Starting phenix.real_space_refine on Fri Aug 22 15:12:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z6x_39807/08_2025/8z6x_39807.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z6x_39807/08_2025/8z6x_39807.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8z6x_39807/08_2025/8z6x_39807.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z6x_39807/08_2025/8z6x_39807.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8z6x_39807/08_2025/8z6x_39807.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z6x_39807/08_2025/8z6x_39807.map" } resolution = 2.96 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= -0.031 sd= 0.144 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 23 5.16 5 C 2991 2.51 5 N 781 2.21 5 O 909 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4704 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1553 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 14, 'TRANS': 181} Chain: "C" Number of atoms: 1502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1502 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 15, 'TRANS': 187} Chain: "B" Number of atoms: 1649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1649 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 12, 'TRANS': 206} Time building chain proxies: 1.25, per 1000 atoms: 0.27 Number of scatterers: 4704 At special positions: 0 Unit cell: (97.58, 77.35, 115.43, 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 23 16.00 O 909 8.00 N 781 7.00 C 2991 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 104 " distance=2.03 Simple disulfide: pdb=" SG CYS C 155 " - pdb=" SG CYS C 214 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 104 " distance=2.03 Simple disulfide: pdb=" SG CYS B 155 " - pdb=" SG CYS B 211 " 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: 0.38 Conformation dependent library (CDL) restraints added in 131.9 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1130 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 12 sheets defined 10.7% alpha, 33.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.993A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.795A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 365 through 370' Processing helix chain 'A' and resid 383 through 390 removed outlier: 3.809A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'C' and resid 95 through 99 removed outlier: 3.681A pdb=" N GLU C 99 " --> pdb=" O ALA C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 148 Processing helix chain 'C' and resid 202 through 208 Processing helix chain 'B' and resid 69 through 72 removed outlier: 4.124A pdb=" N GLN B 72 " --> pdb=" O PRO B 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 69 through 72' Processing helix chain 'B' and resid 95 through 99 removed outlier: 3.727A pdb=" N THR B 99 " --> pdb=" O ALA B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 204 removed outlier: 4.033A pdb=" N LEU B 204 " --> pdb=" O SER B 201 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.961A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.589A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 9 through 13 removed outlier: 3.559A pdb=" N GLY C 13 " --> pdb=" O THR C 125 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N GLN C 43 " --> pdb=" O LEU C 52 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N LEU C 52 " --> pdb=" O GLN C 43 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 9 through 13 removed outlier: 3.559A pdb=" N GLY C 13 " --> pdb=" O THR C 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 19 through 24 Processing sheet with id=AA6, first strand: chain 'C' and resid 135 through 139 removed outlier: 3.541A pdb=" N VAL C 154 " --> pdb=" O PHE C 139 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA C 151 " --> pdb=" O LEU C 201 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N TYR C 193 " --> pdb=" O ASP C 159 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 174 through 176 removed outlier: 4.256A pdb=" N TRP C 169 " --> pdb=" O VAL C 176 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 3 through 6 Processing sheet with id=AA9, first strand: chain 'B' and resid 11 through 13 removed outlier: 6.347A pdb=" N ILE B 39 " --> pdb=" O ILE B 55 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ILE B 55 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N TRP B 41 " --> pdb=" O MET B 53 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 11 through 13 Processing sheet with id=AB2, first strand: chain 'B' and resid 137 through 139 removed outlier: 5.111A pdb=" N ALA B 152 " --> pdb=" O VAL B 199 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N VAL B 199 " --> pdb=" O ALA B 152 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N GLY B 154 " --> pdb=" O VAL B 197 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N VAL B 197 " --> pdb=" O GLY B 154 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N LEU B 156 " --> pdb=" O SER B 195 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N SER B 195 " --> pdb=" O LEU B 156 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N LYS B 158 " --> pdb=" O LEU B 193 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N LEU B 193 " --> pdb=" O LYS B 158 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N SER B 192 " --> pdb=" O ALA B 183 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ALA B 183 " --> pdb=" O SER B 192 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N SER B 194 " --> pdb=" O PHE B 181 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 166 through 169 removed outlier: 3.583A pdb=" N THR B 166 " --> pdb=" O ASN B 214 " (cutoff:3.500A) 156 hydrogen bonds defined for protein. 357 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: 0.59 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: 1036 1.33 - 1.45: 1157 1.45 - 1.57: 2612 1.57 - 1.69: 1 1.69 - 1.81: 29 Bond restraints: 4835 Sorted by residual: bond pdb=" CA VAL C 30 " pdb=" CB VAL C 30 " ideal model delta sigma weight residual 1.540 1.573 -0.033 1.25e-02 6.40e+03 7.07e+00 bond pdb=" CA TYR C 38 " pdb=" C TYR C 38 " ideal model delta sigma weight residual 1.523 1.493 0.031 1.34e-02 5.57e+03 5.20e+00 bond pdb=" C LEU B 153 " pdb=" O LEU B 153 " ideal model delta sigma weight residual 1.235 1.209 0.025 1.18e-02 7.18e+03 4.66e+00 bond pdb=" C ALA B 140 " pdb=" N PRO B 141 " ideal model delta sigma weight residual 1.332 1.356 -0.025 1.32e-02 5.74e+03 3.51e+00 bond pdb=" N VAL C 30 " pdb=" CA VAL C 30 " ideal model delta sigma weight residual 1.461 1.481 -0.021 1.19e-02 7.06e+03 3.02e+00 ... (remaining 4830 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.62: 6531 2.62 - 5.24: 56 5.24 - 7.86: 2 7.86 - 10.48: 0 10.48 - 13.10: 1 Bond angle restraints: 6590 Sorted by residual: angle pdb=" N TYR C 38 " pdb=" CA TYR C 38 " pdb=" C TYR C 38 " ideal model delta sigma weight residual 110.80 97.70 13.10 2.13e+00 2.20e-01 3.78e+01 angle pdb=" N VAL C 30 " pdb=" CA VAL C 30 " pdb=" C VAL C 30 " ideal model delta sigma weight residual 110.62 114.10 -3.48 1.02e+00 9.61e-01 1.16e+01 angle pdb=" C VAL C 30 " pdb=" CA VAL C 30 " pdb=" CB VAL C 30 " ideal model delta sigma weight residual 112.14 107.59 4.55 1.35e+00 5.49e-01 1.14e+01 angle pdb=" C ALA B 140 " pdb=" N PRO B 141 " pdb=" CA PRO B 141 " ideal model delta sigma weight residual 119.76 116.93 2.83 1.00e+00 1.00e+00 8.01e+00 angle pdb=" N VAL C 30 " pdb=" CA VAL C 30 " pdb=" CB VAL C 30 " ideal model delta sigma weight residual 110.54 114.21 -3.67 1.36e+00 5.41e-01 7.27e+00 ... (remaining 6585 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 2763 17.69 - 35.37: 78 35.37 - 53.06: 21 53.06 - 70.75: 3 70.75 - 88.43: 1 Dihedral angle restraints: 2866 sinusoidal: 1083 harmonic: 1783 Sorted by residual: dihedral pdb=" CA GLU C 56 " pdb=" C GLU C 56 " pdb=" N VAL C 57 " pdb=" CA VAL C 57 " ideal model delta harmonic sigma weight residual -180.00 -153.19 -26.81 0 5.00e+00 4.00e-02 2.87e+01 dihedral pdb=" C THR B 150 " pdb=" N THR B 150 " pdb=" CA THR B 150 " pdb=" CB THR B 150 " ideal model delta harmonic sigma weight residual -122.00 -130.45 8.45 0 2.50e+00 1.60e-01 1.14e+01 dihedral pdb=" N THR B 150 " pdb=" C THR B 150 " pdb=" CA THR B 150 " pdb=" CB THR B 150 " ideal model delta harmonic sigma weight residual 123.40 131.42 -8.02 0 2.50e+00 1.60e-01 1.03e+01 ... (remaining 2863 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 628 0.065 - 0.129: 84 0.129 - 0.194: 5 0.194 - 0.258: 1 0.258 - 0.323: 1 Chirality restraints: 719 Sorted by residual: chirality pdb=" CA THR B 150 " pdb=" N THR B 150 " pdb=" C THR B 150 " pdb=" CB THR B 150 " both_signs ideal model delta sigma weight residual False 2.53 2.20 0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" CB VAL C 30 " pdb=" CA VAL C 30 " pdb=" CG1 VAL C 30 " pdb=" CG2 VAL C 30 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 9.56e-01 chirality pdb=" CA TYR C 38 " pdb=" N TYR C 38 " pdb=" C TYR C 38 " pdb=" CB TYR C 38 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.16e-01 ... (remaining 716 not shown) Planarity restraints: 843 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP C 29 " -0.009 2.00e-02 2.50e+03 1.80e-02 3.23e+00 pdb=" C ASP C 29 " 0.031 2.00e-02 2.50e+03 pdb=" O ASP C 29 " -0.012 2.00e-02 2.50e+03 pdb=" N VAL C 30 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR C 184 " -0.022 5.00e-02 4.00e+02 3.33e-02 1.78e+00 pdb=" N PRO C 185 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO C 185 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 185 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 336 " 0.018 5.00e-02 4.00e+02 2.71e-02 1.18e+00 pdb=" N PRO A 337 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO A 337 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 337 " 0.015 5.00e-02 4.00e+02 ... (remaining 840 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 290 2.73 - 3.27: 4607 3.27 - 3.81: 7188 3.81 - 4.36: 9060 4.36 - 4.90: 15812 Nonbonded interactions: 36957 Sorted by model distance: nonbonded pdb=" O ASP C 172 " pdb=" OG SER C 173 " model vdw 2.186 3.040 nonbonded pdb=" OH TYR C 42 " pdb=" O LEU B 114 " model vdw 2.268 3.040 nonbonded pdb=" OG1 THR A 333 " pdb=" N ASN A 334 " model vdw 2.272 3.120 nonbonded pdb=" OH TYR A 369 " pdb=" O PRO A 384 " model vdw 2.283 3.040 nonbonded pdb=" O GLU C 56 " pdb=" N LYS C 66 " model vdw 2.311 3.120 ... (remaining 36952 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 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: 9.190 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.440 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:10.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 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 : 0.003 0.033 4843 Z= 0.153 Angle : 0.544 13.099 6606 Z= 0.293 Chirality : 0.046 0.323 719 Planarity : 0.003 0.033 843 Dihedral : 9.206 88.434 1712 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.19 % Favored : 92.65 % Rotamer: Outliers : 3.07 % Allowed : 5.57 % Favored : 91.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.58 (0.31), residues: 612 helix: -4.14 (0.43), residues: 46 sheet: -0.68 (0.34), residues: 196 loop : -2.05 (0.30), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 75 TYR 0.010 0.001 TYR C 38 PHE 0.004 0.001 PHE C 139 TRP 0.007 0.001 TRP B 52 HIS 0.001 0.000 HIS C 45 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 4835) covalent geometry : angle 0.54406 ( 6590) SS BOND : bond 0.00122 ( 8) SS BOND : angle 0.51190 ( 16) hydrogen bonds : bond 0.26525 ( 145) hydrogen bonds : angle 9.28888 ( 357) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 84 time to evaluate : 0.194 Fit side-chains revert: symmetry clash REVERT: C 150 LYS cc_start: 0.8946 (OUTLIER) cc_final: 0.8495 (mtpp) REVERT: C 215 GLN cc_start: 0.7534 (OUTLIER) cc_final: 0.6763 (mp10) REVERT: B 2 MET cc_start: 0.8525 (mtm) cc_final: 0.8235 (mtm) REVERT: B 212 ASN cc_start: 0.7602 (m110) cc_final: 0.7295 (m-40) outliers start: 16 outliers final: 5 residues processed: 95 average time/residue: 0.6183 time to fit residues: 60.8423 Evaluate side-chains 59 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain C residue 36 TYR Chi-restraints excluded: chain C residue 150 LYS Chi-restraints excluded: chain C residue 215 GLN Chi-restraints excluded: chain B residue 144 LYS 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: 50.3837 > 50: distance: 77 - 81: 11.613 distance: 81 - 82: 22.506 distance: 82 - 83: 17.926 distance: 83 - 84: 4.561 distance: 83 - 85: 15.481 distance: 85 - 86: 4.180 distance: 86 - 87: 8.772 distance: 86 - 89: 15.308 distance: 87 - 88: 5.810 distance: 87 - 92: 5.003 distance: 89 - 90: 14.520 distance: 89 - 91: 15.196 distance: 92 - 93: 3.147 distance: 92 - 211: 8.097 distance: 93 - 94: 5.778 distance: 93 - 96: 7.146 distance: 94 - 95: 12.647 distance: 94 - 102: 7.176 distance: 95 - 208: 6.036 distance: 97 - 99: 4.285 distance: 98 - 100: 5.164 distance: 99 - 101: 4.174 distance: 102 - 103: 9.972 distance: 103 - 104: 8.601 distance: 103 - 106: 8.098 distance: 104 - 105: 37.010 distance: 104 - 109: 15.125 distance: 106 - 107: 6.746 distance: 106 - 108: 6.528 distance: 109 - 110: 25.546 distance: 109 - 202: 23.187 distance: 110 - 113: 8.157 distance: 111 - 112: 5.786 distance: 111 - 120: 6.215 distance: 113 - 114: 5.740 distance: 114 - 115: 5.580 distance: 114 - 116: 7.360 distance: 115 - 117: 8.046 distance: 116 - 118: 5.818 distance: 117 - 119: 9.466 distance: 118 - 119: 9.767 distance: 120 - 121: 19.852 distance: 120 - 126: 18.103 distance: 121 - 122: 10.192 distance: 121 - 124: 7.647 distance: 122 - 123: 16.189 distance: 122 - 127: 12.392 distance: 124 - 125: 8.478 distance: 125 - 126: 11.085 distance: 127 - 128: 8.650 distance: 128 - 129: 5.210 distance: 128 - 131: 13.910 distance: 129 - 130: 15.362 distance: 129 - 132: 7.096 distance: 132 - 133: 20.748 distance: 133 - 134: 15.593 distance: 133 - 136: 16.217 distance: 134 - 135: 10.239 distance: 134 - 139: 33.122 distance: 136 - 137: 21.983 distance: 136 - 138: 19.416 distance: 139 - 140: 18.855 distance: 140 - 141: 14.786 distance: 140 - 143: 14.295 distance: 141 - 142: 18.387 distance: 141 - 147: 26.573 distance: 143 - 144: 11.985 distance: 144 - 145: 7.354 distance: 144 - 146: 15.648 distance: 147 - 148: 4.667 distance: 148 - 149: 7.891 distance: 148 - 151: 8.587 distance: 149 - 150: 8.689 distance: 149 - 156: 16.525 distance: 152 - 153: 5.683 distance: 153 - 155: 4.560