Starting phenix.real_space_refine on Sun Aug 24 11:54:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7k5y_22684/08_2025/7k5y_22684.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k5y_22684/08_2025/7k5y_22684.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7k5y_22684/08_2025/7k5y_22684.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k5y_22684/08_2025/7k5y_22684.map" model { file = "/net/cci-nas-00/data/ceres_data/7k5y_22684/08_2025/7k5y_22684.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k5y_22684/08_2025/7k5y_22684.cif" } resolution = 2.76 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= -0.002 sd= 0.105 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2242 atoms to isotropic. 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 394 5.49 5 S 32 5.16 5 C 10240 2.51 5 N 3340 2.21 5 O 4252 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 43 residue(s): 0.02s 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: 18258 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 799 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "B" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 840 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "D" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 799 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "F" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "G" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 840 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "H" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "I" Number of atoms: 4015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 4015 Classifications: {'DNA': 197} Link IDs: {'rna3p': 196} Chain: "J" Number of atoms: 4062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 4062 Classifications: {'DNA': 197} Link IDs: {'rna3p': 196} Chain: "M" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1777 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 10, 'TRANS': 216} Chain breaks: 1 Chain: "N" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1777 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 10, 'TRANS': 216} Chain breaks: 1 Chain: "U" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 535 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Time building chain proxies: 4.34, per 1000 atoms: 0.24 Number of scatterers: 18258 At special positions: 0 Unit cell: (133.056, 121.968, 197.568, 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 32 16.00 P 394 15.00 O 4252 8.00 N 3340 7.00 C 10240 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.83 Conformation dependent library (CDL) restraints added in 597.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2542 Ramachandran restraints generated. 1271 Oldfield, 0 Emsley, 1271 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2406 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 23 sheets defined 49.0% alpha, 20.8% beta 194 base pairs and 357 stacking pairs defined. Time for finding SS restraints: 3.17 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.801A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.826A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.764A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.353A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 123 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 77 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.604A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.321A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 104 through 124 Processing helix chain 'M' and resid 98 through 102 Processing helix chain 'M' and resid 177 through 179 No H-bonds generated for 'chain 'M' and resid 177 through 179' Processing helix chain 'M' and resid 211 through 214 removed outlier: 3.516A pdb=" N LYS M 214 " --> pdb=" O GLU M 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 211 through 214' Processing helix chain 'M' and resid 236 through 240 Processing helix chain 'N' and resid 98 through 102 Processing helix chain 'N' and resid 177 through 179 No H-bonds generated for 'chain 'N' and resid 177 through 179' Processing helix chain 'N' and resid 211 through 214 removed outlier: 3.600A pdb=" N LYS N 214 " --> pdb=" O GLU N 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 211 through 214' Processing helix chain 'N' and resid 236 through 240 Processing helix chain 'U' and resid 38 through 51 removed outlier: 3.737A pdb=" N LEU U 42 " --> pdb=" O PRO U 38 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N SER U 50 " --> pdb=" O ALA U 46 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS U 51 " --> pdb=" O VAL U 47 " (cutoff:3.500A) Processing helix chain 'U' and resid 58 through 69 Processing helix chain 'U' and resid 71 through 74 removed outlier: 3.639A pdb=" N LYS U 74 " --> pdb=" O ASP U 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 71 through 74' Processing helix chain 'U' and resid 75 through 89 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.726A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.112A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.587A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.601A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 6.999A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'M' and resid 23 through 25 removed outlier: 3.753A pdb=" N ASP M 89 " --> pdb=" O SER M 86 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'M' and resid 29 through 32 removed outlier: 6.213A pdb=" N MET M 30 " --> pdb=" O GLU M 124 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LEU M 52 " --> pdb=" O TYR M 68 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N TYR M 68 " --> pdb=" O LEU M 52 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N TRP M 54 " --> pdb=" O LEU M 66 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 29 through 32 removed outlier: 6.213A pdb=" N MET M 30 " --> pdb=" O GLU M 124 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'M' and resid 152 through 155 Processing sheet with id=AB6, first strand: chain 'M' and resid 159 through 161 removed outlier: 6.208A pdb=" N GLU M 159 " --> pdb=" O THR M 266 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N TYR M 181 " --> pdb=" O TYR M 201 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N TYR M 201 " --> pdb=" O TYR M 181 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ILE M 183 " --> pdb=" O TYR M 199 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N TYR M 199 " --> pdb=" O ILE M 183 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N TRP M 185 " --> pdb=" O ILE M 197 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'M' and resid 159 through 161 removed outlier: 6.208A pdb=" N GLU M 159 " --> pdb=" O THR M 266 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N TYR M 258 " --> pdb=" O ARG M 247 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 23 through 25 removed outlier: 3.778A pdb=" N ASP N 89 " --> pdb=" O SER N 86 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'N' and resid 29 through 32 removed outlier: 6.808A pdb=" N LEU N 52 " --> pdb=" O TYR N 68 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N TYR N 68 " --> pdb=" O LEU N 52 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N TRP N 54 " --> pdb=" O LEU N 66 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'N' and resid 29 through 32 Processing sheet with id=AC2, first strand: chain 'N' and resid 152 through 155 Processing sheet with id=AC3, first strand: chain 'N' and resid 159 through 161 removed outlier: 6.602A pdb=" N ILE N 183 " --> pdb=" O TYR N 199 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N TYR N 199 " --> pdb=" O ILE N 183 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N TRP N 185 " --> pdb=" O ILE N 197 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'N' and resid 159 through 161 removed outlier: 3.859A pdb=" N TYR N 258 " --> pdb=" O ARG N 247 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N SER N 249 " --> pdb=" O LEU N 256 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N LEU N 256 " --> pdb=" O SER N 249 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'U' and resid 56 through 57 612 hydrogen bonds defined for protein. 1683 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 504 hydrogen bonds 1008 hydrogen bond angles 0 basepair planarities 194 basepair parallelities 357 stacking parallelities Total time for adding SS restraints: 4.09 Time building geometry restraints manager: 2.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3473 1.33 - 1.45: 6143 1.45 - 1.57: 8954 1.57 - 1.69: 786 1.69 - 1.81: 52 Bond restraints: 19408 Sorted by residual: bond pdb=" N SER M 26 " pdb=" CA SER M 26 " ideal model delta sigma weight residual 1.463 1.490 -0.027 6.90e-03 2.10e+04 1.50e+01 bond pdb=" C SER M 26 " pdb=" O SER M 26 " ideal model delta sigma weight residual 1.244 1.260 -0.016 9.10e-03 1.21e+04 3.15e+00 bond pdb=" C3' DG J 119 " pdb=" O3' DG J 119 " ideal model delta sigma weight residual 1.422 1.471 -0.049 3.00e-02 1.11e+03 2.68e+00 bond pdb=" CA SER M 26 " pdb=" C SER M 26 " ideal model delta sigma weight residual 1.521 1.505 0.016 1.08e-02 8.57e+03 2.14e+00 bond pdb=" C3' DG I 153 " pdb=" O3' DG I 153 " ideal model delta sigma weight residual 1.422 1.460 -0.038 3.00e-02 1.11e+03 1.59e+00 ... (remaining 19403 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.32: 26392 1.32 - 2.65: 1373 2.65 - 3.97: 125 3.97 - 5.29: 16 5.29 - 6.62: 9 Bond angle restraints: 27915 Sorted by residual: angle pdb=" CA SER M 26 " pdb=" C SER M 26 " pdb=" N PRO M 27 " ideal model delta sigma weight residual 120.58 122.54 -1.96 7.40e-01 1.83e+00 6.99e+00 angle pdb=" N GLY D 104 " pdb=" CA GLY D 104 " pdb=" C GLY D 104 " ideal model delta sigma weight residual 113.18 119.19 -6.01 2.37e+00 1.78e-01 6.42e+00 angle pdb=" C3' DG J 128 " pdb=" C2' DG J 128 " pdb=" C1' DG J 128 " ideal model delta sigma weight residual 101.60 97.81 3.79 1.50e+00 4.44e-01 6.39e+00 angle pdb=" C3' DT J 153 " pdb=" O3' DT J 153 " pdb=" P DC J 154 " ideal model delta sigma weight residual 120.20 123.94 -3.74 1.50e+00 4.44e-01 6.20e+00 angle pdb=" N SER N 50 " pdb=" CA SER N 50 " pdb=" CB SER N 50 " ideal model delta sigma weight residual 113.65 110.00 3.65 1.47e+00 4.63e-01 6.16e+00 ... (remaining 27910 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.24: 8535 34.24 - 68.47: 2039 68.47 - 102.71: 22 102.71 - 136.95: 3 136.95 - 171.18: 2 Dihedral angle restraints: 10601 sinusoidal: 6846 harmonic: 3755 Sorted by residual: dihedral pdb=" CA PRO D 103 " pdb=" C PRO D 103 " pdb=" N GLY D 104 " pdb=" CA GLY D 104 " ideal model delta harmonic sigma weight residual 180.00 159.44 20.56 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" C4' DT J 153 " pdb=" C3' DT J 153 " pdb=" O3' DT J 153 " pdb=" P DC J 154 " ideal model delta sinusoidal sigma weight residual 220.00 48.82 171.18 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DG J 119 " pdb=" C3' DG J 119 " pdb=" O3' DG J 119 " pdb=" P DG J 120 " ideal model delta sinusoidal sigma weight residual 220.00 51.89 168.11 1 3.50e+01 8.16e-04 1.55e+01 ... (remaining 10598 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 2308 0.038 - 0.076: 668 0.076 - 0.113: 147 0.113 - 0.151: 27 0.151 - 0.189: 2 Chirality restraints: 3152 Sorted by residual: chirality pdb=" CG LEU M 252 " pdb=" CB LEU M 252 " pdb=" CD1 LEU M 252 " pdb=" CD2 LEU M 252 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.91e-01 chirality pdb=" CB THR M 177 " pdb=" CA THR M 177 " pdb=" OG1 THR M 177 " pdb=" CG2 THR M 177 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.54e-01 chirality pdb=" CG LEU N 252 " pdb=" CB LEU N 252 " pdb=" CD1 LEU N 252 " pdb=" CD2 LEU N 252 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 5.08e-01 ... (remaining 3149 not shown) Planarity restraints: 2154 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY M 157 " -0.038 5.00e-02 4.00e+02 5.76e-02 5.31e+00 pdb=" N PRO M 158 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO M 158 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO M 158 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 102 " 0.030 5.00e-02 4.00e+02 4.48e-02 3.21e+00 pdb=" N PRO D 103 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO D 103 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO D 103 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 45 " 0.021 2.00e-02 2.50e+03 1.02e-02 2.86e+00 pdb=" N9 DA I 45 " -0.026 2.00e-02 2.50e+03 pdb=" C8 DA I 45 " -0.000 2.00e-02 2.50e+03 pdb=" N7 DA I 45 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DA I 45 " 0.003 2.00e-02 2.50e+03 pdb=" C6 DA I 45 " 0.001 2.00e-02 2.50e+03 pdb=" N6 DA I 45 " 0.005 2.00e-02 2.50e+03 pdb=" N1 DA I 45 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DA I 45 " -0.002 2.00e-02 2.50e+03 pdb=" N3 DA I 45 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DA I 45 " -0.002 2.00e-02 2.50e+03 ... (remaining 2151 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 491 2.67 - 3.22: 15344 3.22 - 3.78: 33372 3.78 - 4.34: 45180 4.34 - 4.90: 64961 Nonbonded interactions: 159348 Sorted by model distance: nonbonded pdb=" OD2 ASP G 90 " pdb=" NH2 ARG N 251 " model vdw 2.108 3.120 nonbonded pdb=" O SER N 156 " pdb=" OG1 THR N 263 " model vdw 2.171 3.040 nonbonded pdb=" OD2 ASP U 71 " pdb=" NZ LYS U 74 " model vdw 2.224 3.120 nonbonded pdb=" OG SER H 56 " pdb=" OP2 DA I 45 " model vdw 2.258 3.040 nonbonded pdb=" O GLN N 155 " pdb=" NE2 GLN N 261 " model vdw 2.275 3.120 ... (remaining 159343 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 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'M' selection = chain 'N' } 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: 3.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 21.060 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:7.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 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 : 0.004 0.049 19408 Z= 0.200 Angle : 0.647 6.616 27915 Z= 0.397 Chirality : 0.038 0.189 3152 Planarity : 0.004 0.058 2154 Dihedral : 27.043 171.183 8195 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % 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: 1.74 (0.23), residues: 1271 helix: 2.37 (0.21), residues: 584 sheet: 0.64 (0.33), residues: 252 loop : -0.19 (0.28), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 69 TYR 0.026 0.002 TYR N 201 PHE 0.015 0.002 PHE D 65 TRP 0.017 0.002 TRP M 185 HIS 0.005 0.001 HIS D 49 Details of bonding type rmsd covalent geometry : bond 0.00435 (19408) covalent geometry : angle 0.64663 (27915) hydrogen bonds : bond 0.09867 ( 1096) hydrogen bonds : angle 4.33555 ( 2691) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2542 Ramachandran restraints generated. 1271 Oldfield, 0 Emsley, 1271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2542 Ramachandran restraints generated. 1271 Oldfield, 0 Emsley, 1271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 270 time to evaluate : 0.608 Fit side-chains revert: symmetry clash REVERT: A 50 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7645 (mt-10) REVERT: E 123 ASP cc_start: 0.8714 (m-30) cc_final: 0.8467 (m-30) REVERT: G 94 ASN cc_start: 0.9158 (t0) cc_final: 0.8954 (t0) REVERT: H 42 TYR cc_start: 0.8151 (t80) cc_final: 0.7855 (t80) REVERT: M 96 ASN cc_start: 0.8143 (m-40) cc_final: 0.7910 (m-40) REVERT: M 160 LEU cc_start: 0.8575 (mm) cc_final: 0.8307 (mm) outliers start: 0 outliers final: 0 residues processed: 270 average time/residue: 0.9837 time to fit residues: 286.2682 Evaluate side-chains 204 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 30.0000 chunk 149 optimal weight: 5.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN D 84 ASN F 93 GLN G 24 GLN H 47 GLN M 25 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.155709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.104190 restraints weight = 22450.579| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 1.30 r_work: 0.3162 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 19408 Z= 0.247 Angle : 0.630 6.931 27915 Z= 0.370 Chirality : 0.039 0.174 3152 Planarity : 0.005 0.049 2154 Dihedral : 30.693 167.186 5711 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.56 % Allowed : 11.32 % Favored : 86.12 % 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: 1.85 (0.23), residues: 1271 helix: 2.33 (0.21), residues: 598 sheet: 0.96 (0.33), residues: 258 loop : -0.22 (0.29), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 33 TYR 0.034 0.002 TYR N 201 PHE 0.008 0.002 PHE N 81 TRP 0.015 0.002 TRP M 185 HIS 0.006 0.001 HIS D 49 Details of bonding type rmsd covalent geometry : bond 0.00565 (19408) covalent geometry : angle 0.63003 (27915) hydrogen bonds : bond 0.04830 ( 1096) hydrogen bonds : angle 3.40880 ( 2691) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2542 Ramachandran restraints generated. 1271 Oldfield, 0 Emsley, 1271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2542 Ramachandran restraints generated. 1271 Oldfield, 0 Emsley, 1271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 208 time to evaluate : 0.553 Fit side-chains revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8706 (OUTLIER) cc_final: 0.7969 (mtp85) REVERT: A 56 LYS cc_start: 0.8832 (OUTLIER) cc_final: 0.8631 (ttmm) REVERT: A 64 LYS cc_start: 0.8867 (mptt) cc_final: 0.8618 (mtpt) REVERT: A 76 GLN cc_start: 0.8725 (OUTLIER) cc_final: 0.8349 (tt0) REVERT: B 77 LYS cc_start: 0.8881 (mtmp) cc_final: 0.8675 (mtmt) REVERT: B 92 ARG cc_start: 0.8909 (ptm-80) cc_final: 0.8555 (ptm160) REVERT: B 95 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.8234 (mtt-85) REVERT: C 99 ARG cc_start: 0.8481 (mmm160) cc_final: 0.8247 (mmm160) REVERT: D 79 ARG cc_start: 0.8428 (mtm180) cc_final: 0.8209 (mtp180) REVERT: E 122 LYS cc_start: 0.8628 (ptpp) cc_final: 0.8378 (ptmm) REVERT: G 94 ASN cc_start: 0.9277 (t0) cc_final: 0.9022 (t0) REVERT: H 79 ARG cc_start: 0.8563 (mtp180) cc_final: 0.8257 (mtp180) REVERT: M 96 ASN cc_start: 0.8609 (m-40) cc_final: 0.8290 (m-40) REVERT: M 160 LEU cc_start: 0.8617 (mm) cc_final: 0.8261 (mm) outliers start: 28 outliers final: 12 residues processed: 222 average time/residue: 0.9401 time to fit residues: 225.7857 Evaluate side-chains 202 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 186 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ARG Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain M residue 39 THR Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain M residue 207 THR Chi-restraints excluded: chain M residue 228 VAL Chi-restraints excluded: chain N residue 84 SER Chi-restraints excluded: chain N residue 211 GLU Chi-restraints excluded: chain N residue 257 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 130 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 90 optimal weight: 20.0000 chunk 84 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 115 optimal weight: 0.0370 chunk 23 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 122 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 overall best weight: 0.9662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN H 84 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.170880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.123386 restraints weight = 24259.049| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 1.29 r_work: 0.3487 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3368 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 19408 Z= 0.165 Angle : 0.545 6.837 27915 Z= 0.325 Chirality : 0.034 0.132 3152 Planarity : 0.004 0.043 2154 Dihedral : 30.122 174.000 5711 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.65 % Allowed : 13.42 % Favored : 83.93 % 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: 2.15 (0.24), residues: 1271 helix: 2.75 (0.21), residues: 586 sheet: 0.86 (0.33), residues: 262 loop : -0.10 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 33 TYR 0.018 0.001 TYR N 201 PHE 0.008 0.001 PHE A 67 TRP 0.008 0.001 TRP M 185 HIS 0.003 0.001 HIS D 49 Details of bonding type rmsd covalent geometry : bond 0.00366 (19408) covalent geometry : angle 0.54497 (27915) hydrogen bonds : bond 0.03639 ( 1096) hydrogen bonds : angle 3.17385 ( 2691) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2542 Ramachandran restraints generated. 1271 Oldfield, 0 Emsley, 1271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2542 Ramachandran restraints generated. 1271 Oldfield, 0 Emsley, 1271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 210 time to evaluate : 0.536 Fit side-chains revert: symmetry clash REVERT: A 64 LYS cc_start: 0.8840 (mptt) cc_final: 0.8618 (mtpt) REVERT: B 92 ARG cc_start: 0.8860 (ptm-80) cc_final: 0.8601 (ptm160) REVERT: C 73 ASN cc_start: 0.8500 (t160) cc_final: 0.8253 (t160) REVERT: E 122 LYS cc_start: 0.8574 (ptpp) cc_final: 0.8373 (ptmm) REVERT: F 95 ARG cc_start: 0.8638 (OUTLIER) cc_final: 0.7635 (mtp-110) REVERT: G 73 ASN cc_start: 0.7803 (m110) cc_final: 0.7495 (t160) REVERT: G 94 ASN cc_start: 0.9282 (t0) cc_final: 0.8946 (t0) REVERT: M 36 GLU cc_start: 0.8595 (pt0) cc_final: 0.8299 (pm20) REVERT: M 37 ARG cc_start: 0.8346 (OUTLIER) cc_final: 0.7897 (mtp-110) REVERT: M 96 ASN cc_start: 0.8457 (m-40) cc_final: 0.7981 (m-40) REVERT: M 159 GLU cc_start: 0.8053 (mm-30) cc_final: 0.7819 (mm-30) REVERT: M 160 LEU cc_start: 0.8585 (mm) cc_final: 0.8224 (mm) REVERT: U 96 LYS cc_start: 0.5566 (OUTLIER) cc_final: 0.4717 (tttp) outliers start: 29 outliers final: 11 residues processed: 224 average time/residue: 0.9130 time to fit residues: 221.4497 Evaluate side-chains 207 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 193 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain H residue 34 LYS Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain M residue 37 ARG Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 207 THR Chi-restraints excluded: chain N residue 84 SER Chi-restraints excluded: chain N residue 167 VAL Chi-restraints excluded: chain N residue 222 ASP Chi-restraints excluded: chain N residue 257 ASP Chi-restraints excluded: chain U residue 96 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- 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: 65.8626 > 50: distance: 40 - 45: 15.971 distance: 45 - 46: 20.755 distance: 46 - 47: 8.885 distance: 46 - 49: 8.618 distance: 47 - 48: 35.766 distance: 47 - 51: 21.910 distance: 49 - 50: 18.799 distance: 51 - 52: 19.608 distance: 52 - 53: 22.427 distance: 53 - 54: 18.944 distance: 53 - 55: 26.151 distance: 55 - 56: 17.973 distance: 55 - 164: 14.977 distance: 56 - 57: 20.466 distance: 56 - 59: 14.266 distance: 57 - 58: 8.398 distance: 57 - 62: 23.866 distance: 58 - 161: 16.767 distance: 59 - 60: 18.728 distance: 59 - 61: 12.451 distance: 62 - 63: 6.801 distance: 63 - 64: 15.052 distance: 63 - 66: 6.935 distance: 64 - 65: 10.076 distance: 64 - 68: 37.511 distance: 66 - 67: 12.498 distance: 68 - 69: 26.240 distance: 69 - 70: 7.682 distance: 69 - 72: 32.087 distance: 70 - 71: 5.812 distance: 70 - 76: 14.272 distance: 71 - 94: 32.221 distance: 72 - 73: 9.359 distance: 73 - 74: 26.167 distance: 73 - 75: 22.646 distance: 76 - 77: 26.374 distance: 77 - 78: 13.850 distance: 77 - 80: 32.648 distance: 78 - 79: 33.319 distance: 78 - 81: 11.909 distance: 79 - 103: 32.356 distance: 81 - 82: 11.366 distance: 82 - 83: 13.842 distance: 82 - 85: 14.498 distance: 83 - 84: 38.374 distance: 83 - 86: 17.907 distance: 84 - 112: 29.072 distance: 86 - 87: 7.136 distance: 87 - 88: 41.467 distance: 87 - 90: 16.852 distance: 88 - 94: 16.940 distance: 89 - 117: 28.148 distance: 90 - 91: 18.624 distance: 91 - 92: 17.411 distance: 91 - 93: 11.829 distance: 94 - 95: 12.332 distance: 95 - 96: 12.842 distance: 95 - 98: 11.817 distance: 96 - 97: 19.541 distance: 96 - 103: 9.338 distance: 97 - 125: 19.508 distance: 98 - 99: 19.483 distance: 99 - 100: 12.226 distance: 100 - 101: 18.007 distance: 101 - 102: 14.063 distance: 103 - 104: 14.845 distance: 104 - 105: 13.327 distance: 104 - 107: 3.817 distance: 105 - 106: 16.075 distance: 105 - 112: 14.328 distance: 106 - 130: 22.686 distance: 107 - 108: 12.469 distance: 108 - 109: 7.945 distance: 109 - 110: 11.180 distance: 110 - 111: 11.499