Starting phenix.real_space_refine on Thu Jul 2 10:25:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8hik_34819/07_2026/8hik_34819.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hik_34819/07_2026/8hik_34819.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hik_34819/07_2026/8hik_34819.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hik_34819/07_2026/8hik_34819.map" model { file = "/net/cci-nas-00/data/ceres_data/8hik_34819/07_2026/8hik_34819.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hik_34819/07_2026/8hik_34819.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8hik_34819/07_2026/8hik_34819.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8hik_34819/07_2026/8hik_34819.cif" } resolution = 3.72 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.016 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 2 5.49 5 S 27 5.16 5 C 5296 2.51 5 N 1376 2.21 5 O 1537 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8238 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 498, 3969 Classifications: {'peptide': 498} Link IDs: {'PTRANS': 17, 'TRANS': 480} Chain breaks: 1 Chain: "H" Number of atoms: 1686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1686 Classifications: {'peptide': 225} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 211} Chain: "N" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 925 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "L" Number of atoms: 1632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1632 Classifications: {'peptide': 212} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 201} Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'TPP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.46, per 1000 atoms: 0.18 Number of scatterers: 8238 At special positions: 0 Unit cell: (66.34, 99.51, 148.73, 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 27 16.00 P 2 15.00 O 1537 8.00 N 1376 7.00 C 5296 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.03 Simple disulfide: pdb=" SG CYS H 154 " - pdb=" SG CYS H 210 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS L 136 " - pdb=" SG CYS L 196 " distance=2.03 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: 0.43 Conformation dependent library (CDL) restraints added in 317.5 milliseconds 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1972 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 14 sheets defined 39.7% alpha, 23.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid -80 through -64 removed outlier: 3.672A pdb=" N LYS A -64 " --> pdb=" O LYS A -68 " (cutoff:3.500A) Processing helix chain 'A' and resid -57 through -43 removed outlier: 3.598A pdb=" N ALA A -43 " --> pdb=" O ALA A -47 " (cutoff:3.500A) Processing helix chain 'A' and resid -38 through -33 removed outlier: 4.020A pdb=" N ASP A -33 " --> pdb=" O PRO A -37 " (cutoff:3.500A) Processing helix chain 'A' and resid -25 through -3 removed outlier: 3.702A pdb=" N LEU A -5 " --> pdb=" O ASP A -9 " (cutoff:3.500A) Processing helix chain 'A' and resid 2 through 18 removed outlier: 3.694A pdb=" N ALA A 6 " --> pdb=" O LYS A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 23 Processing helix chain 'A' and resid 27 through 39 Processing helix chain 'A' and resid 47 through 53 Processing helix chain 'A' and resid 60 through 66 Processing helix chain 'A' and resid 68 through 81 Processing helix chain 'A' and resid 82 through 90 removed outlier: 4.114A pdb=" N LEU A 86 " --> pdb=" O PRO A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 112 Processing helix chain 'A' and resid 115 through 132 removed outlier: 3.884A pdb=" N MET A 119 " --> pdb=" O SER A 115 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N VAL A 128 " --> pdb=" O LEU A 124 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N THR A 129 " --> pdb=" O PHE A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 144 removed outlier: 4.115A pdb=" N SER A 137 " --> pdb=" O ARG A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 176 Processing helix chain 'A' and resid 181 through 202 Processing helix chain 'A' and resid 251 through 259 Processing helix chain 'A' and resid 260 through 262 No H-bonds generated for 'chain 'A' and resid 260 through 262' Processing helix chain 'A' and resid 264 through 296 removed outlier: 3.936A pdb=" N TYR A 287 " --> pdb=" O LEU A 283 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N HIS A 289 " --> pdb=" O VAL A 285 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N ILE A 290 " --> pdb=" O TYR A 286 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP A 296 " --> pdb=" O TRP A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 323 Processing helix chain 'A' and resid 335 through 355 Processing helix chain 'A' and resid 361 through 375 Processing helix chain 'A' and resid 379 through 389 removed outlier: 3.718A pdb=" N ILE A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER A 389 " --> pdb=" O PHE A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 418 Processing helix chain 'A' and resid 427 through 451 Processing helix chain 'H' and resid 90 through 94 removed outlier: 3.532A pdb=" N ASP H 93 " --> pdb=" O ARG H 90 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR H 94 " --> pdb=" O ALA H 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 90 through 94' Processing helix chain 'H' and resid 107 through 112 removed outlier: 3.631A pdb=" N LYS H 112 " --> pdb=" O GLU H 108 " (cutoff:3.500A) Processing helix chain 'L' and resid 80 through 84 removed outlier: 4.097A pdb=" N PHE L 84 " --> pdb=" O PRO L 81 " (cutoff:3.500A) Processing helix chain 'L' and resid 184 through 188 Processing sheet with id=AA1, first strand: chain 'H' and resid 6 through 10 Processing sheet with id=AA2, first strand: chain 'H' and resid 14 through 15 removed outlier: 3.588A pdb=" N VAL H 15 " --> pdb=" O THR H 124 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LEU H 37 " --> pdb=" O TYR H 53 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N TYR H 53 " --> pdb=" O LEU H 37 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 134 through 138 removed outlier: 6.145A pdb=" N TYR H 190 " --> pdb=" O ASP H 158 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 134 through 138 removed outlier: 6.145A pdb=" N TYR H 190 " --> pdb=" O ASP H 158 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 164 through 167 removed outlier: 4.332A pdb=" N TYR H 208 " --> pdb=" O VAL H 225 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.735A pdb=" N SER N 7 " --> pdb=" O SER N 21 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N SER N 21 " --> pdb=" O SER N 7 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'N' and resid 10 through 12 removed outlier: 3.833A pdb=" N THR N 118 " --> pdb=" O GLY N 10 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR N 115 " --> pdb=" O TYR N 94 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR N 94 " --> pdb=" O THR N 115 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N MET N 34 " --> pdb=" O VAL N 50 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N VAL N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'N' and resid 10 through 12 removed outlier: 3.833A pdb=" N THR N 118 " --> pdb=" O GLY N 10 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR N 115 " --> pdb=" O TYR N 94 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR N 94 " --> pdb=" O THR N 115 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N TYR N 110 " --> pdb=" O ILE N 98 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 5 through 6 Processing sheet with id=AB1, first strand: chain 'L' and resid 13 through 14 Processing sheet with id=AB2, first strand: chain 'L' and resid 54 through 55 removed outlier: 3.941A pdb=" N TYR L 50 " --> pdb=" O SER L 54 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN L 91 " --> pdb=" O THR L 99 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N THR L 99 " --> pdb=" O GLN L 91 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 54 through 55 removed outlier: 3.941A pdb=" N TYR L 50 " --> pdb=" O SER L 54 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 116 through 120 removed outlier: 5.961A pdb=" N TYR L 175 " --> pdb=" O ASN L 140 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 147 through 148 446 hydrogen bonds defined for protein. 1248 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: 0.98 Time building geometry restraints manager: 0.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2562 1.34 - 1.46: 2030 1.46 - 1.58: 3807 1.58 - 1.70: 3 1.70 - 1.81: 38 Bond restraints: 8440 Sorted by residual: bond pdb=" C5 TPP A 601 " pdb=" S1 TPP A 601 " ideal model delta sigma weight residual 1.727 1.510 0.217 1.00e-02 1.00e+04 4.69e+02 bond pdb=" C2 TPP A 601 " pdb=" S1 TPP A 601 " ideal model delta sigma weight residual 1.675 1.544 0.131 1.00e-02 1.00e+04 1.71e+02 bond pdb=" C4' TPP A 601 " pdb=" N4' TPP A 601 " ideal model delta sigma weight residual 1.337 1.454 -0.117 1.10e-02 8.26e+03 1.13e+02 bond pdb=" C2 TPP A 601 " pdb=" N3 TPP A 601 " ideal model delta sigma weight residual 1.318 1.424 -0.106 1.30e-02 5.92e+03 6.66e+01 bond pdb=" O3A TPP A 601 " pdb=" PB TPP A 601 " ideal model delta sigma weight residual 1.587 1.662 -0.075 1.10e-02 8.26e+03 4.66e+01 ... (remaining 8435 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.25: 11372 3.25 - 6.49: 91 6.49 - 9.74: 18 9.74 - 12.98: 2 12.98 - 16.23: 1 Bond angle restraints: 11484 Sorted by residual: angle pdb=" PA TPP A 601 " pdb=" O3A TPP A 601 " pdb=" PB TPP A 601 " ideal model delta sigma weight residual 139.87 123.64 16.23 1.00e+00 1.00e+00 2.63e+02 angle pdb=" C2 TPP A 601 " pdb=" S1 TPP A 601 " pdb=" C5 TPP A 601 " ideal model delta sigma weight residual 91.33 104.13 -12.80 1.00e+00 1.00e+00 1.64e+02 angle pdb=" C7 TPP A 601 " pdb=" O7 TPP A 601 " pdb=" PA TPP A 601 " ideal model delta sigma weight residual 124.29 118.57 5.72 1.00e+00 1.00e+00 3.27e+01 angle pdb=" N1' TPP A 601 " pdb=" C2' TPP A 601 " pdb=" N3' TPP A 601 " ideal model delta sigma weight residual 125.71 119.88 5.83 1.07e+00 8.80e-01 2.99e+01 angle pdb=" N3 TPP A 601 " pdb=" C2 TPP A 601 " pdb=" S1 TPP A 601 " ideal model delta sigma weight residual 112.34 107.32 5.02 1.00e+00 1.00e+00 2.52e+01 ... (remaining 11479 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.52: 4807 16.52 - 33.03: 110 33.03 - 49.54: 34 49.54 - 66.06: 1 66.06 - 82.57: 11 Dihedral angle restraints: 4963 sinusoidal: 1886 harmonic: 3077 Sorted by residual: dihedral pdb=" CB CYS H 154 " pdb=" SG CYS H 154 " pdb=" SG CYS H 210 " pdb=" CB CYS H 210 " ideal model delta sinusoidal sigma weight residual 93.00 175.57 -82.57 1 1.00e+01 1.00e-02 8.36e+01 dihedral pdb=" CB CYS L 136 " pdb=" SG CYS L 136 " pdb=" SG CYS L 196 " pdb=" CB CYS L 196 " ideal model delta sinusoidal sigma weight residual -86.00 -120.31 34.31 1 1.00e+01 1.00e-02 1.67e+01 dihedral pdb=" CA ARG A 91 " pdb=" C ARG A 91 " pdb=" N TYR A 92 " pdb=" CA TYR A 92 " ideal model delta harmonic sigma weight residual 180.00 159.67 20.33 0 5.00e+00 4.00e-02 1.65e+01 ... (remaining 4960 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 957 0.049 - 0.097: 267 0.097 - 0.146: 64 0.146 - 0.195: 7 0.195 - 0.243: 1 Chirality restraints: 1296 Sorted by residual: chirality pdb=" CA THR A 69 " pdb=" N THR A 69 " pdb=" C THR A 69 " pdb=" CB THR A 69 " both_signs ideal model delta sigma weight residual False 2.53 2.28 0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CB THR A 69 " pdb=" CA THR A 69 " pdb=" OG1 THR A 69 " pdb=" CG2 THR A 69 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 9.13e-01 chirality pdb=" CA TYR N 104 " pdb=" N TYR N 104 " pdb=" C TYR N 104 " pdb=" CB TYR N 104 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.80e-01 ... (remaining 1293 not shown) Planarity restraints: 1437 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP H 102 " -0.016 2.00e-02 2.50e+03 1.51e-02 5.66e+00 pdb=" CG TRP H 102 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP H 102 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP H 102 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP H 102 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP H 102 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP H 102 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 102 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 102 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP H 102 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP H 105 " 0.038 5.00e-02 4.00e+02 5.76e-02 5.31e+00 pdb=" N PRO H 106 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO H 106 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO H 106 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU H 108 " -0.035 5.00e-02 4.00e+02 5.18e-02 4.29e+00 pdb=" N PRO H 109 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO H 109 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO H 109 " -0.030 5.00e-02 4.00e+02 ... (remaining 1434 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 2236 2.81 - 3.33: 7133 3.33 - 3.85: 13492 3.85 - 4.38: 15090 4.38 - 4.90: 26545 Nonbonded interactions: 64496 Sorted by model distance: nonbonded pdb=" OG SER A 168 " pdb=" O GLY A 307 " model vdw 2.282 3.040 nonbonded pdb=" OG SER L 64 " pdb=" OG1 THR L 75 " model vdw 2.326 3.040 nonbonded pdb=" O GLU A -26 " pdb=" OH TYR A 22 " model vdw 2.336 3.040 nonbonded pdb=" NE ARG A -49 " pdb=" O LEU L 93 " model vdw 2.340 3.120 nonbonded pdb=" O TRP H 111 " pdb=" OH TYR L 92 " model vdw 2.345 3.040 ... (remaining 64491 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.590 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6273 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.217 8445 Z= 0.385 Angle : 0.821 16.228 11494 Z= 0.473 Chirality : 0.047 0.243 1296 Planarity : 0.006 0.058 1437 Dihedral : 9.444 75.327 2976 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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 are not related in a simple way. whole: -3.54 (0.21), residues: 1045 helix: -1.96 (0.20), residues: 380 sheet: -1.92 (0.29), residues: 241 loop : -2.84 (0.25), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 62 TYR 0.023 0.002 TYR H 53 PHE 0.029 0.002 PHE A 103 TRP 0.041 0.002 TRP H 102 HIS 0.006 0.002 HIS H 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00515 / 0.39 ( 8440) covalent geometry : angle 0.82034 / 0.47 (11484) SS BOND : bond 0.00134 / 0.08 ( 5) SS BOND : angle 1.34217 / 0.86 ( 10) hydrogen bonds : bond 0.11935 / 7.62 ( 420) hydrogen bonds : angle 6.64327 / 4.41 ( 1248) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 217 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A -51 LYS cc_start: 0.7460 (tttt) cc_final: 0.7258 (mtmm) REVERT: A -50 MET cc_start: 0.6246 (mmm) cc_final: 0.5921 (mmm) REVERT: A -22 PHE cc_start: 0.7319 (t80) cc_final: 0.6815 (t80) REVERT: A 27 HIS cc_start: 0.5170 (m90) cc_final: 0.4851 (m-70) REVERT: A 73 SER cc_start: 0.6585 (m) cc_final: 0.6353 (t) REVERT: A 140 ILE cc_start: 0.7951 (mt) cc_final: 0.7742 (tp) REVERT: A 281 TYR cc_start: 0.6510 (t80) cc_final: 0.6203 (t80) REVERT: A 304 VAL cc_start: 0.7185 (t) cc_final: 0.5917 (m) REVERT: A 386 GLN cc_start: 0.7578 (mm-40) cc_final: 0.7062 (tm-30) REVERT: A 387 ILE cc_start: 0.7155 (mt) cc_final: 0.6955 (mt) REVERT: H 86 MET cc_start: 0.6378 (mtm) cc_final: 0.6146 (mtm) REVERT: H 99 CYS cc_start: 0.5632 (t) cc_final: 0.5367 (t) REVERT: H 112 LYS cc_start: 0.7716 (mttt) cc_final: 0.7507 (ttmm) REVERT: H 119 GLN cc_start: 0.6958 (mt0) cc_final: 0.6698 (mt0) REVERT: H 135 VAL cc_start: 0.7872 (t) cc_final: 0.7591 (m) REVERT: H 136 PHE cc_start: 0.7526 (m-80) cc_final: 0.7085 (m-80) REVERT: N 34 MET cc_start: 0.6441 (mtp) cc_final: 0.6214 (mtp) REVERT: L 32 SER cc_start: 0.7747 (t) cc_final: 0.7452 (p) REVERT: L 37 TYR cc_start: 0.8262 (m-10) cc_final: 0.7689 (m-80) REVERT: L 43 LYS cc_start: 0.8431 (mttt) cc_final: 0.8095 (ttmm) outliers start: 0 outliers final: 0 residues processed: 217 average time/residue: 0.0753 time to fit residues: 22.9584 Evaluate side-chains 184 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.0070 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A -77 ASN A -42 GLN A 27 HIS A 120 GLN A 358 HIS H 178 HIS ** H 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 28 GLN L 39 GLN L 90 GLN L 162 GLN ** L 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 191 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.170418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.151691 restraints weight = 13135.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.155496 restraints weight = 7261.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.157999 restraints weight = 4574.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.159689 restraints weight = 3212.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.160824 restraints weight = 2449.010| |-----------------------------------------------------------------------------| r_work (final): 0.4047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6504 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 8445 Z= 0.217 Angle : 0.648 10.014 11494 Z= 0.337 Chirality : 0.043 0.170 1296 Planarity : 0.005 0.052 1437 Dihedral : 5.243 43.862 1159 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 2.24 % Allowed : 9.85 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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 are not related in a simple way. whole: -2.19 (0.24), residues: 1045 helix: -0.38 (0.25), residues: 388 sheet: -1.48 (0.31), residues: 240 loop : -2.39 (0.28), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A -49 TYR 0.030 0.002 TYR A 126 PHE 0.018 0.002 PHE L 211 TRP 0.035 0.003 TRP H 102 HIS 0.005 0.001 HIS H 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.22 ( 8440) covalent geometry : angle 0.64287 / 0.33 (11484) SS BOND : bond 0.00719 / 0.36 ( 5) SS BOND : angle 2.91382 / 1.71 ( 10) hydrogen bonds : bond 0.04003 / 2.63 ( 420) hydrogen bonds : angle 5.51520 / 3.73 ( 1248) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 221 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A -51 LYS cc_start: 0.7674 (tttt) cc_final: 0.7313 (mtmm) REVERT: A -50 MET cc_start: 0.6424 (mmm) cc_final: 0.5992 (mmm) REVERT: A 27 HIS cc_start: 0.5905 (m-70) cc_final: 0.5648 (m-70) REVERT: A 73 SER cc_start: 0.7496 (m) cc_final: 0.7163 (t) REVERT: A 99 GLN cc_start: 0.7890 (tt0) cc_final: 0.7449 (tt0) REVERT: A 281 TYR cc_start: 0.6721 (t80) cc_final: 0.6374 (t80) REVERT: A 294 GLU cc_start: 0.6928 (tt0) cc_final: 0.6662 (tt0) REVERT: A 386 GLN cc_start: 0.7461 (mm-40) cc_final: 0.7112 (tm-30) REVERT: A 387 ILE cc_start: 0.7141 (mt) cc_final: 0.6836 (mt) REVERT: H 7 LEU cc_start: 0.7527 (mm) cc_final: 0.7319 (mt) REVERT: H 46 LYS cc_start: 0.8403 (mmtt) cc_final: 0.8160 (mmmm) REVERT: H 63 TYR cc_start: 0.7695 (m-10) cc_final: 0.7176 (m-10) REVERT: H 86 MET cc_start: 0.6684 (mtm) cc_final: 0.6463 (mtm) REVERT: H 110 TRP cc_start: 0.7961 (t60) cc_final: 0.7068 (t60) REVERT: H 135 VAL cc_start: 0.7908 (t) cc_final: 0.7569 (m) REVERT: H 136 PHE cc_start: 0.7550 (m-80) cc_final: 0.7233 (m-80) REVERT: H 197 THR cc_start: 0.7173 (p) cc_final: 0.6972 (p) REVERT: N 59 PHE cc_start: 0.7030 (m-80) cc_final: 0.6791 (m-80) REVERT: L 36 TRP cc_start: 0.8123 (m100) cc_final: 0.7782 (m100) REVERT: L 37 TYR cc_start: 0.8336 (m-10) cc_final: 0.8034 (m-80) REVERT: L 43 LYS cc_start: 0.8619 (mttt) cc_final: 0.8326 (mmmm) REVERT: L 47 LEU cc_start: 0.8590 (tp) cc_final: 0.8318 (tt) REVERT: L 74 LEU cc_start: 0.8144 (tt) cc_final: 0.7939 (tp) REVERT: L 87 TYR cc_start: 0.8413 (m-80) cc_final: 0.7947 (m-10) REVERT: L 117 VAL cc_start: 0.8265 (t) cc_final: 0.7953 (p) REVERT: L 141 PHE cc_start: 0.8627 (p90) cc_final: 0.8419 (p90) REVERT: L 166 THR cc_start: 0.8448 (t) cc_final: 0.7946 (m) REVERT: L 177 LEU cc_start: 0.8129 (tt) cc_final: 0.7928 (tt) outliers start: 20 outliers final: 10 residues processed: 228 average time/residue: 0.0680 time to fit residues: 21.8793 Evaluate side-chains 208 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 198 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue -18 PHE Chi-restraints excluded: chain A residue -11 ILE Chi-restraints excluded: chain A residue -7 LEU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 51 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 44 optimal weight: 0.6980 chunk 83 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 86 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 57 optimal weight: 0.0670 chunk 52 optimal weight: 0.2980 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A -77 ASN A -20 HIS ** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 377 GLN L 28 GLN L 160 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.168493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.149997 restraints weight = 13075.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.153676 restraints weight = 7289.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.156063 restraints weight = 4616.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.157718 restraints weight = 3267.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.158726 restraints weight = 2507.125| |-----------------------------------------------------------------------------| r_work (final): 0.4013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6552 moved from start: 0.3576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 8445 Z= 0.173 Angle : 0.609 7.574 11494 Z= 0.310 Chirality : 0.042 0.154 1296 Planarity : 0.004 0.048 1437 Dihedral : 5.005 38.245 1159 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.69 % Allowed : 10.64 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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 are not related in a simple way. whole: -1.59 (0.26), residues: 1045 helix: 0.21 (0.26), residues: 387 sheet: -1.22 (0.31), residues: 243 loop : -2.12 (0.30), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A -49 TYR 0.024 0.002 TYR A 126 PHE 0.017 0.001 PHE A 212 TRP 0.025 0.002 TRP H 102 HIS 0.003 0.001 HIS H 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.17 ( 8440) covalent geometry : angle 0.60785 / 0.31 (11484) SS BOND : bond 0.00570 / 0.29 ( 5) SS BOND : angle 1.59392 / 1.01 ( 10) hydrogen bonds : bond 0.03808 / 2.50 ( 420) hydrogen bonds : angle 5.17453 / 3.50 ( 1248) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 209 time to evaluate : 0.184 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A -56 LYS cc_start: 0.8159 (tttt) cc_final: 0.7946 (ttpt) REVERT: A 73 SER cc_start: 0.7768 (m) cc_final: 0.7358 (t) REVERT: A 99 GLN cc_start: 0.7558 (tt0) cc_final: 0.7058 (tt0) REVERT: A 294 GLU cc_start: 0.6861 (tt0) cc_final: 0.6572 (tt0) REVERT: A 373 ARG cc_start: 0.6022 (mmm-85) cc_final: 0.5760 (mmm-85) REVERT: A 386 GLN cc_start: 0.7432 (mm-40) cc_final: 0.6983 (tm-30) REVERT: A 387 ILE cc_start: 0.7096 (mt) cc_final: 0.6884 (mt) REVERT: H 135 VAL cc_start: 0.7893 (t) cc_final: 0.7532 (m) REVERT: H 136 PHE cc_start: 0.7709 (m-80) cc_final: 0.7448 (m-80) REVERT: H 197 THR cc_start: 0.7080 (p) cc_final: 0.6873 (p) REVERT: N 39 GLN cc_start: 0.5923 (mp10) cc_final: 0.4010 (mp10) REVERT: L 36 TRP cc_start: 0.8094 (m100) cc_final: 0.7812 (m100) REVERT: L 43 LYS cc_start: 0.8665 (mttt) cc_final: 0.8385 (mtpp) REVERT: L 48 LEU cc_start: 0.8011 (tp) cc_final: 0.7679 (tp) REVERT: L 74 LEU cc_start: 0.8170 (tt) cc_final: 0.7924 (tp) REVERT: L 104 THR cc_start: 0.7898 (p) cc_final: 0.7626 (p) outliers start: 24 outliers final: 19 residues processed: 218 average time/residue: 0.0643 time to fit residues: 20.0628 Evaluate side-chains 216 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 197 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue -69 LEU Chi-restraints excluded: chain A residue -18 PHE Chi-restraints excluded: chain A residue -11 ILE Chi-restraints excluded: chain A residue -7 LEU Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 160 PHE Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain L residue 90 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 53.8828 > 50: distance: 66 - 77: 27.833 distance: 77 - 78: 53.883 distance: 78 - 79: 5.711 distance: 79 - 80: 12.718 distance: 79 - 81: 17.804 distance: 81 - 82: 10.806 distance: 82 - 83: 5.042 distance: 82 - 85: 7.395 distance: 83 - 93: 5.593 distance: 85 - 86: 13.952 distance: 86 - 87: 8.397 distance: 86 - 88: 8.856 distance: 87 - 89: 12.531 distance: 88 - 90: 8.843 distance: 89 - 91: 11.460 distance: 90 - 91: 11.119 distance: 91 - 92: 7.301 distance: 93 - 94: 6.565 distance: 94 - 95: 3.184 distance: 94 - 97: 5.834 distance: 95 - 96: 8.713 distance: 97 - 98: 7.467 distance: 98 - 99: 3.808 distance: 98 - 100: 4.484 distance: 99 - 101: 4.545 distance: 100 - 102: 7.084 distance: 100 - 103: 5.901 distance: 101 - 102: 5.238 distance: 103 - 105: 3.405 distance: 104 - 106: 6.085 distance: 105 - 106: 6.975 distance: 108 - 109: 3.966 distance: 109 - 114: 4.420 distance: 111 - 112: 3.767 distance: 114 - 115: 3.705 distance: 115 - 116: 5.793 distance: 116 - 117: 4.382 distance: 116 - 118: 3.462 distance: 117 - 148: 4.092 distance: 118 - 119: 4.755 distance: 119 - 120: 3.018 distance: 119 - 122: 4.638 distance: 120 - 121: 4.473 distance: 120 - 127: 3.218 distance: 122 - 123: 8.595 distance: 123 - 124: 6.436 distance: 124 - 125: 4.520 distance: 124 - 126: 11.737 distance: 127 - 128: 6.586 distance: 127 - 133: 8.384 distance: 128 - 129: 16.579 distance: 128 - 131: 16.235 distance: 129 - 130: 12.194 distance: 129 - 134: 12.390 distance: 131 - 132: 9.629 distance: 132 - 133: 8.617 distance: 134 - 135: 11.352 distance: 135 - 136: 10.723 distance: 135 - 138: 10.012 distance: 136 - 137: 19.684 distance: 136 - 148: 11.609 distance: 138 - 139: 4.223 distance: 139 - 140: 5.859 distance: 139 - 141: 9.655 distance: 140 - 142: 5.456 distance: 141 - 143: 5.570 distance: 141 - 144: 3.368 distance: 142 - 143: 4.127 distance: 143 - 145: 4.964 distance: 144 - 146: 6.306 distance: 146 - 147: 4.985 distance: 149 - 152: 6.719 distance: 150 - 151: 3.905 distance: 152 - 153: 7.115 distance: 153 - 154: 8.088 distance: 153 - 155: 3.991 distance: 155 - 157: 4.853 distance: 155 - 158: 3.415 distance: 156 - 157: 3.503 distance: 159 - 161: 3.461 distance: 160 - 161: 3.371 distance: 162 - 163: 6.316 distance: 163 - 164: 5.651 distance: 163 - 166: 5.566 distance: 164 - 171: 5.398 distance: 167 - 168: 7.737 distance: 168 - 169: 5.227 distance: 169 - 170: 11.946