Starting phenix.real_space_refine on Fri Aug 22 18:16:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7m71_23707/08_2025/7m71_23707.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m71_23707/08_2025/7m71_23707.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7m71_23707/08_2025/7m71_23707.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m71_23707/08_2025/7m71_23707.map" model { file = "/net/cci-nas-00/data/ceres_data/7m71_23707/08_2025/7m71_23707.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m71_23707/08_2025/7m71_23707.cif" } resolution = 2.66 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= -0.003 sd= 0.072 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: 4 Type Number sf(0) Gaussians S 29 5.16 5 C 4212 2.51 5 N 1112 2.21 5 O 1293 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6646 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1657 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 12, 'TRANS': 196} Chain: "B" Number of atoms: 1657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1657 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 12, 'TRANS': 196} Chain: "H" Number of atoms: 1645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1645 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 11, 'TRANS': 208} Chain: "L" Number of atoms: 1631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1631 Classifications: {'peptide': 214} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 202} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 1.28, per 1000 atoms: 0.19 Number of scatterers: 6646 At special positions: 0 Unit cell: (115.193, 92.6293, 129.444, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 29 16.00 O 1293 8.00 N 1112 7.00 C 4212 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.07 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.04 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.07 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 146 " - pdb=" SG CYS H 202 " distance=2.03 Simple disulfide: pdb=" SG CYS H 222 " - pdb=" SG CYS L 214 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.07 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " 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 Links applied NAG-ASN " NAG A1301 " - " ASN A 331 " " NAG A1302 " - " ASN A 343 " " NAG B1301 " - " ASN B 331 " " NAG B1302 " - " ASN B 343 " Time building additional restraints: 0.35 Conformation dependent library (CDL) restraints added in 263.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1574 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 20 sheets defined 14.0% alpha, 29.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.941A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.606A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.446A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.860A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 370 removed outlier: 3.715A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 388 removed outlier: 3.504A pdb=" N ASN B 388 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.222A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 162 through 164 No H-bonds generated for 'chain 'H' and resid 162 through 164' Processing helix chain 'H' and resid 191 through 197 removed outlier: 4.268A pdb=" N GLY H 196 " --> pdb=" O SER H 193 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 126 removed outlier: 3.906A pdb=" N LYS L 126 " --> pdb=" O ASP L 122 " (cutoff:3.500A) Processing helix chain 'L' and resid 150 through 153 Processing helix chain 'L' and resid 183 through 187 Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA2, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.703A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL A 524 " --> pdb=" O PHE A 392 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA5, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AA6, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.699A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA8, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AA9, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AB1, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.761A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.776A pdb=" N TYR H 108 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 126 through 130 removed outlier: 3.893A pdb=" N GLY H 145 " --> pdb=" O LEU H 130 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N GLY H 145 " --> pdb=" O VAL H 188 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N VAL H 188 " --> pdb=" O GLY H 145 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N LEU H 147 " --> pdb=" O SER H 186 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N SER H 186 " --> pdb=" O LEU H 147 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N LYS H 149 " --> pdb=" O LEU H 184 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N LEU H 184 " --> pdb=" O LYS H 149 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR H 151 " --> pdb=" O TYR H 182 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 137 through 138 removed outlier: 5.283A pdb=" N GLY H 145 " --> pdb=" O VAL H 188 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N VAL H 188 " --> pdb=" O GLY H 145 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N LEU H 147 " --> pdb=" O SER H 186 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N SER H 186 " --> pdb=" O LEU H 147 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N LYS H 149 " --> pdb=" O LEU H 184 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N LEU H 184 " --> pdb=" O LYS H 149 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR H 151 " --> pdb=" O TYR H 182 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 156 through 160 Processing sheet with id=AB6, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AB7, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.410A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 117 through 118 Processing sheet with id=AB9, first strand: chain 'L' and resid 129 through 131 Processing sheet with id=AC1, first strand: chain 'L' and resid 145 through 148 Processing sheet with id=AC2, first strand: chain 'L' and resid 161 through 164 removed outlier: 4.153A pdb=" N SER L 174 " --> pdb=" O THR L 164 " (cutoff:3.500A) 207 hydrogen bonds defined for protein. 465 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: 0.96 Time building geometry restraints manager: 0.52 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: 1616 1.33 - 1.45: 1469 1.45 - 1.58: 3693 1.58 - 1.70: 0 1.70 - 1.82: 32 Bond restraints: 6810 Sorted by residual: bond pdb=" CA PHE L 118 " pdb=" C PHE L 118 " ideal model delta sigma weight residual 1.522 1.564 -0.042 1.06e-02 8.90e+03 1.55e+01 bond pdb=" C5 NAG A1302 " pdb=" O5 NAG A1302 " ideal model delta sigma weight residual 1.413 1.486 -0.073 2.00e-02 2.50e+03 1.34e+01 bond pdb=" CZ ARG A 454 " pdb=" NH2 ARG A 454 " ideal model delta sigma weight residual 1.330 1.285 0.045 1.30e-02 5.92e+03 1.22e+01 bond pdb=" C5 NAG B1302 " pdb=" O5 NAG B1302 " ideal model delta sigma weight residual 1.413 1.482 -0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" CA PRO L 119 " pdb=" C PRO L 119 " ideal model delta sigma weight residual 1.517 1.549 -0.032 9.30e-03 1.16e+04 1.18e+01 ... (remaining 6805 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 6411 1.84 - 3.69: 2379 3.69 - 5.53: 420 5.53 - 7.38: 41 7.38 - 9.22: 7 Bond angle restraints: 9258 Sorted by residual: angle pdb=" CA PHE H 68 " pdb=" CB PHE H 68 " pdb=" CG PHE H 68 " ideal model delta sigma weight residual 113.80 121.12 -7.32 1.00e+00 1.00e+00 5.36e+01 angle pdb=" CA GLY A 416 " pdb=" C GLY A 416 " pdb=" N LYS A 417 " ideal model delta sigma weight residual 114.23 120.16 -5.93 8.80e-01 1.29e+00 4.54e+01 angle pdb=" CB ASN A 331 " pdb=" CG ASN A 331 " pdb=" ND2 ASN A 331 " ideal model delta sigma weight residual 116.40 107.47 8.93 1.50e+00 4.44e-01 3.54e+01 angle pdb=" C LYS H 215 " pdb=" N LYS H 216 " pdb=" CA LYS H 216 " ideal model delta sigma weight residual 120.95 128.90 -7.95 1.40e+00 5.10e-01 3.22e+01 angle pdb=" CA PHE L 209 " pdb=" CB PHE L 209 " pdb=" CG PHE L 209 " ideal model delta sigma weight residual 113.80 119.13 -5.33 1.00e+00 1.00e+00 2.84e+01 ... (remaining 9253 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 3785 17.69 - 35.37: 271 35.37 - 53.05: 45 53.05 - 70.74: 10 70.74 - 88.42: 4 Dihedral angle restraints: 4115 sinusoidal: 1642 harmonic: 2473 Sorted by residual: dihedral pdb=" CA THR L 178 " pdb=" C THR L 178 " pdb=" N LEU L 179 " pdb=" CA LEU L 179 " ideal model delta harmonic sigma weight residual 180.00 150.15 29.85 0 5.00e+00 4.00e-02 3.56e+01 dihedral pdb=" CA ARG H 72 " pdb=" C ARG H 72 " pdb=" N ASP H 73 " pdb=" CA ASP H 73 " ideal model delta harmonic sigma weight residual 180.00 150.43 29.57 0 5.00e+00 4.00e-02 3.50e+01 dihedral pdb=" CA LEU L 104 " pdb=" C LEU L 104 " pdb=" N GLU L 105 " pdb=" CA GLU L 105 " ideal model delta harmonic sigma weight residual -180.00 -150.73 -29.27 0 5.00e+00 4.00e-02 3.43e+01 ... (remaining 4112 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.274: 1010 0.274 - 0.548: 13 0.548 - 0.822: 0 0.822 - 1.096: 0 1.096 - 1.370: 1 Chirality restraints: 1024 Sorted by residual: chirality pdb=" C1 NAG A1301 " pdb=" ND2 ASN A 331 " pdb=" C2 NAG A1301 " pdb=" O5 NAG A1301 " both_signs ideal model delta sigma weight residual False -2.40 -1.03 -1.37 2.00e-01 2.50e+01 4.69e+01 chirality pdb=" CA ASP H 150 " pdb=" N ASP H 150 " pdb=" C ASP H 150 " pdb=" CB ASP H 150 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.19e+00 chirality pdb=" CA ASN B 331 " pdb=" N ASN B 331 " pdb=" C ASN B 331 " pdb=" CB ASN B 331 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.06e+00 ... (remaining 1021 not shown) Planarity restraints: 1197 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 331 " -0.098 2.00e-02 2.50e+03 1.02e-01 1.31e+02 pdb=" CG ASN A 331 " 0.075 2.00e-02 2.50e+03 pdb=" OD1 ASN A 331 " -0.015 2.00e-02 2.50e+03 pdb=" ND2 ASN A 331 " 0.153 2.00e-02 2.50e+03 pdb=" C1 NAG A1301 " -0.116 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR L 49 " 0.131 2.00e-02 2.50e+03 7.39e-02 1.09e+02 pdb=" CG TYR L 49 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TYR L 49 " -0.057 2.00e-02 2.50e+03 pdb=" CD2 TYR L 49 " -0.065 2.00e-02 2.50e+03 pdb=" CE1 TYR L 49 " -0.049 2.00e-02 2.50e+03 pdb=" CE2 TYR L 49 " -0.039 2.00e-02 2.50e+03 pdb=" CZ TYR L 49 " -0.008 2.00e-02 2.50e+03 pdb=" OH TYR L 49 " 0.118 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 353 " -0.121 2.00e-02 2.50e+03 6.35e-02 1.01e+02 pdb=" CG TRP B 353 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 TRP B 353 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TRP B 353 " 0.091 2.00e-02 2.50e+03 pdb=" NE1 TRP B 353 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 TRP B 353 " 0.027 2.00e-02 2.50e+03 pdb=" CE3 TRP B 353 " 0.085 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 353 " -0.051 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 353 " -0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP B 353 " -0.074 2.00e-02 2.50e+03 ... (remaining 1194 not shown) Histogram of nonbonded interaction distances: 2.53 - 3.00: 3298 3.00 - 3.48: 6121 3.48 - 3.95: 11157 3.95 - 4.43: 12531 4.43 - 4.90: 20762 Nonbonded interactions: 53869 Sorted by model distance: nonbonded pdb=" OD1 ASP A 364 " pdb=" OG SER A 366 " model vdw 2.531 3.040 nonbonded pdb=" OE1 GLU A 406 " pdb=" OH TYR A 495 " model vdw 2.549 3.040 nonbonded pdb=" OE1 GLU B 406 " pdb=" OH TYR B 495 " model vdw 2.561 3.040 nonbonded pdb=" OD1 ASP B 467 " pdb=" OG SER B 469 " model vdw 2.577 3.040 nonbonded pdb=" OG SER B 438 " pdb=" OD2 ASP B 442 " model vdw 2.579 3.040 ... (remaining 53864 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' } 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: 4.040 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.610 Find NCS groups from input model: 0.050 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:8.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 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 : 0.013 0.073 6827 Z= 0.752 Angle : 1.872 9.869 9296 Z= 1.236 Chirality : 0.112 1.370 1024 Planarity : 0.016 0.190 1193 Dihedral : 12.979 88.419 2502 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 0.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 0.41 % Allowed : 3.81 % Favored : 95.78 % Cbeta Deviations : 0.64 % Peptide Plane: Cis-proline : 2.17 % 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: -0.93 (0.27), residues: 844 helix: -4.22 (0.28), residues: 79 sheet: 0.09 (0.32), residues: 253 loop : -0.31 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 403 TYR 0.131 0.019 TYR L 49 PHE 0.077 0.013 PHE L 118 TRP 0.121 0.024 TRP B 353 HIS 0.007 0.003 HIS H 206 Details of bonding type rmsd covalent geometry : bond 0.01282 ( 6810) covalent geometry : angle 1.86108 ( 9258) SS BOND : bond 0.02022 ( 13) SS BOND : angle 2.54002 ( 26) hydrogen bonds : bond 0.12603 ( 199) hydrogen bonds : angle 9.08133 ( 465) link_NAG-ASN : bond 0.00964 ( 4) link_NAG-ASN : angle 5.38630 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 54 time to evaluate : 0.268 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 56 average time/residue: 0.7447 time to fit residues: 43.2784 Evaluate side-chains 28 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 27 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 165 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 20.0000 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 20.0000 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 9.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 439 ASN A 487 ASN B 354 ASN L 37 GLN L 198 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.053852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.034462 restraints weight = 33073.027| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 3.44 r_work: 0.2743 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8900 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6827 Z= 0.140 Angle : 0.638 7.770 9296 Z= 0.332 Chirality : 0.045 0.159 1024 Planarity : 0.005 0.039 1193 Dihedral : 6.179 47.838 1017 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.82 % Allowed : 7.21 % Favored : 91.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -0.39 (0.29), residues: 844 helix: -3.16 (0.57), residues: 65 sheet: 0.12 (0.30), residues: 288 loop : 0.04 (0.29), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 346 TYR 0.024 0.001 TYR L 186 PHE 0.016 0.002 PHE B 497 TRP 0.013 0.001 TRP A 436 HIS 0.003 0.001 HIS L 198 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 6810) covalent geometry : angle 0.62813 ( 9258) SS BOND : bond 0.00304 ( 13) SS BOND : angle 0.81001 ( 26) hydrogen bonds : bond 0.03560 ( 199) hydrogen bonds : angle 6.98718 ( 465) link_NAG-ASN : bond 0.00206 ( 4) link_NAG-ASN : angle 3.13271 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 33 time to evaluate : 0.183 Fit side-chains REVERT: A 406 GLU cc_start: 0.8873 (mt-10) cc_final: 0.8555 (mt-10) REVERT: B 340 GLU cc_start: 0.9033 (mm-30) cc_final: 0.8652 (mp0) REVERT: L 187 GLU cc_start: 0.8837 (mm-30) cc_final: 0.8627 (mm-30) outliers start: 6 outliers final: 2 residues processed: 38 average time/residue: 0.6806 time to fit residues: 27.0153 Evaluate side-chains 28 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 26 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain L residue 134 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 71 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 46 optimal weight: 4.9990 chunk 36 optimal weight: 0.8980 chunk 49 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 354 ASN ** L 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.053011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.033673 restraints weight = 33229.915| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 3.42 r_work: 0.2722 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8925 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 6827 Z= 0.147 Angle : 0.587 6.653 9296 Z= 0.304 Chirality : 0.044 0.151 1024 Planarity : 0.005 0.041 1193 Dihedral : 5.491 49.628 1014 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.54 % Allowed : 8.98 % Favored : 90.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -0.25 (0.29), residues: 844 helix: -2.81 (0.59), residues: 65 sheet: 0.30 (0.30), residues: 278 loop : 0.04 (0.29), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 346 TYR 0.019 0.001 TYR A 495 PHE 0.012 0.001 PHE H 29 TRP 0.013 0.001 TRP H 47 HIS 0.002 0.001 HIS L 198 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 6810) covalent geometry : angle 0.57999 ( 9258) SS BOND : bond 0.00331 ( 13) SS BOND : angle 0.78674 ( 26) hydrogen bonds : bond 0.03442 ( 199) hydrogen bonds : angle 6.48561 ( 465) link_NAG-ASN : bond 0.00123 ( 4) link_NAG-ASN : angle 2.48853 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.227 Fit side-chains REVERT: A 406 GLU cc_start: 0.8909 (mt-10) cc_final: 0.8511 (mt-10) REVERT: B 340 GLU cc_start: 0.9012 (mm-30) cc_final: 0.8672 (mp0) REVERT: B 516 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8083 (pp20) REVERT: L 105 GLU cc_start: 0.8147 (mm-30) cc_final: 0.7911 (mp0) REVERT: L 143 GLU cc_start: 0.8270 (pm20) cc_final: 0.8003 (pm20) outliers start: 4 outliers final: 2 residues processed: 36 average time/residue: 0.7132 time to fit residues: 26.8438 Evaluate side-chains 31 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 28 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain L residue 154 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 79 optimal weight: 10.0000 chunk 74 optimal weight: 8.9990 chunk 81 optimal weight: 10.0000 chunk 23 optimal weight: 0.8980 chunk 32 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 70 optimal weight: 6.9990 chunk 47 optimal weight: 6.9990 chunk 57 optimal weight: 10.0000 chunk 14 optimal weight: 6.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- 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 = 0.3499 r_free = 0.3499 target = 0.051240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.031879 restraints weight = 34183.959| |-----------------------------------------------------------------------------| r_work (start): 0.2783 rms_B_bonded: 3.51 r_work: 0.2655 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8990 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.052 6827 Z= 0.386 Angle : 0.697 7.644 9296 Z= 0.362 Chirality : 0.048 0.147 1024 Planarity : 0.005 0.045 1193 Dihedral : 6.378 47.358 1014 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.09 % Allowed : 9.93 % Favored : 88.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -0.69 (0.29), residues: 844 helix: -3.03 (0.53), residues: 73 sheet: 0.02 (0.30), residues: 281 loop : -0.24 (0.29), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 142 TYR 0.019 0.002 TYR A 495 PHE 0.017 0.002 PHE L 83 TRP 0.018 0.002 TRP H 47 HIS 0.002 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00884 ( 6810) covalent geometry : angle 0.68584 ( 9258) SS BOND : bond 0.00580 ( 13) SS BOND : angle 1.18203 ( 26) hydrogen bonds : bond 0.04115 ( 199) hydrogen bonds : angle 6.85731 ( 465) link_NAG-ASN : bond 0.00562 ( 4) link_NAG-ASN : angle 3.22507 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 26 time to evaluate : 0.249 Fit side-chains REVERT: B 516 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8125 (pp20) REVERT: L 143 GLU cc_start: 0.8515 (pm20) cc_final: 0.8286 (pm20) outliers start: 8 outliers final: 5 residues processed: 32 average time/residue: 0.5934 time to fit residues: 19.9921 Evaluate side-chains 26 residues out of total 735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 20 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 203 ASN Chi-restraints excluded: chain L residue 134 CYS Chi-restraints excluded: chain L residue 154 LEU 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: 71.6066 > 50: distance: 87 - 96: 34.005 distance: 96 - 97: 42.104 distance: 97 - 98: 41.593 distance: 97 - 100: 49.507 distance: 98 - 99: 23.509 distance: 98 - 105: 27.216 distance: 100 - 101: 39.901 distance: 101 - 102: 50.686 distance: 102 - 103: 43.523 distance: 103 - 104: 14.363 distance: 105 - 106: 48.496 distance: 106 - 107: 8.679 distance: 106 - 109: 13.032 distance: 107 - 108: 12.794 distance: 107 - 111: 53.982 distance: 109 - 110: 55.338 distance: 111 - 112: 33.633 distance: 112 - 113: 20.109 distance: 112 - 115: 43.407 distance: 113 - 114: 41.770 distance: 113 - 119: 23.249 distance: 115 - 116: 28.067 distance: 116 - 117: 26.466 distance: 116 - 118: 18.539 distance: 119 - 120: 38.881 distance: 120 - 121: 50.429 distance: 120 - 123: 24.397 distance: 121 - 122: 31.197 distance: 123 - 124: 58.571 distance: 124 - 125: 58.728 distance: 124 - 126: 50.057 distance: 127 - 128: 17.127 distance: 128 - 129: 22.881 distance: 128 - 131: 9.555 distance: 129 - 130: 33.234 distance: 129 - 136: 29.926 distance: 131 - 132: 24.678 distance: 132 - 133: 20.939 distance: 133 - 134: 41.562 distance: 134 - 135: 37.010 distance: 136 - 137: 35.894 distance: 136 - 142: 40.576 distance: 137 - 138: 27.439 distance: 137 - 140: 59.724 distance: 138 - 139: 32.414 distance: 138 - 143: 36.253 distance: 140 - 141: 24.087 distance: 141 - 142: 31.738 distance: 143 - 144: 8.711 distance: 144 - 145: 18.221 distance: 144 - 147: 17.309 distance: 145 - 146: 28.473 distance: 145 - 154: 12.709 distance: 147 - 148: 13.848 distance: 148 - 149: 15.453 distance: 148 - 150: 49.341 distance: 149 - 151: 25.352 distance: 150 - 152: 15.912 distance: 151 - 153: 40.767 distance: 152 - 153: 8.820 distance: 154 - 155: 11.269 distance: 155 - 156: 14.115 distance: 155 - 158: 24.181 distance: 156 - 157: 7.520 distance: 156 - 163: 26.824 distance: 158 - 159: 19.395 distance: 159 - 160: 13.124 distance: 160 - 161: 33.937 distance: 163 - 164: 39.226 distance: 164 - 165: 13.270 distance: 164 - 167: 54.962 distance: 165 - 166: 13.953 distance: 165 - 174: 53.697 distance: 167 - 168: 24.794 distance: 168 - 169: 53.963 distance: 169 - 170: 3.658 distance: 170 - 171: 28.229 distance: 171 - 172: 11.487 distance: 171 - 173: 10.847 distance: 174 - 175: 32.755 distance: 175 - 176: 31.868 distance: 175 - 178: 20.131 distance: 176 - 177: 17.117 distance: 176 - 182: 30.550 distance: 178 - 179: 3.694 distance: 179 - 180: 12.180 distance: 179 - 181: 35.219