (cutoff:3.500A) Proline residue: A 164 - end of helix Processing helix chain 'A' and resid 181 through 199 removed outlier: 3.521A pdb=" N TRP A 190 " --> pdb=" O ARG A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 207 removed outlier: 3.986A pdb=" N ILE A 207 " --> pdb=" O PRO A 203 " (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 Processing helix chain 'B' and resid 64 through 67 Processing helix chain 'B' and resid 68 through 90 Processing helix chain 'B' and resid 105 through 122 removed outlier: 4.182A pdb=" N THR B 109 " --> pdb=" O ASP B 105 " (cutoff:3.500A) Proline residue: B 111 - end of helix Processing helix chain 'B' and resid 125 through 146 Processing helix chain 'B' and resid 149 through 177 removed outlier: 3.878A pdb=" N ALA B 153 " --> pdb=" O ALA B 149 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TRP B 161 " --> pdb=" O LEU B 157 " (cutoff:3.500A) Proline residue: B 164 - end of helix Processing helix chain 'B' and resid 181 through 199 removed outlier: 3.521A pdb=" N TRP B 190 " --> pdb=" O ARG B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 207 removed outlier: 3.986A pdb=" N ILE B 207 " --> pdb=" O PRO B 203 " (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 Processing helix chain 'C' and resid 64 through 67 Processing helix chain 'C' and resid 68 through 90 Processing helix chain 'C' and resid 105 through 122 removed outlier: 4.182A pdb=" N THR C 109 " --> pdb=" O ASP C 105 " (cutoff:3.500A) Proline residue: C 111 - end of helix Processing helix chain 'C' and resid 125 through 146 Processing helix chain 'C' and resid 149 through 177 removed outlier: 3.878A pdb=" N ALA C 153 " --> pdb=" O ALA C 149 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TRP C 161 " --> pdb=" O LEU C 157 " (cutoff:3.500A) Proline residue: C 164 - end of helix Processing helix chain 'C' and resid 181 through 199 removed outlier: 3.521A pdb=" N TRP C 190 " --> pdb=" O ARG C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 207 removed outlier: 3.986A pdb=" N ILE C 207 " --> pdb=" O PRO C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 233 Processing helix chain 'C' and resid 233 through 252 414 hydrogen bonds defined for protein. 1233 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: 1.03 Time building geometry restraints manager: 0.89 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: 1169 1.33 - 1.46: 2602 1.46 - 1.59: 3288 1.59 - 1.72: 6 1.72 - 1.85: 63 Bond restraints: 7128 Sorted by residual: bond pdb=" C6 PSC A 404 " pdb=" C7 PSC A 404 " ideal model delta sigma weight residual 1.523 1.314 0.209 2.00e-02 2.50e+03 1.09e+02 bond pdb=" C6 PSC C 404 " pdb=" C7 PSC C 404 " ideal model delta sigma weight residual 1.523 1.314 0.209 2.00e-02 2.50e+03 1.09e+02 bond pdb=" C6 PSC B 404 " pdb=" C7 PSC B 404 " ideal model delta sigma weight residual 1.523 1.314 0.209 2.00e-02 2.50e+03 1.09e+02 bond pdb=" CA SER A 217 " pdb=" CB SER A 217 " ideal model delta sigma weight residual 1.528 1.461 0.067 1.61e-02 3.86e+03 1.75e+01 bond pdb=" CA SER C 217 " pdb=" CB SER C 217 " ideal model delta sigma weight residual 1.528 1.461 0.067 1.61e-02 3.86e+03 1.72e+01 ... (remaining 7123 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.08: 9373 4.08 - 8.16: 101 8.16 - 12.24: 12 12.24 - 16.32: 12 16.32 - 20.41: 3 Bond angle restraints: 9501 Sorted by residual: angle pdb=" C01 PSC B 402 " pdb=" C02 PSC B 402 " pdb=" O01 PSC B 402 " ideal model delta sigma weight residual 107.00 127.41 -20.41 3.00e+00 1.11e-01 4.63e+01 angle pdb=" C01 PSC C 402 " pdb=" C02 PSC C 402 " pdb=" O01 PSC C 402 " ideal model delta sigma weight residual 107.00 127.40 -20.40 3.00e+00 1.11e-01 4.62e+01 angle pdb=" C01 PSC A 402 " pdb=" C02 PSC A 402 " pdb=" O01 PSC A 402 " ideal model delta sigma weight residual 107.00 127.39 -20.39 3.00e+00 1.11e-01 4.62e+01 angle pdb=" N PRO C 182 " pdb=" CA PRO C 182 " pdb=" C PRO C 182 " ideal model delta sigma weight residual 113.75 121.44 -7.69 1.49e+00 4.50e-01 2.67e+01 angle pdb=" N PRO A 182 " pdb=" CA PRO A 182 " pdb=" C PRO A 182 " ideal model delta sigma weight residual 113.75 121.44 -7.69 1.49e+00 4.50e-01 2.66e+01 ... (remaining 9496 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.13: 3900 32.13 - 64.27: 213 64.27 - 96.40: 12 96.40 - 128.53: 3 128.53 - 160.67: 3 Dihedral angle restraints: 4131 sinusoidal: 1869 harmonic: 2262 Sorted by residual: dihedral pdb=" N PSC A 402 " pdb=" C04 PSC A 402 " pdb=" C05 PSC A 402 " pdb=" O12 PSC A 402 " ideal model delta sinusoidal sigma weight residual -70.45 90.22 -160.67 1 3.00e+01 1.11e-03 2.07e+01 dihedral pdb=" N PSC B 402 " pdb=" C04 PSC B 402 " pdb=" C05 PSC B 402 " pdb=" O12 PSC B 402 " ideal model delta sinusoidal sigma weight residual -70.45 90.21 -160.66 1 3.00e+01 1.11e-03 2.07e+01 dihedral pdb=" N PSC C 402 " pdb=" C04 PSC C 402 " pdb=" C05 PSC C 402 " pdb=" O12 PSC C 402 " ideal model delta sinusoidal sigma weight residual -70.45 90.20 -160.65 1 3.00e+01 1.11e-03 2.07e+01 ... (remaining 4128 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 460 0.049 - 0.098: 261 0.098 - 0.147: 139 0.147 - 0.196: 43 0.196 - 0.245: 24 Chirality restraints: 927 Sorted by residual: chirality pdb=" CB VAL B 17 " pdb=" CA VAL B 17 " pdb=" CG1 VAL B 17 " pdb=" CG2 VAL B 17 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.24 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CB VAL C 17 " pdb=" CA VAL C 17 " pdb=" CG1 VAL C 17 " pdb=" CG2 VAL C 17 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CB VAL A 17 " pdb=" CA VAL A 17 " pdb=" CG1 VAL A 17 " pdb=" CG2 VAL A 17 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.48e+00 ... (remaining 924 not shown) Planarity restraints: 1137 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 PSC A 402 " -0.246 2.00e-02 2.50e+03 1.85e-01 3.43e+02 pdb=" C11 PSC A 402 " 0.088 2.00e-02 2.50e+03 pdb=" C8 PSC A 402 " -0.089 2.00e-02 2.50e+03 pdb=" C9 PSC A 402 " 0.247 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 PSC C 402 " 0.246 2.00e-02 2.50e+03 1.85e-01 3.43e+02 pdb=" C11 PSC C 402 " -0.088 2.00e-02 2.50e+03 pdb=" C8 PSC C 402 " 0.089 2.00e-02 2.50e+03 pdb=" C9 PSC C 402 " -0.247 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 PSC B 402 " 0.246 2.00e-02 2.50e+03 1.85e-01 3.42e+02 pdb=" C11 PSC B 402 " -0.088 2.00e-02 2.50e+03 pdb=" C8 PSC B 402 " 0.089 2.00e-02 2.50e+03 pdb=" C9 PSC B 402 " -0.247 2.00e-02 2.50e+03 ... (remaining 1134 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2114 2.82 - 3.34: 6640 3.34 - 3.86: 12755 3.86 - 4.38: 16441 4.38 - 4.90: 25046 Nonbonded interactions: 62996 Sorted by model distance: nonbonded pdb=" OH TYR A 180 " pdb=" O HOH A 501 " model vdw 2.300 3.040 nonbonded pdb=" OH TYR C 180 " pdb=" O HOH C 501 " model vdw 2.301 3.040 nonbonded pdb=" OH TYR B 180 " pdb=" O HOH B 501 " model vdw 2.301 3.040 nonbonded pdb=" N GLY A 52 " pdb=" OE1 GLU A 248 " model vdw 2.333 3.120 nonbonded pdb=" N GLY B 52 " pdb=" OE1 GLU B 248 " model vdw 2.333 3.120 ... (remaining 62991 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: 0.280 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.400 Find NCS groups from input model: 0.060 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:6.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 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 : 0.011 0.209 7131 Z= 0.729 Angle : 1.547 20.406 9501 Z= 0.941 Chirality : 0.080 0.245 927 Planarity : 0.017 0.185 1137 Dihedral : 18.835 160.666 2691 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.91 % Allowed : 1.82 % Favored : 97.27 % 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: -1.32 (0.27), residues: 771 helix: -1.08 (0.18), residues: 516 sheet: None (None), residues: 0 loop : 0.02 (0.42), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.002 ARG B 46 TYR 0.043 0.010 TYR A 101 PHE 0.050 0.010 PHE A 150 TRP 0.049 0.011 TRP C 42 HIS 0.012 0.006 HIS C 225 Details of bonding type rmsd covalent geometry : bond 0.01079 ( 7128) covalent geometry : angle 1.54697 ( 9501) hydrogen bonds : bond 0.17238 ( 414) hydrogen bonds : angle 7.56513 ( 1233) Misc. bond : bond 0.16257 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 83 time to evaluate : 0.257 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 ASP cc_start: 0.8294 (m-30) cc_final: 0.7947 (m-30) REVERT: A 171 ARG cc_start: 0.7193 (ttt-90) cc_final: 0.6401 (ttp-170) REVERT: A 174 LYS cc_start: 0.7676 (mtpm) cc_final: 0.7077 (mtmt) REVERT: A 186 ARG cc_start: 0.8079 (ttt180) cc_final: 0.7023 (ttm110) REVERT: A 204 LEU cc_start: 0.7840 (tp) cc_final: 0.7525 (mt) REVERT: A 235 ILE cc_start: 0.7628 (mm) cc_final: 0.7405 (mt) REVERT: B 4 TYR cc_start: 0.8153 (t80) cc_final: 0.7940 (t80) REVERT: B 5 ASP cc_start: 0.8288 (m-30) cc_final: 0.8018 (m-30) REVERT: B 14 ARG cc_start: 0.7816 (mtp-110) cc_final: 0.6862 (mmp-170) REVERT: B 171 ARG cc_start: 0.7391 (ttt-90) cc_final: 0.6602 (ttp-170) REVERT: B 174 LYS cc_start: 0.7774 (mtpm) cc_final: 0.7222 (mtmp) REVERT: B 204 LEU cc_start: 0.7739 (tp) cc_final: 0.7474 (mt) REVERT: C 5 ASP cc_start: 0.8412 (m-30) cc_final: 0.8078 (m-30) REVERT: C 43 MET cc_start: 0.7930 (mtt) cc_final: 0.7695 (mtt) REVERT: C 171 ARG cc_start: 0.7205 (ttt-90) cc_final: 0.6382 (ttp-170) REVERT: C 174 LYS cc_start: 0.7698 (mtpm) cc_final: 0.7172 (mtmp) REVERT: C 186 ARG cc_start: 0.7992 (ttt180) cc_final: 0.6898 (ttm110) REVERT: C 204 LEU cc_start: 0.7704 (tp) cc_final: 0.7489 (mt) REVERT: C 230 LEU cc_start: 0.7623 (tp) cc_final: 0.7392 (tp) outliers start: 6 outliers final: 2 residues processed: 89 average time/residue: 0.7004 time to fit residues: 65.1236 Evaluate side-chains 82 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 80 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain C residue 165 LEU 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: 70.1114 > 50: distance: 18 - 30: 3.189 distance: 32 - 36: 31.954 distance: 33 - 59: 36.065 distance: 36 - 37: 37.097 distance: 36 - 42: 41.177 distance: 37 - 38: 40.472 distance: 37 - 40: 35.486 distance: 38 - 39: 40.516 distance: 39 - 67: 53.070 distance: 40 - 41: 48.515 distance: 41 - 42: 55.715 distance: 44 - 45: 56.732 distance: 44 - 47: 55.799 distance: 45 - 46: 39.545 distance: 45 - 51: 29.797 distance: 46 - 74: 5.914 distance: 47 - 48: 67.367 distance: 48 - 49: 30.044 distance: 48 - 50: 54.008 distance: 51 - 52: 50.035 distance: 52 - 53: 67.273 distance: 52 - 55: 27.171 distance: 53 - 54: 46.291 distance: 53 - 59: 54.956 distance: 54 - 82: 49.655 distance: 55 - 56: 32.987 distance: 56 - 57: 12.428 distance: 56 - 58: 9.791 distance: 59 - 60: 45.386 distance: 60 - 61: 41.972 distance: 60 - 63: 51.953 distance: 61 - 62: 51.378 distance: 61 - 67: 23.475 distance: 62 - 93: 35.585 distance: 63 - 64: 37.904 distance: 63 - 65: 41.156 distance: 64 - 66: 27.394 distance: 67 - 68: 19.247 distance: 68 - 69: 10.194 distance: 68 - 71: 26.510 distance: 69 - 70: 32.917 distance: 69 - 74: 38.165 distance: 70 - 98: 50.029 distance: 71 - 72: 40.613 distance: 71 - 73: 55.472 distance: 74 - 75: 25.433 distance: 75 - 76: 21.143 distance: 75 - 78: 39.898 distance: 76 - 77: 33.028 distance: 76 - 82: 41.393 distance: 77 - 109: 34.745 distance: 78 - 79: 33.620 distance: 79 - 80: 26.090 distance: 79 - 81: 22.771 distance: 82 - 83: 19.037 distance: 83 - 84: 3.528 distance: 83 - 86: 27.453 distance: 84 - 85: 3.701 distance: 84 - 93: 5.333 distance: 85 - 116: 5.063 distance: 86 - 87: 31.856 distance: 87 - 88: 28.430 distance: 87 - 89: 15.726 distance: 88 - 90: 15.265 distance: 89 - 91: 21.263 distance: 90 - 92: 15.771 distance: 91 - 92: 12.007 distance: 93 - 94: 13.327 distance: 94 - 95: 14.827 distance: 94 - 97: 12.508 distance: 95 - 96: 10.721 distance: 95 - 98: 23.592 distance: 96 - 124: 9.096 distance: 98 - 99: 30.310 distance: 99 - 100: 11.936 distance: 99 - 102: 4.592 distance: 100 - 101: 24.431 distance: 100 - 109: 37.074 distance: 102 - 103: 20.145 distance: 103 - 104: 29.166 distance: 103 - 105: 16.584 distance: 104 - 106: 56.563 distance: 105 - 107: 17.406 distance: 106 - 108: 27.474 distance: 107 - 108: 7.184 distance: 109 - 110: 22.067 distance: 110 - 111: 24.856 distance: 110 - 113: 3.157 distance: 111 - 112: 36.758 distance: 111 - 116: 26.179 distance: 113 - 114: 63.059 distance: 113 - 115: 49.113 distance: 137 - 150: 3.015 distance: 153 - 160: 3.112 distance: 200 - 210: 3.046