Starting phenix.real_space_refine on Thu Jul 2 00:19:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wml_66096/07_2026/9wml_66096_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wml_66096/07_2026/9wml_66096.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9wml_66096/07_2026/9wml_66096.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wml_66096/07_2026/9wml_66096.map" model { file = "/net/cci-nas-00/data/ceres_data/9wml_66096/07_2026/9wml_66096_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wml_66096/07_2026/9wml_66096_neut.cif" } resolution = 2.79 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= 0.132 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: 6 Type Number sf(0) Gaussians S 33 5.16 5 Cl 1 4.86 5 Na 2 4.78 5 C 3010 2.51 5 N 663 2.21 5 O 729 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4438 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 4273 Classifications: {'peptide': 541} Link IDs: {'PTRANS': 26, 'TRANS': 514} Chain breaks: 1 Chain: "A" Number of atoms: 165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 162 Ad-hoc single atom residues: {' NA': 2, ' CL': 1} Unusual residues: {'CLR': 3, 'Y01': 2} Inner-chain residues flagged as termini: ['pdbres="8LJ A 704 "'] Classifications: {'peptide': 1, 'undetermined': 5} Modifications used: {'COO': 1} Link IDs: {None: 5} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'8LJ%COO:plan-2': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 1.05, per 1000 atoms: 0.24 Number of scatterers: 4438 At special positions: 0 Unit cell: (86.4, 72.36, 72.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 33 16.00 Na 2 11.00 O 729 8.00 N 663 7.00 C 3010 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 157 " - pdb=" SG CYS A 166 " 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: 0.40 Conformation dependent library (CDL) restraints added in 161.9 milliseconds 1074 Ramachandran restraints generated. 537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 984 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 1 sheets defined 79.9% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'A' and resid 44 through 53 Processing helix chain 'A' and resid 56 through 61 removed outlier: 3.631A pdb=" N VAL A 60 " --> pdb=" O GLY A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 70 removed outlier: 3.544A pdb=" N TYR A 65 " --> pdb=" O TRP A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 86 removed outlier: 3.616A pdb=" N LEU A 76 " --> pdb=" O GLY A 72 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL A 77 " --> pdb=" O GLY A 73 " (cutoff:3.500A) Proline residue: A 78 - end of helix Processing helix chain 'A' and resid 86 through 102 Processing helix chain 'A' and resid 106 through 114 Proline residue: A 113 - end of helix Processing helix chain 'A' and resid 115 through 147 removed outlier: 3.968A pdb=" N GLY A 119 " --> pdb=" O PHE A 115 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA A 120 " --> pdb=" O LYS A 116 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN A 134 " --> pdb=" O ALA A 130 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N MET A 135 " --> pdb=" O ILE A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 197 Processing helix chain 'A' and resid 200 through 204 Processing helix chain 'A' and resid 214 through 234 Processing helix chain 'A' and resid 247 through 263 removed outlier: 3.602A pdb=" N TYR A 251 " --> pdb=" O ALA A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 276 removed outlier: 3.863A pdb=" N GLY A 270 " --> pdb=" O GLY A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 284 removed outlier: 3.641A pdb=" N SER A 284 " --> pdb=" O HIS A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 300 Processing helix chain 'A' and resid 304 through 312 removed outlier: 4.144A pdb=" N TYR A 312 " --> pdb=" O THR A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 353 removed outlier: 3.652A pdb=" N VAL A 326 " --> pdb=" O ASP A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 359 removed outlier: 3.649A pdb=" N VAL A 359 " --> pdb=" O VAL A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 365 No H-bonds generated for 'chain 'A' and resid 363 through 365' Processing helix chain 'A' and resid 366 through 377 Proline residue: A 372 - end of helix removed outlier: 3.506A pdb=" N MET A 377 " --> pdb=" O GLN A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 415 removed outlier: 3.566A pdb=" N TRP A 384 " --> pdb=" O LEU A 380 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER A 399 " --> pdb=" O LEU A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 420 Processing helix chain 'A' and resid 422 through 439 Processing helix chain 'A' and resid 440 through 444 removed outlier: 3.607A pdb=" N THR A 443 " --> pdb=" O ILE A 440 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ASP A 444 " --> pdb=" O LEU A 441 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 440 through 444' Processing helix chain 'A' and resid 445 through 457 removed outlier: 3.773A pdb=" N TRP A 449 " --> pdb=" O GLY A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 475 Processing helix chain 'A' and resid 478 through 491 Processing helix chain 'A' and resid 495 through 504 Processing helix chain 'A' and resid 504 through 520 Processing helix chain 'A' and resid 532 through 561 removed outlier: 3.727A pdb=" N SER A 546 " --> pdb=" O MET A 542 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ILE A 550 " --> pdb=" O SER A 546 " (cutoff:3.500A) Proline residue: A 551 - end of helix Processing helix chain 'A' and resid 564 through 574 Processing helix chain 'A' and resid 588 through 592 removed outlier: 3.732A pdb=" N TYR A 591 " --> pdb=" O THR A 588 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL A 592 " --> pdb=" O GLY A 589 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 588 through 592' Processing sheet with id=AA1, first strand: chain 'A' and resid 525 through 526 282 hydrogen bonds defined for protein. 822 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: 0.83 Time building geometry restraints manager: 0.49 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: 651 1.32 - 1.45: 1323 1.45 - 1.57: 2554 1.57 - 1.69: 2 1.69 - 1.82: 53 Bond restraints: 4583 Sorted by residual: bond pdb=" CG 8LJ A 704 " pdb=" CD 8LJ A 704 " ideal model delta sigma weight residual 1.334 1.587 -0.253 2.00e-02 2.50e+03 1.60e+02 bond pdb=" N 8LJ A 704 " pdb=" CD 8LJ A 704 " ideal model delta sigma weight residual 1.473 1.579 -0.106 1.40e-02 5.10e+03 5.71e+01 bond pdb=" N PHE A 63 " pdb=" CA PHE A 63 " ideal model delta sigma weight residual 1.462 1.488 -0.026 7.70e-03 1.69e+04 1.12e+01 bond pdb=" N ASN A 59 " pdb=" CA ASN A 59 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.33e-02 5.65e+03 6.92e+00 bond pdb=" N ASN A 162 " pdb=" CA ASN A 162 " ideal model delta sigma weight residual 1.456 1.488 -0.031 1.21e-02 6.83e+03 6.70e+00 ... (remaining 4578 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 6074 1.65 - 3.30: 149 3.30 - 4.95: 39 4.95 - 6.60: 8 6.60 - 8.26: 3 Bond angle restraints: 6273 Sorted by residual: angle pdb=" CA TYR A 297 " pdb=" C TYR A 297 " pdb=" O TYR A 297 " ideal model delta sigma weight residual 121.00 116.12 4.88 1.05e+00 9.07e-01 2.16e+01 angle pdb=" CA GLU A 567 " pdb=" C GLU A 567 " pdb=" O GLU A 567 " ideal model delta sigma weight residual 120.42 115.55 4.87 1.06e+00 8.90e-01 2.11e+01 angle pdb=" N 8LJ A 704 " pdb=" CA 8LJ A 704 " pdb=" CB 8LJ A 704 " ideal model delta sigma weight residual 103.00 107.61 -4.61 1.10e+00 8.26e-01 1.76e+01 angle pdb=" N 8LJ A 704 " pdb=" CA 8LJ A 704 " pdb=" C 8LJ A 704 " ideal model delta sigma weight residual 112.10 103.84 8.26 2.50e+00 1.60e-01 1.09e+01 angle pdb=" N GLY A 42 " pdb=" CA GLY A 42 " pdb=" C GLY A 42 " ideal model delta sigma weight residual 110.38 115.08 -4.70 1.48e+00 4.57e-01 1.01e+01 ... (remaining 6268 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.07: 2637 24.07 - 48.13: 173 48.13 - 72.20: 26 72.20 - 96.26: 2 96.26 - 120.33: 6 Dihedral angle restraints: 2844 sinusoidal: 1291 harmonic: 1553 Sorted by residual: dihedral pdb=" C10 CLR A 706 " pdb=" C1 CLR A 706 " pdb=" C2 CLR A 706 " pdb=" C3 CLR A 706 " ideal model delta sinusoidal sigma weight residual -56.83 63.50 -120.33 1 3.00e+01 1.11e-03 1.61e+01 dihedral pdb=" CB CYS A 157 " pdb=" SG CYS A 157 " pdb=" SG CYS A 166 " pdb=" CB CYS A 166 " ideal model delta sinusoidal sigma weight residual -86.00 -118.94 32.94 1 1.00e+01 1.00e-02 1.54e+01 dihedral pdb=" C1 CLR A 709 " pdb=" C2 CLR A 709 " pdb=" C3 CLR A 709 " pdb=" O1 CLR A 709 " ideal model delta sinusoidal sigma weight residual 180.04 67.53 112.51 1 3.00e+01 1.11e-03 1.48e+01 ... (remaining 2841 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 490 0.035 - 0.070: 158 0.070 - 0.105: 49 0.105 - 0.139: 13 0.139 - 0.174: 4 Chirality restraints: 714 Sorted by residual: chirality pdb=" CA ILE A 51 " pdb=" N ILE A 51 " pdb=" C ILE A 51 " pdb=" CB ILE A 51 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.58e-01 chirality pdb=" CB ILE A 51 " pdb=" CA ILE A 51 " pdb=" CG1 ILE A 51 " pdb=" CG2 ILE A 51 " both_signs ideal model delta sigma weight residual False 2.64 2.80 -0.16 2.00e-01 2.50e+01 6.08e-01 chirality pdb=" CA ASN A 59 " pdb=" N ASN A 59 " pdb=" C ASN A 59 " pdb=" CB ASN A 59 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.61e-01 ... (remaining 711 not shown) Planarity restraints: 735 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" N 8LJ A 704 " 0.034 2.00e-02 2.50e+03 4.53e-02 2.06e+01 pdb=" CB 8LJ A 704 " -0.036 2.00e-02 2.50e+03 pdb=" CG 8LJ A 704 " 0.054 2.00e-02 2.50e+03 pdb=" CD 8LJ A 704 " -0.053 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 37 " -0.213 9.50e-02 1.11e+02 9.60e-02 7.30e+00 pdb=" NE ARG A 37 " 0.020 2.00e-02 2.50e+03 pdb=" CZ ARG A 37 " -0.020 2.00e-02 2.50e+03 pdb=" NH1 ARG A 37 " 0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG A 37 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 297 " 0.029 2.00e-02 2.50e+03 1.71e-02 5.85e+00 pdb=" CG TYR A 297 " -0.004 2.00e-02 2.50e+03 pdb=" CD1 TYR A 297 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 TYR A 297 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR A 297 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR A 297 " -0.010 2.00e-02 2.50e+03 pdb=" CZ TYR A 297 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR A 297 " 0.015 2.00e-02 2.50e+03 ... (remaining 732 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 31 2.57 - 3.15: 3722 3.15 - 3.73: 7318 3.73 - 4.32: 10383 4.32 - 4.90: 17362 Nonbonded interactions: 38816 Sorted by model distance: nonbonded pdb=" OD1 ASN A 59 " pdb="NA NA A 701 " model vdw 1.986 3.210 nonbonded pdb=" OG SER A 298 " pdb="NA NA A 701 " model vdw 1.989 3.210 nonbonded pdb=" ND2 ASN A 59 " pdb=" OG SER A 298 " model vdw 2.232 3.120 nonbonded pdb=" O GLU A 405 " pdb=" OG1 THR A 409 " model vdw 2.254 3.040 nonbonded pdb=" O GLN A 373 " pdb=" OG1 THR A 376 " model vdw 2.274 3.040 ... (remaining 38811 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: 1.350 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: 0.020 Process input model: 6.170 Find NCS groups from input model: 0.040 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:6.690 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 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 0.253 4584 Z= 0.291 Angle : 0.679 8.255 6275 Z= 0.362 Chirality : 0.041 0.174 714 Planarity : 0.006 0.096 735 Dihedral : 16.127 120.329 1857 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.00 % Allowed : 16.11 % Favored : 83.89 % 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 are not related in a simple way. whole: 0.11 (0.36), residues: 537 helix: 0.54 (0.27), residues: 371 sheet: None (None), residues: 0 loop : -0.79 (0.48), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG A 37 TYR 0.030 0.002 TYR A 297 PHE 0.021 0.001 PHE A 401 TRP 0.021 0.002 TRP A 109 HIS 0.002 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00533 / 0.29 ( 4583) covalent geometry : angle 0.67798 / 0.36 ( 6273) SS BOND : bond 0.00347 / 0.18 ( 1) SS BOND : angle 1.71753 / 0.97 ( 2) hydrogen bonds : bond 0.14381 / 10.24 ( 282) hydrogen bonds : angle 7.24171 / 5.49 ( 822) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1074 Ramachandran restraints generated. 537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1074 Ramachandran restraints generated. 537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.171 Fit side-chains REVERT: A 272 GLN cc_start: 0.7822 (tt0) cc_final: 0.7605 (tt0) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.5102 time to fit residues: 44.1166 Evaluate side-chains 73 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 24 optimal weight: 0.7980 chunk 48 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.0970 chunk 25 optimal weight: 0.7980 chunk 50 optimal weight: 0.6980 chunk 53 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.149338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.130595 restraints weight = 5229.304| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 1.52 r_work: 0.3485 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3380 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.1198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4584 Z= 0.148 Angle : 0.592 7.096 6275 Z= 0.287 Chirality : 0.040 0.203 714 Planarity : 0.004 0.044 735 Dihedral : 9.368 59.724 926 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.87 % Allowed : 15.23 % Favored : 81.90 % 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 are not related in a simple way. whole: 1.02 (0.36), residues: 537 helix: 1.19 (0.27), residues: 377 sheet: None (None), residues: 0 loop : -0.41 (0.52), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 62 TYR 0.019 0.002 TYR A 418 PHE 0.014 0.001 PHE A 401 TRP 0.013 0.001 TRP A 109 HIS 0.002 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 ( 4583) covalent geometry : angle 0.59164 / 0.29 ( 6273) SS BOND : bond 0.00003 / 0.00 ( 1) SS BOND : angle 1.75430 / 0.94 ( 2) hydrogen bonds : bond 0.04783 / 3.20 ( 282) hydrogen bonds : angle 5.19089 / 3.94 ( 822) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1074 Ramachandran restraints generated. 537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1074 Ramachandran restraints generated. 537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 0.165 Fit side-chains REVERT: A 272 GLN cc_start: 0.7900 (OUTLIER) cc_final: 0.7697 (tt0) REVERT: A 541 LEU cc_start: 0.7478 (OUTLIER) cc_final: 0.7202 (mp) REVERT: A 562 GLU cc_start: 0.7279 (mm-30) cc_final: 0.7071 (tp30) REVERT: A 567 GLU cc_start: 0.7187 (tp30) cc_final: 0.6877 (mp0) outliers start: 13 outliers final: 5 residues processed: 88 average time/residue: 0.4776 time to fit residues: 43.8232 Evaluate side-chains 83 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 76 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 159 ASN Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 272 GLN Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 544 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 38 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 24 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 chunk 1 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.137395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.117376 restraints weight = 5097.273| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 1.67 r_work: 0.3283 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4584 Z= 0.156 Angle : 0.566 6.375 6275 Z= 0.277 Chirality : 0.040 0.202 714 Planarity : 0.004 0.041 735 Dihedral : 9.124 59.843 926 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.97 % Allowed : 14.79 % Favored : 81.24 % 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 are not related in a simple way. whole: 1.17 (0.36), residues: 537 helix: 1.33 (0.26), residues: 376 sheet: None (None), residues: 0 loop : -0.43 (0.52), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 62 TYR 0.019 0.002 TYR A 418 PHE 0.015 0.001 PHE A 401 TRP 0.013 0.001 TRP A 109 HIS 0.002 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 ( 4583) covalent geometry : angle 0.56497 / 0.28 ( 6273) SS BOND : bond 0.00018 / 0.01 ( 1) SS BOND : angle 1.88382 / 1.00 ( 2) hydrogen bonds : bond 0.04638 / 3.10 ( 282) hydrogen bonds : angle 4.99943 / 3.77 ( 822) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1074 Ramachandran restraints generated. 537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1074 Ramachandran restraints generated. 537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 0.161 Fit side-chains REVERT: A 124 LEU cc_start: 0.8588 (tp) cc_final: 0.8213 (mt) REVERT: A 541 LEU cc_start: 0.7199 (OUTLIER) cc_final: 0.6909 (mp) REVERT: A 567 GLU cc_start: 0.6869 (tp30) cc_final: 0.6641 (mp0) outliers start: 18 outliers final: 10 residues processed: 91 average time/residue: 0.4446 time to fit residues: 42.3257 Evaluate side-chains 87 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 582 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 38 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 17 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 40 optimal weight: 0.1980 chunk 8 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 18 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 162 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.145445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.127172 restraints weight = 5148.746| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 1.52 r_work: 0.3457 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3355 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4584 Z= 0.161 Angle : 0.558 6.102 6275 Z= 0.273 Chirality : 0.040 0.195 714 Planarity : 0.004 0.039 735 Dihedral : 9.212 58.191 926 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.31 % Allowed : 15.45 % Favored : 81.24 % 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 are not related in a simple way. whole: 1.23 (0.37), residues: 537 helix: 1.36 (0.26), residues: 376 sheet: None (None), residues: 0 loop : -0.38 (0.52), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 62 TYR 0.020 0.002 TYR A 418 PHE 0.017 0.001 PHE A 401 TRP 0.012 0.001 TRP A 109 HIS 0.002 0.000 HIS A 316 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.16 ( 4583) covalent geometry : angle 0.55729 / 0.27 ( 6273) SS BOND : bond 0.00032 / 0.02 ( 1) SS BOND : angle 1.91260 / 1.02 ( 2) hydrogen bonds : bond 0.04653 / 3.09 ( 282) hydrogen bonds : angle 4.91766 / 3.69 ( 822) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1074 Ramachandran restraints generated. 537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1074 Ramachandran restraints generated. 537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 0.169 Fit side-chains REVERT: A 124 LEU cc_start: 0.8684 (tp) cc_final: 0.8326 (mt) REVERT: A 272 GLN cc_start: 0.7833 (tt0) cc_final: 0.7245 (tp40) REVERT: A 541 LEU cc_start: 0.7361 (OUTLIER) cc_final: 0.7075 (mp) outliers start: 15 outliers final: 10 residues processed: 82 average time/residue: 0.4815 time to fit residues: 41.1671 Evaluate side-chains 84 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 582 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 41 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 45 optimal weight: 0.0980 chunk 39 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 32 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 156 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.144932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.126702 restraints weight = 5170.330| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 1.50 r_work: 0.3451 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3350 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4584 Z= 0.134 Angle : 0.530 5.927 6275 Z= 0.259 Chirality : 0.039 0.193 714 Planarity : 0.004 0.037 735 Dihedral : 9.109 58.439 926 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.31 % Allowed : 14.57 % Favored : 82.12 % 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 are not related in a simple way. whole: 1.41 (0.37), residues: 537 helix: 1.46 (0.26), residues: 378 sheet: None (None), residues: 0 loop : -0.21 (0.54), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 62 TYR 0.021 0.001 TYR A 418 PHE 0.015 0.001 PHE A 401 TRP 0.012 0.001 TRP A 109 HIS 0.002 0.000 HIS A 316 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 ( 4583) covalent geometry : angle 0.52927 / 0.26 ( 6273) SS BOND : bond 0.00044 / 0.02 ( 1) SS BOND : angle 1.60035 / 0.86 ( 2) hydrogen bonds : bond 0.04380 / 2.91 ( 282) hydrogen bonds : angle 4.77961 / 3.58 ( 822) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1074 Ramachandran restraints generated. 537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1074 Ramachandran restraints generated. 537 Oldfield, 0 Emsley, 537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 0.160 Fit side-chains REVERT: A 110 LYS cc_start: 0.8452 (ttmm) cc_final: 0.8200 (ttmm) REVERT: A 124 LEU cc_start: 0.8692 (tp) cc_final: 0.8359 (mt) REVERT: A 541 LEU cc_start: 0.7421 (OUTLIER) cc_final: 0.7160 (mp) outliers start: 15 outliers final: 10 residues processed: 84 average time/residue: 0.4980 time to fit residues: 43.6438 Evaluate side-chains 85 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 422 LYS Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 582 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 51.5384 > 50: distance: 2 - 25: 8.205 distance: 8 - 32: 5.124 distance: 23 - 25: 6.458 distance: 25 - 26: 13.725 distance: 26 - 27: 7.947 distance: 26 - 29: 16.332 distance: 27 - 28: 20.263 distance: 27 - 32: 7.157 distance: 29 - 30: 15.841 distance: 29 - 31: 11.832 distance: 32 - 33: 4.744 distance: 33 - 34: 6.162 distance: 33 - 36: 12.285 distance: 34 - 35: 10.616 distance: 34 - 39: 11.296 distance: 36 - 37: 6.458 distance: 36 - 38: 11.335 distance: 39 - 40: 19.908 distance: 40 - 41: 13.718 distance: 40 - 43: 8.335 distance: 41 - 42: 16.042 distance: 41 - 47: 11.799 distance: 43 - 44: 6.166 distance: 44 - 45: 11.740 distance: 44 - 46: 25.162 distance: 47 - 48: 8.922 distance: 47 - 53: 21.575 distance: 48 - 49: 19.834 distance: 48 - 51: 29.334 distance: 49 - 50: 21.793 distance: 49 - 54: 14.036 distance: 51 - 52: 15.106 distance: 52 - 53: 20.623 distance: 54 - 55: 4.687 distance: 55 - 56: 14.697 distance: 56 - 57: 15.522 distance: 56 - 58: 15.414 distance: 58 - 59: 9.603 distance: 59 - 60: 8.470 distance: 59 - 62: 8.648 distance: 60 - 61: 14.096 distance: 60 - 63: 5.770 distance: 61 - 90: 12.169 distance: 64 - 65: 5.998 distance: 64 - 67: 5.403 distance: 65 - 66: 5.616 distance: 65 - 77: 3.247 distance: 66 - 98: 13.340 distance: 67 - 68: 9.126 distance: 68 - 69: 8.431 distance: 68 - 70: 4.417 distance: 69 - 71: 11.118 distance: 70 - 72: 11.844 distance: 70 - 73: 4.444 distance: 72 - 74: 7.133 distance: 73 - 75: 6.960 distance: 74 - 76: 5.029 distance: 75 - 76: 11.871 distance: 77 - 78: 11.546 distance: 78 - 79: 12.692 distance: 78 - 81: 10.923 distance: 79 - 80: 11.722 distance: 79 - 86: 18.344 distance: 80 - 107: 25.622 distance: 81 - 82: 12.917 distance: 82 - 83: 5.565 distance: 83 - 84: 3.366 distance: 84 - 85: 17.199 distance: 86 - 87: 11.128 distance: 87 - 88: 12.814 distance: 88 - 89: 11.771 distance: 88 - 90: 5.412 distance: 89 - 114: 19.236 distance: 90 - 91: 4.594 distance: 91 - 92: 4.258 distance: 91 - 94: 12.567 distance: 92 - 93: 8.874 distance: 92 - 98: 7.011 distance: 93 - 121: 15.770 distance: 94 - 95: 15.855 distance: 94 - 96: 12.491 distance: 95 - 97: 9.026