Starting phenix.real_space_refine on Fri Aug 22 14:37:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y2e_38852/08_2025/8y2e_38852.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y2e_38852/08_2025/8y2e_38852.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8y2e_38852/08_2025/8y2e_38852.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y2e_38852/08_2025/8y2e_38852.map" model { file = "/net/cci-nas-00/data/ceres_data/8y2e_38852/08_2025/8y2e_38852.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y2e_38852/08_2025/8y2e_38852.cif" } resolution = 3.03 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.042 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 2813 2.51 5 N 659 2.21 5 O 719 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 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: 4214 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4163 Classifications: {'peptide': 528} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 504} Chain breaks: 2 Chain: "A" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 51 Unusual residues: {'CXQ': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: 0.30 Number of scatterers: 4214 At special positions: 0 Unit cell: (74.8, 69.7, 91.8, 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 719 8.00 N 659 7.00 C 2813 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 180 " - pdb=" SG CYS A 189 " distance=2.04 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 A 701 " - " ASN A 181 " " NAG A 702 " - " ASN A 188 " Time building additional restraints: 0.32 Conformation dependent library (CDL) restraints added in 156.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 972 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 1 sheets defined 79.4% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'A' and resid 66 through 78 removed outlier: 3.780A pdb=" N PHE A 76 " --> pdb=" O SER A 72 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 84 Processing helix chain 'A' and resid 84 through 94 removed outlier: 3.782A pdb=" N TYR A 88 " --> pdb=" O TRP A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 110 removed outlier: 3.598A pdb=" N ILE A 108 " --> pdb=" O LEU A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 125 Processing helix chain 'A' and resid 140 through 170 removed outlier: 3.610A pdb=" N VAL A 145 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ILE A 146 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N PHE A 155 " --> pdb=" O TYR A 151 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ASN A 157 " --> pdb=" O GLY A 153 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N VAL A 158 " --> pdb=" O PHE A 154 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ILE A 159 " --> pdb=" O PHE A 155 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ILE A 160 " --> pdb=" O TYR A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 220 Processing helix chain 'A' and resid 223 through 227 Processing helix chain 'A' and resid 237 through 255 Processing helix chain 'A' and resid 271 through 286 Processing helix chain 'A' and resid 289 through 296 removed outlier: 3.874A pdb=" N GLY A 293 " --> pdb=" O GLY A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 306 removed outlier: 3.830A pdb=" N LEU A 305 " --> pdb=" O ASP A 301 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N CYS A 306 " --> pdb=" O PHE A 302 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 301 through 306' Processing helix chain 'A' and resid 308 through 323 removed outlier: 3.523A pdb=" N CYS A 319 " --> pdb=" O ALA A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 334 removed outlier: 3.874A pdb=" N ALA A 331 " --> pdb=" O GLY A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 376 Processing helix chain 'A' and resid 378 through 382 removed outlier: 3.685A pdb=" N VAL A 382 " --> pdb=" O ILE A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 400 Proline residue: A 395 - end of helix Processing helix chain 'A' and resid 403 through 438 removed outlier: 3.521A pdb=" N TRP A 407 " --> pdb=" O LEU A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 461 Processing helix chain 'A' and resid 462 through 464 No H-bonds generated for 'chain 'A' and resid 462 through 464' Processing helix chain 'A' and resid 467 through 479 removed outlier: 4.111A pdb=" N VAL A 471 " --> pdb=" O GLY A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 498 Processing helix chain 'A' and resid 500 through 513 Processing helix chain 'A' and resid 517 through 526 Processing helix chain 'A' and resid 526 through 542 removed outlier: 3.506A pdb=" N PHE A 531 " --> pdb=" O VAL A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 570 removed outlier: 3.544A pdb=" N ASN A 558 " --> pdb=" O PRO A 554 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N SER A 568 " --> pdb=" O ILE A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 583 removed outlier: 4.293A pdb=" N ILE A 574 " --> pdb=" O ALA A 570 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR A 575 " --> pdb=" O MET A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 596 removed outlier: 3.593A pdb=" N TYR A 593 " --> pdb=" O GLU A 589 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE A 595 " --> pdb=" O LEU A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 599 No H-bonds generated for 'chain 'A' and resid 597 through 599' Processing helix chain 'A' and resid 600 through 605 Processing helix chain 'A' and resid 609 through 612 Processing helix chain 'A' and resid 613 through 618 removed outlier: 3.898A pdb=" N TRP A 617 " --> pdb=" O THR A 613 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 547 through 548 268 hydrogen bonds defined for protein. 789 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: 0.51 Time building geometry restraints manager: 0.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 1101 1.34 - 1.46: 925 1.46 - 1.58: 2282 1.58 - 1.70: 3 1.70 - 1.82: 34 Bond restraints: 4345 Sorted by residual: bond pdb=" C1 CXQ A 703 " pdb=" C5 CXQ A 703 " ideal model delta sigma weight residual 1.519 1.633 -0.114 2.00e-02 2.50e+03 3.26e+01 bond pdb=" C1 CXQ A 703 " pdb=" C4 CXQ A 703 " ideal model delta sigma weight residual 1.513 1.594 -0.081 2.00e-02 2.50e+03 1.63e+01 bond pdb=" C17 CXQ A 703 " pdb=" N1 CXQ A 703 " ideal model delta sigma weight residual 1.448 1.510 -0.062 2.00e-02 2.50e+03 9.70e+00 bond pdb=" C1 CXQ A 703 " pdb=" O1 CXQ A 703 " ideal model delta sigma weight residual 1.397 1.458 -0.061 2.00e-02 2.50e+03 9.41e+00 bond pdb=" N ILE A 268 " pdb=" CA ILE A 268 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.25e-02 6.40e+03 6.49e+00 ... (remaining 4340 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.86: 5799 1.86 - 3.71: 114 3.71 - 5.57: 15 5.57 - 7.43: 2 7.43 - 9.28: 1 Bond angle restraints: 5931 Sorted by residual: angle pdb=" CA PRO A 584 " pdb=" N PRO A 584 " pdb=" CD PRO A 584 " ideal model delta sigma weight residual 112.00 106.62 5.38 1.40e+00 5.10e-01 1.48e+01 angle pdb=" CA ASP A 191 " pdb=" C ASP A 191 " pdb=" O ASP A 191 " ideal model delta sigma weight residual 120.92 117.41 3.51 1.04e+00 9.25e-01 1.14e+01 angle pdb=" CA PHE A 531 " pdb=" CB PHE A 531 " pdb=" CG PHE A 531 " ideal model delta sigma weight residual 113.80 117.14 -3.34 1.00e+00 1.00e+00 1.12e+01 angle pdb=" CA ARG A 606 " pdb=" CB ARG A 606 " pdb=" CG ARG A 606 " ideal model delta sigma weight residual 114.10 120.47 -6.37 2.00e+00 2.50e-01 1.02e+01 angle pdb=" CA LEU A 250 " pdb=" CB LEU A 250 " pdb=" CG LEU A 250 " ideal model delta sigma weight residual 116.30 125.58 -9.28 3.50e+00 8.16e-02 7.04e+00 ... (remaining 5926 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.42: 2330 28.42 - 56.85: 151 56.85 - 85.27: 11 85.27 - 113.70: 0 113.70 - 142.12: 2 Dihedral angle restraints: 2494 sinusoidal: 973 harmonic: 1521 Sorted by residual: dihedral pdb=" C1 CXQ A 703 " pdb=" C6 CXQ A 703 " pdb=" O1 CXQ A 703 " pdb=" C8 CXQ A 703 " ideal model delta sinusoidal sigma weight residual 158.12 16.00 142.12 1 3.00e+01 1.11e-03 1.91e+01 dihedral pdb=" C1 CXQ A 703 " pdb=" C6 CXQ A 703 " pdb=" O1 CXQ A 703 " pdb=" C7 CXQ A 703 " ideal model delta sinusoidal sigma weight residual 280.48 139.54 140.94 1 3.00e+01 1.11e-03 1.89e+01 dihedral pdb=" CA TRP A 132 " pdb=" C TRP A 132 " pdb=" N LYS A 133 " pdb=" CA LYS A 133 " ideal model delta harmonic sigma weight residual 180.00 162.14 17.86 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 2491 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 529 0.046 - 0.093: 116 0.093 - 0.139: 30 0.139 - 0.185: 2 0.185 - 0.231: 1 Chirality restraints: 678 Sorted by residual: chirality pdb=" CA ILE A 268 " pdb=" N ILE A 268 " pdb=" C ILE A 268 " pdb=" CB ILE A 268 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" C2 CXQ A 703 " pdb=" C13 CXQ A 703 " pdb=" C7 CXQ A 703 " pdb=" N1 CXQ A 703 " both_signs ideal model delta sigma weight residual False 2.74 2.92 -0.18 2.00e-01 2.50e+01 8.16e-01 chirality pdb=" CA PRO A 584 " pdb=" N PRO A 584 " pdb=" C PRO A 584 " pdb=" CB PRO A 584 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.90e-01 ... (remaining 675 not shown) Planarity restraints: 725 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 394 " -0.039 5.00e-02 4.00e+02 5.89e-02 5.54e+00 pdb=" N PRO A 395 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO A 395 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 395 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 189 " -0.010 2.00e-02 2.50e+03 2.03e-02 4.11e+00 pdb=" C CYS A 189 " 0.035 2.00e-02 2.50e+03 pdb=" O CYS A 189 " -0.013 2.00e-02 2.50e+03 pdb=" N SER A 190 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 181 " -0.016 2.00e-02 2.50e+03 1.47e-02 2.71e+00 pdb=" CG ASN A 181 " 0.021 2.00e-02 2.50e+03 pdb=" OD1 ASN A 181 " -0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN A 181 " 0.013 2.00e-02 2.50e+03 pdb=" C1 NAG A 701 " -0.015 2.00e-02 2.50e+03 ... (remaining 722 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 1154 2.81 - 3.33: 3834 3.33 - 3.85: 6643 3.85 - 4.38: 7416 4.38 - 4.90: 13745 Nonbonded interactions: 32792 Sorted by model distance: nonbonded pdb=" NH1 ARG A 237 " pdb=" OD1 ASN A 466 " model vdw 2.283 3.120 nonbonded pdb=" O ARG A 237 " pdb=" OG1 THR A 241 " model vdw 2.312 3.040 nonbonded pdb=" OG SER A 186 " pdb=" OE2 GLU A 215 " model vdw 2.340 3.040 nonbonded pdb=" N ASP A 79 " pdb=" OD1 ASP A 79 " model vdw 2.409 3.120 nonbonded pdb=" O PHE A 498 " pdb=" NE2 GLN A 611 " model vdw 2.419 3.120 ... (remaining 32787 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 2.340 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: 0.010 Set scattering table: 0.020 Process input model: 5.680 Find NCS groups from input model: 0.020 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:0.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 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 0.114 4348 Z= 0.232 Angle : 0.614 9.283 5939 Z= 0.318 Chirality : 0.041 0.231 678 Planarity : 0.005 0.059 723 Dihedral : 17.534 142.121 1519 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 0.00 % Allowed : 23.76 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.57 (0.38), residues: 522 helix: 1.92 (0.28), residues: 360 sheet: None (None), residues: 0 loop : -1.00 (0.49), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 125 TYR 0.010 0.001 TYR A 575 PHE 0.016 0.001 PHE A 451 TRP 0.013 0.001 TRP A 132 HIS 0.002 0.001 HIS A 225 Details of bonding type rmsd covalent geometry : bond 0.00485 ( 4345) covalent geometry : angle 0.60991 ( 5931) SS BOND : bond 0.00707 ( 1) SS BOND : angle 1.67162 ( 2) hydrogen bonds : bond 0.14037 ( 268) hydrogen bonds : angle 4.41491 ( 789) link_NAG-ASN : bond 0.01612 ( 2) link_NAG-ASN : angle 2.17487 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.108 Fit side-chains REVERT: A 126 GLU cc_start: 0.7627 (mt-10) cc_final: 0.7415 (mt-10) REVERT: A 531 PHE cc_start: 0.8123 (t80) cc_final: 0.7252 (t80) outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.0618 time to fit residues: 3.8753 Evaluate side-chains 44 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 53.1769 > 50: distance: 75 - 101: 15.671 distance: 82 - 109: 20.614 distance: 89 - 93: 8.747 distance: 93 - 94: 5.391 distance: 94 - 95: 14.454 distance: 94 - 97: 9.255 distance: 95 - 96: 18.722 distance: 95 - 101: 19.437 distance: 97 - 98: 11.568 distance: 97 - 99: 4.653 distance: 98 - 100: 8.706 distance: 101 - 102: 18.744 distance: 102 - 103: 7.714 distance: 102 - 105: 10.631 distance: 103 - 104: 38.789 distance: 103 - 109: 16.170 distance: 105 - 106: 11.507 distance: 105 - 107: 18.364 distance: 106 - 108: 12.727 distance: 109 - 110: 27.843 distance: 110 - 113: 5.193 distance: 111 - 112: 11.575 distance: 111 - 121: 5.912 distance: 112 - 142: 17.048 distance: 113 - 114: 8.826 distance: 114 - 115: 11.718 distance: 114 - 116: 12.300 distance: 115 - 117: 14.187 distance: 116 - 118: 12.616 distance: 117 - 119: 15.359 distance: 118 - 119: 10.031 distance: 119 - 120: 4.928 distance: 121 - 122: 6.784 distance: 121 - 127: 14.998 distance: 122 - 123: 12.616 distance: 122 - 125: 12.593 distance: 123 - 124: 8.933 distance: 123 - 128: 8.946 distance: 124 - 150: 11.136 distance: 125 - 126: 32.155 distance: 126 - 127: 20.626 distance: 128 - 129: 9.454 distance: 129 - 130: 20.434 distance: 129 - 132: 9.482 distance: 130 - 131: 11.147 distance: 130 - 137: 14.437 distance: 131 - 155: 30.092 distance: 132 - 133: 20.713 distance: 133 - 134: 11.687 distance: 134 - 135: 5.543 distance: 134 - 136: 10.091 distance: 137 - 138: 20.839 distance: 138 - 139: 12.155 distance: 138 - 141: 7.760 distance: 139 - 140: 21.198 distance: 139 - 142: 19.629 distance: 142 - 143: 9.940 distance: 143 - 144: 8.991 distance: 143 - 146: 11.688 distance: 144 - 145: 24.539 distance: 144 - 150: 14.923 distance: 146 - 147: 16.448 distance: 146 - 148: 12.127 distance: 147 - 149: 9.560 distance: 150 - 151: 11.433 distance: 151 - 152: 14.059 distance: 151 - 154: 20.995 distance: 152 - 153: 17.473 distance: 152 - 155: 34.537 distance: 155 - 156: 13.542 distance: 156 - 157: 19.849 distance: 156 - 159: 20.978 distance: 157 - 158: 13.351 distance: 157 - 162: 32.300 distance: 159 - 160: 14.357 distance: 159 - 161: 31.855 distance: 162 - 163: 14.819 distance: 163 - 164: 17.153 distance: 163 - 166: 24.182 distance: 164 - 165: 9.850 distance: 164 - 170: 5.098 distance: 166 - 167: 17.134 distance: 167 - 168: 5.229 distance: 167 - 169: 11.363 distance: 185 - 196: 3.236