Starting phenix.real_space_refine on Fri Aug 22 14:14:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jsu_61783/08_2025/9jsu_61783.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jsu_61783/08_2025/9jsu_61783.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9jsu_61783/08_2025/9jsu_61783.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jsu_61783/08_2025/9jsu_61783.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jsu_61783/08_2025/9jsu_61783.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jsu_61783/08_2025/9jsu_61783.map" } resolution = 1.79 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= 0.006 sd= 0.050 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 S 8 5.16 5 C 1336 2.51 5 N 352 2.21 5 O 344 1.98 5 H 2000 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.00s 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: 4040 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 505 Classifications: {'peptide': 33} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'TRANS': 31} Chain: "B" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 505 Classifications: {'peptide': 33} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'TRANS': 31} Chain: "C" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 505 Classifications: {'peptide': 33} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'TRANS': 31} Chain: "D" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 505 Classifications: {'peptide': 33} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'TRANS': 31} Chain: "E" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 505 Classifications: {'peptide': 33} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'TRANS': 31} Chain: "F" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 505 Classifications: {'peptide': 33} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'TRANS': 31} Chain: "G" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 505 Classifications: {'peptide': 33} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'TRANS': 31} Chain: "H" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 505 Classifications: {'peptide': 33} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'TRANS': 31} Time building chain proxies: 1.07, per 1000 atoms: 0.26 Number of scatterers: 4040 At special positions: 0 Unit cell: (71.1504, 76.4208, 38.6496, 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 8 16.00 O 344 8.00 N 352 7.00 C 1336 6.00 H 2000 1.00 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: 0.33 Conformation dependent library (CDL) restraints added in 94.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 496 Ramachandran restraints generated. 248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 416 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 4 sheets defined 0.0% alpha, 66.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 152 through 162 removed outlier: 6.366A pdb=" N TRP A 153 " --> pdb=" O LYS B 154 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N TRP B 156 " --> pdb=" O TRP A 153 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N THR A 155 " --> pdb=" O TRP B 156 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N GLN B 158 " --> pdb=" O THR A 155 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N GLY A 157 " --> pdb=" O GLN B 158 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N TRP B 160 " --> pdb=" O GLY A 157 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N TYR A 159 " --> pdb=" O TRP B 160 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N VAL B 162 " --> pdb=" O TYR A 159 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N GLN A 161 " --> pdb=" O VAL B 162 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 167 through 179 removed outlier: 8.759A pdb=" N SER A 168 " --> pdb=" O GLY B 169 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N SER B 171 " --> pdb=" O SER A 168 " (cutoff:3.500A) removed outlier: 8.878A pdb=" N LEU A 170 " --> pdb=" O SER B 171 " (cutoff:3.500A) removed outlier: 10.384A pdb=" N GLY B 173 " --> pdb=" O LEU A 170 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ILE A 172 " --> pdb=" O GLY B 173 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N GLY B 175 " --> pdb=" O ILE A 172 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N THR A 174 " --> pdb=" O GLY B 175 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N ALA B 177 " --> pdb=" O THR A 174 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ARG A 176 " --> pdb=" O ALA B 177 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N LEU B 179 " --> pdb=" O ARG A 176 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N MET A 178 " --> pdb=" O LEU B 179 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU B 170 " --> pdb=" O GLY C 169 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N SER C 171 " --> pdb=" O LEU B 170 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ILE B 172 " --> pdb=" O SER C 171 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N GLY C 173 " --> pdb=" O ILE B 172 " (cutoff:3.500A) removed outlier: 8.756A pdb=" N SER C 168 " --> pdb=" O GLY D 169 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N SER D 171 " --> pdb=" O SER C 168 " (cutoff:3.500A) removed outlier: 8.969A pdb=" N LEU C 170 " --> pdb=" O SER D 171 " (cutoff:3.500A) removed outlier: 10.410A pdb=" N GLY D 173 " --> pdb=" O LEU C 170 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ILE C 172 " --> pdb=" O GLY D 173 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N GLY D 175 " --> pdb=" O ILE C 172 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N THR C 174 " --> pdb=" O GLY D 175 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N ALA D 177 " --> pdb=" O THR C 174 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ARG C 176 " --> pdb=" O ALA D 177 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N LEU D 179 " --> pdb=" O ARG C 176 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N MET C 178 " --> pdb=" O LEU D 179 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 152 through 162 removed outlier: 6.345A pdb=" N TRP E 153 " --> pdb=" O LYS F 154 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N TRP F 156 " --> pdb=" O TRP E 153 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N THR E 155 " --> pdb=" O TRP F 156 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N GLN F 158 " --> pdb=" O THR E 155 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLY E 157 " --> pdb=" O GLN F 158 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N TRP F 160 " --> pdb=" O GLY E 157 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N TYR E 159 " --> pdb=" O TRP F 160 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N VAL F 162 " --> pdb=" O TYR E 159 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N GLN E 161 " --> pdb=" O VAL F 162 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 167 through 179 removed outlier: 8.749A pdb=" N SER E 168 " --> pdb=" O GLY F 169 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N SER F 171 " --> pdb=" O SER E 168 " (cutoff:3.500A) removed outlier: 8.888A pdb=" N LEU E 170 " --> pdb=" O SER F 171 " (cutoff:3.500A) removed outlier: 10.352A pdb=" N GLY F 173 " --> pdb=" O LEU E 170 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ILE E 172 " --> pdb=" O GLY F 173 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N GLY F 175 " --> pdb=" O ILE E 172 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N THR E 174 " --> pdb=" O GLY F 175 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N ALA F 177 " --> pdb=" O THR E 174 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ARG E 176 " --> pdb=" O ALA F 177 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N LEU F 179 " --> pdb=" O ARG E 176 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N MET E 178 " --> pdb=" O LEU F 179 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LEU F 170 " --> pdb=" O GLY G 169 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N SER G 171 " --> pdb=" O LEU F 170 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ILE F 172 " --> pdb=" O SER G 171 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLY G 173 " --> pdb=" O ILE F 172 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LEU G 170 " --> pdb=" O GLY H 169 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N SER H 171 " --> pdb=" O LEU G 170 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ILE G 172 " --> pdb=" O SER H 171 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N GLY H 173 " --> pdb=" O ILE G 172 " (cutoff:3.500A) 64 hydrogen bonds defined for protein. 192 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: 0.73 Time building geometry restraints manager: 0.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.12: 2000 1.12 - 1.30: 289 1.30 - 1.47: 919 1.47 - 1.64: 888 1.64 - 1.81: 16 Bond restraints: 4112 Sorted by residual: bond pdb=" CZ3 TRP C 153 " pdb=" HZ3 TRP C 153 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" N MET D 178 " pdb=" H MET D 178 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.66e+01 bond pdb=" N TRP F 153 " pdb=" H TRP F 153 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.66e+01 bond pdb=" N LYS F 154 " pdb=" H LYS F 154 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.66e+01 bond pdb=" CD1 TRP F 153 " pdb=" HD1 TRP F 153 " ideal model delta sigma weight residual 0.930 1.080 -0.150 2.00e-02 2.50e+03 5.66e+01 ... (remaining 4107 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 5068 1.55 - 3.09: 1588 3.09 - 4.64: 383 4.64 - 6.18: 261 6.18 - 7.73: 60 Bond angle restraints: 7360 Sorted by residual: angle pdb=" N GLY G 175 " pdb=" CA GLY G 175 " pdb=" C GLY G 175 " ideal model delta sigma weight residual 110.58 118.31 -7.73 1.35e+00 5.49e-01 3.27e+01 angle pdb=" N GLY C 175 " pdb=" CA GLY C 175 " pdb=" C GLY C 175 " ideal model delta sigma weight residual 110.58 117.98 -7.40 1.35e+00 5.49e-01 3.01e+01 angle pdb=" N GLY B 175 " pdb=" CA GLY B 175 " pdb=" C GLY B 175 " ideal model delta sigma weight residual 110.45 117.52 -7.07 1.30e+00 5.92e-01 2.96e+01 angle pdb=" N GLY F 175 " pdb=" CA GLY F 175 " pdb=" C GLY F 175 " ideal model delta sigma weight residual 110.45 117.43 -6.98 1.30e+00 5.92e-01 2.88e+01 angle pdb=" OE1 GLN H 158 " pdb=" CD GLN H 158 " pdb=" NE2 GLN H 158 " ideal model delta sigma weight residual 122.60 118.28 4.32 1.00e+00 1.00e+00 1.86e+01 ... (remaining 7355 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.02: 1663 14.02 - 28.04: 105 28.04 - 42.06: 41 42.06 - 56.08: 43 56.08 - 70.10: 52 Dihedral angle restraints: 1904 sinusoidal: 984 harmonic: 920 Sorted by residual: dihedral pdb=" CA TRP H 160 " pdb=" C TRP H 160 " pdb=" N GLN H 161 " pdb=" CA GLN H 161 " ideal model delta harmonic sigma weight residual 180.00 156.43 23.57 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" CA TRP E 160 " pdb=" C TRP E 160 " pdb=" N GLN E 161 " pdb=" CA GLN E 161 " ideal model delta harmonic sigma weight residual 180.00 156.78 23.22 0 5.00e+00 4.00e-02 2.16e+01 dihedral pdb=" CA TRP D 160 " pdb=" C TRP D 160 " pdb=" N GLN D 161 " pdb=" CA GLN D 161 " ideal model delta harmonic sigma weight residual 180.00 156.79 23.21 0 5.00e+00 4.00e-02 2.15e+01 ... (remaining 1901 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 103 0.039 - 0.077: 93 0.077 - 0.116: 72 0.116 - 0.155: 24 0.155 - 0.193: 4 Chirality restraints: 296 Sorted by residual: chirality pdb=" CA THR G 183 " pdb=" N THR G 183 " pdb=" C THR G 183 " pdb=" CB THR G 183 " both_signs ideal model delta sigma weight residual False 2.53 2.33 0.19 2.00e-01 2.50e+01 9.34e-01 chirality pdb=" CA THR C 183 " pdb=" N THR C 183 " pdb=" C THR C 183 " pdb=" CB THR C 183 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.19 2.00e-01 2.50e+01 8.86e-01 chirality pdb=" CA THR B 183 " pdb=" N THR B 183 " pdb=" C THR B 183 " pdb=" CB THR B 183 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.19 2.00e-01 2.50e+01 8.63e-01 ... (remaining 293 not shown) Planarity restraints: 584 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 153 " 0.076 2.00e-02 2.50e+03 3.26e-02 4.24e+01 pdb=" CG TRP A 153 " 0.001 2.00e-02 2.50e+03 pdb=" CD1 TRP A 153 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TRP A 153 " -0.041 2.00e-02 2.50e+03 pdb=" NE1 TRP A 153 " -0.030 2.00e-02 2.50e+03 pdb=" CE2 TRP A 153 " -0.026 2.00e-02 2.50e+03 pdb=" CE3 TRP A 153 " -0.046 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 153 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 153 " -0.015 2.00e-02 2.50e+03 pdb=" CH2 TRP A 153 " 0.014 2.00e-02 2.50e+03 pdb=" HD1 TRP A 153 " 0.028 2.00e-02 2.50e+03 pdb=" HE1 TRP A 153 " -0.021 2.00e-02 2.50e+03 pdb=" HE3 TRP A 153 " -0.027 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 153 " 0.024 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 153 " 0.015 2.00e-02 2.50e+03 pdb=" HH2 TRP A 153 " 0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 160 " -0.035 2.00e-02 2.50e+03 3.14e-02 3.94e+01 pdb=" CG TRP A 160 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 TRP A 160 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 TRP A 160 " -0.033 2.00e-02 2.50e+03 pdb=" NE1 TRP A 160 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 TRP A 160 " -0.027 2.00e-02 2.50e+03 pdb=" CE3 TRP A 160 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 160 " -0.032 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 160 " 0.025 2.00e-02 2.50e+03 pdb=" CH2 TRP A 160 " -0.006 2.00e-02 2.50e+03 pdb=" HD1 TRP A 160 " 0.029 2.00e-02 2.50e+03 pdb=" HE1 TRP A 160 " 0.071 2.00e-02 2.50e+03 pdb=" HE3 TRP A 160 " 0.020 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 160 " -0.037 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 160 " 0.049 2.00e-02 2.50e+03 pdb=" HH2 TRP A 160 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 160 " -0.034 2.00e-02 2.50e+03 3.02e-02 3.65e+01 pdb=" CG TRP E 160 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 TRP E 160 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TRP E 160 " -0.033 2.00e-02 2.50e+03 pdb=" NE1 TRP E 160 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 TRP E 160 " -0.029 2.00e-02 2.50e+03 pdb=" CE3 TRP E 160 " 0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 160 " -0.027 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 160 " 0.021 2.00e-02 2.50e+03 pdb=" CH2 TRP E 160 " -0.006 2.00e-02 2.50e+03 pdb=" HD1 TRP E 160 " 0.026 2.00e-02 2.50e+03 pdb=" HE1 TRP E 160 " 0.070 2.00e-02 2.50e+03 pdb=" HE3 TRP E 160 " 0.028 2.00e-02 2.50e+03 pdb=" HZ2 TRP E 160 " -0.033 2.00e-02 2.50e+03 pdb=" HZ3 TRP E 160 " 0.040 2.00e-02 2.50e+03 pdb=" HH2 TRP E 160 " -0.010 2.00e-02 2.50e+03 ... (remaining 581 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.36: 852 2.36 - 2.92: 8389 2.92 - 3.48: 10759 3.48 - 4.04: 15237 4.04 - 4.60: 20099 Nonbonded interactions: 55336 Sorted by model distance: nonbonded pdb=" HE3 MET B 178 " pdb=" HE ARG C 176 " model vdw 1.806 2.270 nonbonded pdb=" O THR C 183 " pdb=" HG1 THR D 183 " model vdw 1.816 2.450 nonbonded pdb=" O THR F 183 " pdb=" HG1 THR G 183 " model vdw 1.817 2.450 nonbonded pdb=" O THR B 183 " pdb=" HG1 THR C 183 " model vdw 1.819 2.450 nonbonded pdb=" H LEU F 163 " pdb=" O VAL G 162 " model vdw 1.820 2.450 ... (remaining 55331 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 0.050 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: 0.020 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.720 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.000 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:5.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6900 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.041 2112 Z= 0.743 Angle : 1.698 7.725 2880 Z= 1.106 Chirality : 0.073 0.193 296 Planarity : 0.010 0.052 336 Dihedral : 11.861 65.051 672 Min Nonbonded Distance : 2.673 Molprobity Statistics. All-atom Clashscore : 0.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 100.00 % 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: -2.92 (0.33), residues: 248 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.22 (0.25), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 176 TYR 0.035 0.007 TYR E 159 TRP 0.054 0.013 TRP A 153 HIS 0.006 0.002 HIS D 182 Details of bonding type rmsd covalent geometry : bond 0.01239 ( 2112) covalent geometry : angle 1.69846 ( 2880) hydrogen bonds : bond 0.09928 ( 64) hydrogen bonds : angle 8.62075 ( 192) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 496 Ramachandran restraints generated. 248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 496 Ramachandran restraints generated. 248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.121 Fit side-chains revert: symmetry clash REVERT: A 154 LYS cc_start: 0.7602 (mttt) cc_final: 0.7300 (mttt) REVERT: A 178 MET cc_start: 0.7652 (mtm) cc_final: 0.7252 (mtp) REVERT: B 152 VAL cc_start: 0.7749 (t) cc_final: 0.7504 (p) REVERT: B 154 LYS cc_start: 0.7397 (mttt) cc_final: 0.7063 (mttt) REVERT: B 163 LEU cc_start: 0.7973 (mt) cc_final: 0.7675 (mm) REVERT: B 176 ARG cc_start: 0.7080 (mtp85) cc_final: 0.6726 (mtm180) REVERT: C 154 LYS cc_start: 0.7334 (mttt) cc_final: 0.6999 (mtpt) REVERT: C 176 ARG cc_start: 0.7075 (mtp180) cc_final: 0.6833 (mtm180) REVERT: D 152 VAL cc_start: 0.7528 (t) cc_final: 0.7167 (p) REVERT: D 176 ARG cc_start: 0.7319 (mtp85) cc_final: 0.7080 (ttm170) REVERT: D 178 MET cc_start: 0.7814 (mtm) cc_final: 0.7433 (mtp) REVERT: E 154 LYS cc_start: 0.7572 (mttt) cc_final: 0.7290 (mttt) REVERT: E 178 MET cc_start: 0.7633 (mtm) cc_final: 0.7205 (mtp) REVERT: F 154 LYS cc_start: 0.7448 (mttt) cc_final: 0.7200 (mttt) REVERT: F 163 LEU cc_start: 0.8005 (mt) cc_final: 0.7701 (mm) REVERT: F 176 ARG cc_start: 0.7109 (mtp85) cc_final: 0.6685 (mtm180) REVERT: G 154 LYS cc_start: 0.7406 (mttt) cc_final: 0.7090 (mtpt) REVERT: G 176 ARG cc_start: 0.7209 (mtp85) cc_final: 0.6967 (ttm170) REVERT: H 152 VAL cc_start: 0.7601 (t) cc_final: 0.7228 (p) REVERT: H 178 MET cc_start: 0.7840 (mtm) cc_final: 0.7399 (mtp) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 1.0234 time to fit residues: 53.1681 Evaluate side-chains 47 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 12 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 9 optimal weight: 6.9990 chunk 11 optimal weight: 6.9990 chunk 18 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.144040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.112396 restraints weight = 4495.055| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 1.61 r_work: 0.3452 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3371 rms_B_bonded: 2.50 restraints_weight: 0.2500 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9206 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2112 Z= 0.141 Angle : 0.590 4.810 2880 Z= 0.305 Chirality : 0.047 0.147 296 Planarity : 0.004 0.022 336 Dihedral : 6.926 19.326 280 Min Nonbonded Distance : 2.694 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 100.00 % 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: -3.00 (0.33), residues: 248 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.28 (0.25), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 176 TYR 0.005 0.001 TYR A 151 TRP 0.011 0.002 TRP C 160 HIS 0.003 0.001 HIS A 182 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 2112) covalent geometry : angle 0.58993 ( 2880) hydrogen bonds : bond 0.03652 ( 64) hydrogen bonds : angle 6.47303 ( 192) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 496 Ramachandran restraints generated. 248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 496 Ramachandran restraints generated. 248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.072 Fit side-chains REVERT: D 152 VAL cc_start: 0.8579 (t) cc_final: 0.8343 (p) outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 1.1916 time to fit residues: 56.8755 Evaluate side-chains 46 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 chunk 15 optimal weight: 9.9990 chunk 22 optimal weight: 9.9990 chunk 23 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 6 optimal weight: 20.0000 chunk 19 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 9.9990 chunk 14 optimal weight: 5.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.143663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.112425 restraints weight = 4308.398| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 1.56 r_work: 0.3437 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3356 rms_B_bonded: 2.42 restraints_weight: 0.2500 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9176 moved from start: 0.3436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 2112 Z= 0.106 Angle : 0.521 3.804 2880 Z= 0.272 Chirality : 0.046 0.136 296 Planarity : 0.004 0.022 336 Dihedral : 6.492 18.188 280 Min Nonbonded Distance : 2.698 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 100.00 % 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: -3.06 (0.34), residues: 248 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.32 (0.26), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 176 TYR 0.004 0.001 TYR G 151 TRP 0.010 0.001 TRP A 153 HIS 0.001 0.000 HIS A 182 Details of bonding type rmsd covalent geometry : bond 0.00222 ( 2112) covalent geometry : angle 0.52091 ( 2880) hydrogen bonds : bond 0.03039 ( 64) hydrogen bonds : angle 5.96018 ( 192) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 496 Ramachandran restraints generated. 248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 496 Ramachandran restraints generated. 248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.135 Fit side-chains REVERT: D 152 VAL cc_start: 0.8576 (t) cc_final: 0.8328 (p) outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 1.3203 time to fit residues: 62.9494 Evaluate side-chains 46 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 20 optimal weight: 20.0000 chunk 17 optimal weight: 8.9990 chunk 15 optimal weight: 8.9990 chunk 11 optimal weight: 9.9990 chunk 19 optimal weight: 10.0000 chunk 4 optimal weight: 10.0000 chunk 21 optimal weight: 9.9990 chunk 7 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.143497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.112395 restraints weight = 4409.601| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 1.58 r_work: 0.3469 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3388 rms_B_bonded: 2.42 restraints_weight: 0.2500 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9192 moved from start: 0.3645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 2112 Z= 0.115 Angle : 0.525 3.547 2880 Z= 0.274 Chirality : 0.046 0.138 296 Planarity : 0.004 0.023 336 Dihedral : 6.391 17.841 280 Min Nonbonded Distance : 2.694 Molprobity Statistics. All-atom Clashscore : 1.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.00 % Allowed : 10.50 % Favored : 88.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 100.00 % 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: -2.98 (0.35), residues: 248 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.26 (0.27), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 176 TYR 0.005 0.001 TYR C 151 TRP 0.008 0.001 TRP B 153 HIS 0.001 0.000 HIS E 182 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 2112) covalent geometry : angle 0.52458 ( 2880) hydrogen bonds : bond 0.03171 ( 64) hydrogen bonds : angle 5.76812 ( 192) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 496 Ramachandran restraints generated. 248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 496 Ramachandran restraints generated. 248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 48 time to evaluate : 0.126 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 49 average time/residue: 1.2749 time to fit residues: 63.4799 Evaluate side-chains 46 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- 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: 65.1544 > 50: distance: 17 - 36: 7.324 distance: 36 - 37: 20.516 distance: 36 - 50: 19.392 distance: 37 - 38: 25.744 distance: 37 - 40: 4.519 distance: 37 - 51: 25.556 distance: 38 - 39: 27.248 distance: 38 - 60: 37.156 distance: 40 - 41: 5.923 distance: 40 - 52: 27.507 distance: 40 - 53: 19.436 distance: 41 - 42: 10.863 distance: 41 - 43: 9.491 distance: 42 - 44: 12.424 distance: 42 - 54: 13.026 distance: 43 - 45: 18.215 distance: 43 - 46: 13.472 distance: 44 - 45: 13.422 distance: 44 - 55: 10.761 distance: 45 - 47: 21.485 distance: 46 - 48: 6.693 distance: 46 - 56: 8.179 distance: 47 - 49: 11.610 distance: 47 - 57: 8.599 distance: 48 - 49: 13.577 distance: 48 - 58: 11.691 distance: 49 - 59: 10.280 distance: 60 - 61: 17.759 distance: 60 - 69: 24.535 distance: 61 - 62: 5.374 distance: 61 - 64: 4.408 distance: 61 - 70: 6.194 distance: 62 - 63: 12.657 distance: 62 - 77: 13.736 distance: 64 - 65: 12.131 distance: 64 - 71: 7.412 distance: 64 - 72: 6.962 distance: 65 - 66: 11.514 distance: 65 - 73: 6.108 distance: 65 - 74: 8.313 distance: 66 - 67: 19.661 distance: 66 - 68: 8.616 distance: 68 - 75: 9.988 distance: 68 - 76: 8.839 distance: 77 - 78: 17.459 distance: 77 - 84: 5.383 distance: 78 - 79: 21.824 distance: 78 - 81: 13.857 distance: 78 - 85: 16.414 distance: 79 - 80: 24.958 distance: 79 - 93: 22.295 distance: 81 - 82: 9.752 distance: 81 - 83: 15.994 distance: 81 - 86: 4.818 distance: 82 - 87: 11.122 distance: 82 - 88: 8.902 distance: 82 - 89: 11.282 distance: 83 - 90: 11.413 distance: 83 - 91: 8.741 distance: 83 - 92: 9.333 distance: 93 - 94: 16.716 distance: 93 - 101: 4.274 distance: 94 - 95: 3.877 distance: 94 - 97: 14.577 distance: 94 - 102: 12.047 distance: 95 - 96: 32.253 distance: 95 - 112: 22.717 distance: 97 - 98: 10.112 distance: 97 - 103: 8.268 distance: 97 - 104: 3.527 distance: 98 - 99: 9.950 distance: 98 - 100: 4.863 distance: 98 - 105: 3.127 distance: 99 - 106: 5.137 distance: 99 - 107: 5.947 distance: 99 - 108: 3.735 distance: 100 - 109: 3.433 distance: 100 - 110: 5.114 distance: 100 - 111: 4.480 distance: 112 - 113: 9.538 distance: 112 - 116: 20.568 distance: 113 - 114: 22.454 distance: 113 - 117: 5.908 distance: 113 - 118: 18.047 distance: 114 - 115: 15.315 distance: 114 - 119: 19.920 distance: 119 - 120: 38.232 distance: 119 - 123: 26.310 distance: 120 - 121: 17.945 distance: 120 - 124: 65.154 distance: 120 - 125: 37.615 distance: 121 - 122: 7.798 distance: 121 - 126: 11.239 distance: 126 - 127: 19.586 distance: 126 - 132: 24.613 distance: 127 - 128: 9.785 distance: 127 - 130: 10.919 distance: 127 - 133: 24.022 distance: 128 - 129: 22.180 distance: 128 - 140: 6.463 distance: 130 - 131: 27.004 distance: 130 - 134: 23.043 distance: 130 - 135: 10.906 distance: 131 - 132: 11.754 distance: 131 - 136: 8.143 distance: 131 - 137: 7.432 distance: 132 - 138: 28.368 distance: 132 - 139: 27.974 distance: 140 - 141: 31.888 distance: 140 - 147: 20.419 distance: 141 - 142: 26.327 distance: 141 - 144: 14.795 distance: 141 - 148: 22.427 distance: 142 - 143: 11.426 distance: 142 - 156: 27.193 distance: 144 - 145: 11.628 distance: 144 - 146: 11.184 distance: 144 - 149: 12.810 distance: 145 - 150: 3.957 distance: 145 - 151: 25.011 distance: 145 - 152: 13.232 distance: 146 - 153: 6.873 distance: 146 - 155: 3.284 distance: 156 - 157: 3.813 distance: 156 - 162: 17.870 distance: 157 - 158: 18.696 distance: 157 - 160: 20.647 distance: 157 - 163: 13.251 distance: 158 - 159: 9.334 distance: 158 - 167: 24.915 distance: 160 - 161: 9.548 distance: 160 - 164: 11.002 distance: 160 - 165: 3.640 distance: 161 - 166: 13.868 distance: 167 - 168: 13.147 distance: 167 - 171: 21.848 distance: 168 - 169: 6.988 distance: 168 - 172: 18.421 distance: 168 - 173: 15.607 distance: 169 - 170: 11.064 distance: 169 - 174: 4.559