Starting phenix.real_space_refine on Fri Aug 22 12:57:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iyx_61003/08_2025/9iyx_61003.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iyx_61003/08_2025/9iyx_61003.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9iyx_61003/08_2025/9iyx_61003.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iyx_61003/08_2025/9iyx_61003.map" model { file = "/net/cci-nas-00/data/ceres_data/9iyx_61003/08_2025/9iyx_61003.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iyx_61003/08_2025/9iyx_61003.cif" } resolution = 3.6 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= 0.001 sd= 0.043 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 Zn 2 6.06 5 S 18 5.16 5 C 1772 2.51 5 N 414 2.21 5 O 420 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 2626 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1302 Classifications: {'peptide': 179} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 16, 'TRANS': 162} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 174 Unresolved non-hydrogen angles: 234 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'ASN:plan1': 2, 'PHE:plan': 5, 'TRP:plan': 4, 'GLN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 83 Chain: "B" Number of atoms: 1322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1322 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 16, 'TRANS': 155} Chain breaks: 2 Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 134 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 2, 'TRP:plan': 3, 'PHE:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 54 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 347 SG CYS A 48 56.811 25.413 16.460 1.00 2.92 S ATOM 417 SG CYS A 65 53.101 25.858 17.554 1.00 3.68 S ATOM 442 SG CYS A 69 54.091 23.123 15.110 1.00 3.57 S ATOM 1605 SG CYS B 48 68.977 38.696 20.531 1.00 1.71 S ATOM 1673 SG CYS B 65 70.381 38.605 24.224 1.00 1.25 S ATOM 1700 SG CYS B 69 72.048 40.812 21.357 1.00 1.49 S Time building chain proxies: 1.01, per 1000 atoms: 0.38 Number of scatterers: 2626 At special positions: 0 Unit cell: (98.072, 75.686, 79.95, 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) Zn 2 29.99 S 18 16.00 O 420 8.00 N 414 7.00 C 1772 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: 0.20 Conformation dependent library (CDL) restraints added in 68.9 milliseconds Enol-peptide restraints added in 1.2 microseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" NE2 HIS A 60 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 69 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 65 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 48 " pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 60 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 48 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 69 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 65 " Number of angles added : 6 678 Ramachandran restraints generated. 339 Oldfield, 0 Emsley, 339 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 660 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 0 sheets defined 79.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.05 Creating SS restraints... Processing helix chain 'A' and resid 3 through 26 Proline residue: A 11 - end of helix Processing helix chain 'A' and resid 27 through 41 removed outlier: 3.567A pdb=" N PHE A 41 " --> pdb=" O THR A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 99 removed outlier: 4.214A pdb=" N TRP A 74 " --> pdb=" O PRO A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 102 No H-bonds generated for 'chain 'A' and resid 100 through 102' Processing helix chain 'A' and resid 156 through 170 Processing helix chain 'A' and resid 170 through 186 removed outlier: 4.402A pdb=" N SER A 174 " --> pdb=" O PHE A 170 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU A 175 " --> pdb=" O SER A 171 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU A 176 " --> pdb=" O TRP A 172 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL A 177 " --> pdb=" O LEU A 173 " (cutoff:3.500A) Proline residue: A 178 - end of helix Processing helix chain 'A' and resid 187 through 207 Proline residue: A 203 - end of helix Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 211 through 226 removed outlier: 3.696A pdb=" N LEU A 215 " --> pdb=" O PRO A 211 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU A 216 " --> pdb=" O PHE A 212 " (cutoff:3.500A) Proline residue: A 217 - end of helix Processing helix chain 'B' and resid 10 through 41 Proline residue: B 29 - end of helix removed outlier: 3.752A pdb=" N PHE B 41 " --> pdb=" O THR B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 102 removed outlier: 4.276A pdb=" N ARG B 73 " --> pdb=" O CYS B 69 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N TRP B 74 " --> pdb=" O PRO B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 171 Processing helix chain 'B' and resid 172 through 186 Proline residue: B 178 - end of helix Processing helix chain 'B' and resid 189 through 210 removed outlier: 3.590A pdb=" N SER B 193 " --> pdb=" O THR B 189 " (cutoff:3.500A) Proline residue: B 203 - end of helix Processing helix chain 'B' and resid 211 through 213 No H-bonds generated for 'chain 'B' and resid 211 through 213' Processing helix chain 'B' and resid 214 through 226 removed outlier: 3.723A pdb=" N ILE B 218 " --> pdb=" O PRO B 214 " (cutoff:3.500A) 184 hydrogen bonds defined for protein. 552 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: 0.22 Time building geometry restraints manager: 0.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 386 1.32 - 1.44: 814 1.44 - 1.57: 1496 1.57 - 1.69: 1 1.69 - 1.81: 24 Bond restraints: 2721 Sorted by residual: bond pdb=" CA THR A 46 " pdb=" C THR A 46 " ideal model delta sigma weight residual 1.523 1.581 -0.058 1.34e-02 5.57e+03 1.86e+01 bond pdb=" N THR A 46 " pdb=" CA THR A 46 " ideal model delta sigma weight residual 1.457 1.498 -0.041 1.29e-02 6.01e+03 1.00e+01 bond pdb=" CA THR A 45 " pdb=" C THR A 45 " ideal model delta sigma weight residual 1.524 1.560 -0.036 1.26e-02 6.30e+03 8.35e+00 bond pdb=" C ASN A 40 " pdb=" O ASN A 40 " ideal model delta sigma weight residual 1.236 1.201 0.035 1.25e-02 6.40e+03 7.98e+00 bond pdb=" CA PHE A 41 " pdb=" C PHE A 41 " ideal model delta sigma weight residual 1.531 1.499 0.032 1.46e-02 4.69e+03 4.89e+00 ... (remaining 2716 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 3645 2.19 - 4.38: 89 4.38 - 6.57: 12 6.57 - 8.76: 1 8.76 - 10.95: 1 Bond angle restraints: 3748 Sorted by residual: angle pdb=" N THR A 45 " pdb=" CA THR A 45 " pdb=" C THR A 45 " ideal model delta sigma weight residual 111.14 122.09 -10.95 1.08e+00 8.57e-01 1.03e+02 angle pdb=" C ASN A 40 " pdb=" N PHE A 41 " pdb=" CA PHE A 41 " ideal model delta sigma weight residual 123.03 118.01 5.02 1.34e+00 5.57e-01 1.40e+01 angle pdb=" CA THR A 46 " pdb=" C THR A 46 " pdb=" N VAL A 47 " ideal model delta sigma weight residual 116.84 122.76 -5.92 1.71e+00 3.42e-01 1.20e+01 angle pdb=" C PHE A 41 " pdb=" CA PHE A 41 " pdb=" CB PHE A 41 " ideal model delta sigma weight residual 111.85 106.87 4.98 1.47e+00 4.63e-01 1.15e+01 angle pdb=" C MET B 198 " pdb=" N TRP B 199 " pdb=" CA TRP B 199 " ideal model delta sigma weight residual 120.28 124.53 -4.25 1.34e+00 5.57e-01 1.01e+01 ... (remaining 3743 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.12: 1382 15.12 - 30.23: 119 30.23 - 45.35: 30 45.35 - 60.47: 2 60.47 - 75.58: 2 Dihedral angle restraints: 1535 sinusoidal: 522 harmonic: 1013 Sorted by residual: dihedral pdb=" C THR A 46 " pdb=" N THR A 46 " pdb=" CA THR A 46 " pdb=" CB THR A 46 " ideal model delta harmonic sigma weight residual -122.00 -134.41 12.41 0 2.50e+00 1.60e-01 2.46e+01 dihedral pdb=" N THR A 46 " pdb=" C THR A 46 " pdb=" CA THR A 46 " pdb=" CB THR A 46 " ideal model delta harmonic sigma weight residual 123.40 132.57 -9.17 0 2.50e+00 1.60e-01 1.34e+01 dihedral pdb=" CB MET B 75 " pdb=" CG MET B 75 " pdb=" SD MET B 75 " pdb=" CE MET B 75 " ideal model delta sinusoidal sigma weight residual 180.00 129.77 50.23 3 1.50e+01 4.44e-03 8.87e+00 ... (remaining 1532 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 350 0.054 - 0.109: 64 0.109 - 0.163: 14 0.163 - 0.217: 1 0.217 - 0.272: 1 Chirality restraints: 430 Sorted by residual: chirality pdb=" CA THR A 46 " pdb=" N THR A 46 " pdb=" C THR A 46 " pdb=" CB THR A 46 " both_signs ideal model delta sigma weight residual False 2.53 2.25 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CA THR A 45 " pdb=" N THR A 45 " pdb=" C THR A 45 " pdb=" CB THR A 45 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.19 2.00e-01 2.50e+01 9.10e-01 chirality pdb=" CA ASN B 59 " pdb=" N ASN B 59 " pdb=" C ASN B 59 " pdb=" CB ASN B 59 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.23e-01 ... (remaining 427 not shown) Planarity restraints: 454 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS A 65 " 0.041 5.00e-02 4.00e+02 6.36e-02 6.46e+00 pdb=" N PRO A 66 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO A 66 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 66 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 44 " -0.012 2.00e-02 2.50e+03 2.38e-02 5.65e+00 pdb=" C GLY A 44 " 0.041 2.00e-02 2.50e+03 pdb=" O GLY A 44 " -0.016 2.00e-02 2.50e+03 pdb=" N THR A 45 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 216 " 0.036 5.00e-02 4.00e+02 5.52e-02 4.88e+00 pdb=" N PRO B 217 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO B 217 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 217 " 0.031 5.00e-02 4.00e+02 ... (remaining 451 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 52 2.69 - 3.24: 2972 3.24 - 3.79: 4240 3.79 - 4.35: 5062 4.35 - 4.90: 7896 Nonbonded interactions: 20222 Sorted by model distance: nonbonded pdb=" O TRP A 35 " pdb=" OG SER A 38 " model vdw 2.132 3.040 nonbonded pdb=" OE1 GLN B 30 " pdb=" NH2 ARG B 79 " model vdw 2.138 3.120 nonbonded pdb=" O TRP A 201 " pdb=" N LEU A 205 " model vdw 2.156 3.120 nonbonded pdb=" O PRO A 62 " pdb=" NH2 ARG A 78 " model vdw 2.187 3.120 nonbonded pdb=" O PHE B 170 " pdb=" OG SER B 171 " model vdw 2.238 3.040 ... (remaining 20217 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' and (resid 9 through 11 or (resid 12 through 13 and (name N or name C \ A or name C or name O or name CB )) or resid 14 through 15 or (resid 16 through \ 17 and (name N or name CA or name C or name O or name CB )) or resid 18 through \ 50 or resid 58 through 178 or (resid 179 through 181 and (name N or name CA or n \ ame C or name O or name CB )) or resid 182 through 1001)) selection = (chain 'B' and (resid 9 through 12 or (resid 13 and (name N or name CA or name C \ or name O or name CB )) or resid 14 through 58 or (resid 59 and (name N or name \ CA or name C or name O or name CB )) or resid 60 through 67 or (resid 68 and (n \ ame N or name CA or name C or name O or name CB )) or resid 69 through 169 or (r \ esid 170 through 177 and (name N or name CA or name C or name O or name CB )) or \ resid 178 through 182 or (resid 183 through 184 and (name N or name CA or name \ C or name O or name CB )) or resid 185 through 188 or (resid 189 through 194 and \ (name N or name CA or name C or name O or name CB )) or resid 195 through 196 o \ r (resid 197 through 198 and (name N or name CA or name C or name O or name CB ) \ ) or resid 199 through 200 or (resid 201 and (name N or name CA or name C or nam \ e O or name CB )) or resid 202 through 203 or (resid 204 through 205 and (name N \ or name CA or name C or name O or name CB )) or resid 206 or (resid 207 through \ 210 and (name N or name CA or name C or name O or name CB )) or resid 211 or (r \ esid 212 through 213 and (name N or name CA or name C or name O or name CB )) or \ resid 214 through 216 or (resid 217 and (name N or name CA or name C or name O \ or name CB )) or resid 218 or (resid 219 through 226 and (name N or name CA or n \ ame C or name O or name CB )) or resid 301)) } 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: 3.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.040 Check model and map are aligned: 0.020 Set scattering table: 0.000 Process input model: 4.240 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6669 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 0.058 2729 Z= 0.250 Angle : 0.791 10.952 3754 Z= 0.473 Chirality : 0.044 0.272 430 Planarity : 0.009 0.064 454 Dihedral : 12.810 75.584 875 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.40 % Allowed : 0.79 % Favored : 98.81 % Cbeta Deviations : 0.30 % 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: 1.26 (0.49), residues: 339 helix: 0.99 (0.34), residues: 244 sheet: None (None), residues: 0 loop : 0.76 (0.74), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 73 TYR 0.008 0.001 TYR B 200 PHE 0.018 0.002 PHE B 219 TRP 0.013 0.001 TRP B 36 HIS 0.004 0.002 HIS A 60 Details of bonding type rmsd covalent geometry : bond 0.00449 ( 2721) covalent geometry : angle 0.78017 ( 3748) hydrogen bonds : bond 0.17505 ( 184) hydrogen bonds : angle 7.90669 ( 552) metal coordination : bond 0.01410 ( 8) metal coordination : angle 3.35346 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 678 Ramachandran restraints generated. 339 Oldfield, 0 Emsley, 339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 678 Ramachandran restraints generated. 339 Oldfield, 0 Emsley, 339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 60 time to evaluate : 0.056 Fit side-chains REVERT: A 103 MET cc_start: 0.7181 (tpp) cc_final: 0.6956 (tpp) outliers start: 1 outliers final: 1 residues processed: 61 average time/residue: 0.0354 time to fit residues: 2.7091 Evaluate side-chains 51 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 50 time to evaluate : 0.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.8835 > 50: distance: 53 - 57: 35.309 distance: 57 - 58: 5.817 distance: 58 - 59: 7.970 distance: 58 - 61: 19.751 distance: 59 - 60: 17.504 distance: 61 - 62: 15.239 distance: 62 - 168: 28.717 distance: 63 - 64: 36.243 distance: 63 - 69: 41.045 distance: 64 - 65: 40.231 distance: 64 - 67: 8.354 distance: 65 - 66: 20.420 distance: 67 - 68: 52.118 distance: 70 - 71: 13.419 distance: 71 - 72: 48.112 distance: 71 - 74: 7.212 distance: 72 - 77: 39.937 distance: 74 - 75: 8.315 distance: 77 - 78: 15.815 distance: 78 - 79: 21.783 distance: 78 - 81: 22.331 distance: 79 - 80: 41.628 distance: 79 - 84: 20.652 distance: 81 - 83: 34.734 distance: 84 - 85: 24.626 distance: 85 - 86: 36.455 distance: 85 - 88: 24.579 distance: 86 - 90: 37.479 distance: 88 - 89: 41.618 distance: 89 - 168: 28.322 distance: 90 - 91: 4.117 distance: 90 - 96: 10.762 distance: 91 - 92: 23.779 distance: 91 - 94: 6.204 distance: 92 - 93: 47.175 distance: 92 - 97: 16.788 distance: 94 - 95: 28.988 distance: 95 - 96: 30.750 distance: 98 - 99: 3.884 distance: 99 - 100: 37.005 distance: 99 - 101: 13.125 distance: 100 - 138: 35.232 distance: 101 - 102: 28.658 distance: 102 - 103: 12.663 distance: 102 - 105: 27.650 distance: 103 - 104: 14.653 distance: 103 - 113: 14.569 distance: 104 - 146: 19.186 distance: 105 - 106: 38.974 distance: 106 - 107: 24.575 distance: 106 - 108: 6.107 distance: 107 - 109: 25.464 distance: 108 - 110: 19.890 distance: 109 - 111: 20.485 distance: 113 - 114: 32.438 distance: 114 - 115: 7.678 distance: 114 - 117: 19.236 distance: 115 - 116: 16.689 distance: 115 - 124: 15.005 distance: 116 - 152: 27.023 distance: 117 - 118: 8.248 distance: 118 - 119: 32.635 distance: 121 - 123: 16.286 distance: 124 - 125: 29.596 distance: 125 - 126: 16.982 distance: 125 - 128: 15.606 distance: 126 - 127: 16.882 distance: 126 - 138: 28.767 distance: 127 - 159: 36.059 distance: 128 - 129: 27.865 distance: 129 - 130: 37.133 distance: 129 - 131: 32.027 distance: 130 - 132: 17.997 distance: 131 - 133: 23.625 distance: 131 - 134: 12.160 distance: 132 - 133: 6.036 distance: 133 - 135: 7.351 distance: 134 - 136: 7.913 distance: 135 - 137: 10.115 distance: 136 - 137: 28.628