Starting phenix.real_space_refine on Thu Jul 2 05:53:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jhk_61485/07_2026/9jhk_61485.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jhk_61485/07_2026/9jhk_61485.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9jhk_61485/07_2026/9jhk_61485.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jhk_61485/07_2026/9jhk_61485.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jhk_61485/07_2026/9jhk_61485.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jhk_61485/07_2026/9jhk_61485.map" } resolution = 3.42 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= 0.012 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 Mn 1 7.51 5 P 42 5.49 5 S 20 5.16 5 C 4313 2.51 5 N 1139 2.21 5 O 1383 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-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6898 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 745, 6036 Classifications: {'peptide': 745} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 27, 'TRANS': 717} Chain: "C" Number of atoms: 442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 442 Classifications: {'DNA': 21} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 20} Chain: "E" Number of atoms: 419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 419 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' MN': 1} Chain breaks: 1 Time building chain proxies: 1.69, per 1000 atoms: 0.24 Number of scatterers: 6898 At special positions: 0 Unit cell: (72.16, 85.28, 104.14, 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) Mn 1 24.99 S 20 16.00 P 42 15.00 O 1383 8.00 N 1139 7.00 C 4313 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.58 Conformation dependent library (CDL) restraints added in 348.1 milliseconds 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1394 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 12 sheets defined 31.1% alpha, 17.4% beta 6 base pairs and 33 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 40 through 42 No H-bonds generated for 'chain 'A' and resid 40 through 42' Processing helix chain 'A' and resid 43 through 54 Processing helix chain 'A' and resid 98 through 115 removed outlier: 4.242A pdb=" N LYS A 115 " --> pdb=" O LEU A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 194 Processing helix chain 'A' and resid 233 through 240 Processing helix chain 'A' and resid 244 through 249 removed outlier: 4.158A pdb=" N ASP A 249 " --> pdb=" O TYR A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 256 Processing helix chain 'A' and resid 281 through 289 Processing helix chain 'A' and resid 289 through 301 removed outlier: 4.538A pdb=" N GLN A 298 " --> pdb=" O LYS A 294 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N LEU A 299 " --> pdb=" O GLU A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 319 Processing helix chain 'A' and resid 364 through 369 Processing helix chain 'A' and resid 388 through 404 Processing helix chain 'A' and resid 439 through 451 Processing helix chain 'A' and resid 474 through 485 Processing helix chain 'A' and resid 494 through 503 Processing helix chain 'A' and resid 508 through 522 Processing helix chain 'A' and resid 584 through 603 Processing helix chain 'A' and resid 620 through 631 removed outlier: 3.831A pdb=" N TYR A 624 " --> pdb=" O ASP A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 711 Processing helix chain 'A' and resid 723 through 735 Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 12 removed outlier: 3.516A pdb=" N ASN A 655 " --> pdb=" O ASN A 652 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 163 through 166 removed outlier: 3.846A pdb=" N TYR A 175 " --> pdb=" O SER A 163 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N VAL A 172 " --> pdb=" O GLY A 17 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 60 through 61 removed outlier: 3.795A pdb=" N LEU A 67 " --> pdb=" O TYR A 29 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR A 27 " --> pdb=" O THR A 69 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 117 through 118 Processing sheet with id=AA5, first strand: chain 'A' and resid 125 through 127 Processing sheet with id=AA6, first strand: chain 'A' and resid 268 through 271 removed outlier: 3.671A pdb=" N VAL A 262 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N TYR A 271 " --> pdb=" O VAL A 260 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL A 260 " --> pdb=" O TYR A 271 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LEU A 214 " --> pdb=" O VAL A 203 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 343 through 346 removed outlier: 6.731A pdb=" N ILE A 637 " --> pdb=" O SER A 693 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ILE A 609 " --> pdb=" O ASN A 636 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N ILE A 638 " --> pdb=" O ILE A 609 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N ILE A 611 " --> pdb=" O ILE A 638 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL A 640 " --> pdb=" O ILE A 611 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N ARG A 613 " --> pdb=" O VAL A 640 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 358 through 359 removed outlier: 4.697A pdb=" N LEU A 352 " --> pdb=" O ILE A 359 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 423 through 424 removed outlier: 6.277A pdb=" N VAL A 378 " --> pdb=" O GLU A 424 " (cutoff:3.500A) removed outlier: 9.132A pdb=" N GLU A 433 " --> pdb=" O PHE A 380 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N VAL A 382 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N TYR A 435 " --> pdb=" O VAL A 382 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N TYR A 384 " --> pdb=" O TYR A 435 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 423 through 424 removed outlier: 6.277A pdb=" N VAL A 378 " --> pdb=" O GLU A 424 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 407 through 408 removed outlier: 3.536A pdb=" N GLU A 411 " --> pdb=" O TYR A 408 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 462 through 463 229 hydrogen bonds defined for protein. 648 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 14 hydrogen bonds 28 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 33 stacking parallelities Total time for adding SS restraints: 1.37 Time building geometry restraints manager: 0.77 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: 1269 1.32 - 1.44: 1927 1.44 - 1.56: 3814 1.56 - 1.69: 78 1.69 - 1.81: 35 Bond restraints: 7123 Sorted by residual: bond pdb=" C5' DG C 2 " pdb=" C4' DG C 2 " ideal model delta sigma weight residual 1.512 1.461 0.051 7.00e-03 2.04e+04 5.41e+01 bond pdb=" C3' DA C 7 " pdb=" O3' DA C 7 " ideal model delta sigma weight residual 1.435 1.346 0.089 1.30e-02 5.92e+03 4.66e+01 bond pdb=" C3' DC E 8 " pdb=" O3' DC E 8 " ideal model delta sigma weight residual 1.435 1.355 0.080 1.30e-02 5.92e+03 3.79e+01 bond pdb=" C3' DG C 8 " pdb=" O3' DG C 8 " ideal model delta sigma weight residual 1.435 1.370 0.065 1.30e-02 5.92e+03 2.48e+01 bond pdb=" C4' DA C 7 " pdb=" C3' DA C 7 " ideal model delta sigma weight residual 1.529 1.479 0.050 1.00e-02 1.00e+04 2.48e+01 ... (remaining 7118 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 8862 1.95 - 3.90: 798 3.90 - 5.85: 92 5.85 - 7.80: 24 7.80 - 9.75: 7 Bond angle restraints: 9783 Sorted by residual: angle pdb=" O4' DG C 4 " pdb=" C4' DG C 4 " pdb=" C3' DG C 4 " ideal model delta sigma weight residual 106.00 101.93 4.07 6.00e-01 2.78e+00 4.60e+01 angle pdb=" O4' DC E 7 " pdb=" C4' DC E 7 " pdb=" C3' DC E 7 " ideal model delta sigma weight residual 106.00 102.04 3.96 6.00e-01 2.78e+00 4.35e+01 angle pdb=" O4' DC E 8 " pdb=" C4' DC E 8 " pdb=" C3' DC E 8 " ideal model delta sigma weight residual 106.00 102.26 3.74 6.00e-01 2.78e+00 3.88e+01 angle pdb=" O4' DT E 12 " pdb=" C4' DT E 12 " pdb=" C3' DT E 12 " ideal model delta sigma weight residual 106.00 102.83 3.17 6.00e-01 2.78e+00 2.78e+01 angle pdb=" O4' DT E 9 " pdb=" C4' DT E 9 " pdb=" C3' DT E 9 " ideal model delta sigma weight residual 106.00 102.99 3.01 6.00e-01 2.78e+00 2.51e+01 ... (remaining 9778 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.30: 3928 25.30 - 50.59: 236 50.59 - 75.89: 40 75.89 - 101.18: 5 101.18 - 126.48: 1 Dihedral angle restraints: 4210 sinusoidal: 2023 harmonic: 2187 Sorted by residual: dihedral pdb=" CA ILE A 471 " pdb=" C ILE A 471 " pdb=" N GLU A 472 " pdb=" CA GLU A 472 " ideal model delta harmonic sigma weight residual -180.00 -139.34 -40.66 0 5.00e+00 4.00e-02 6.61e+01 dihedral pdb=" CA GLU A 470 " pdb=" C GLU A 470 " pdb=" N ILE A 471 " pdb=" CA ILE A 471 " ideal model delta harmonic sigma weight residual -180.00 -141.07 -38.93 0 5.00e+00 4.00e-02 6.06e+01 dihedral pdb=" CA LYS A 63 " pdb=" C LYS A 63 " pdb=" N ASP A 64 " pdb=" CA ASP A 64 " ideal model delta harmonic sigma weight residual -180.00 -144.17 -35.83 0 5.00e+00 4.00e-02 5.14e+01 ... (remaining 4207 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 660 0.056 - 0.111: 291 0.111 - 0.166: 82 0.166 - 0.222: 27 0.222 - 0.277: 12 Chirality restraints: 1072 Sorted by residual: chirality pdb=" C3' DG C 4 " pdb=" C4' DG C 4 " pdb=" O3' DG C 4 " pdb=" C2' DG C 4 " both_signs ideal model delta sigma weight residual False -2.73 -2.45 -0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" CB THR A 725 " pdb=" CA THR A 725 " pdb=" OG1 THR A 725 " pdb=" CG2 THR A 725 " both_signs ideal model delta sigma weight residual False 2.55 2.28 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" C3' DT E 12 " pdb=" C4' DT E 12 " pdb=" O3' DT E 12 " pdb=" C2' DT E 12 " both_signs ideal model delta sigma weight residual False -2.73 -2.47 -0.26 2.00e-01 2.50e+01 1.75e+00 ... (remaining 1069 not shown) Planarity restraints: 1097 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 470 " 0.014 2.00e-02 2.50e+03 2.75e-02 7.55e+00 pdb=" C GLU A 470 " -0.048 2.00e-02 2.50e+03 pdb=" O GLU A 470 " 0.018 2.00e-02 2.50e+03 pdb=" N ILE A 471 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 623 " 0.017 2.00e-02 2.50e+03 1.56e-02 6.12e+00 pdb=" CG TRP A 623 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 TRP A 623 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP A 623 " -0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP A 623 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A 623 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 623 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 623 " 0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 623 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP A 623 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 154 " -0.016 2.00e-02 2.50e+03 1.72e-02 5.18e+00 pdb=" CG PHE A 154 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE A 154 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE A 154 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE A 154 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 154 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 154 " -0.003 2.00e-02 2.50e+03 ... (remaining 1094 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 29 2.44 - 3.06: 4273 3.06 - 3.67: 10867 3.67 - 4.29: 16318 4.29 - 4.90: 26642 Nonbonded interactions: 58129 Sorted by model distance: nonbonded pdb=" OD1 ASN A 451 " pdb=" CZ3 TRP A 482 " model vdw 1.829 3.340 nonbonded pdb=" OP1 DA C 3 " pdb="MN MN C 801 " model vdw 1.846 3.060 nonbonded pdb=" OP2 DT C 1 " pdb="MN MN C 801 " model vdw 1.858 3.060 nonbonded pdb=" O LEU A 751 " pdb="MN MN C 801 " model vdw 1.874 3.060 nonbonded pdb=" ND2 ASN A 451 " pdb=" CZ3 TRP A 482 " model vdw 2.005 3.420 ... (remaining 58124 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: 1.200 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.130 Find NCS groups from input model: 0.030 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:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6775 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 : 0.014 0.139 7123 Z= 0.791 Angle : 1.185 9.751 9783 Z= 0.736 Chirality : 0.073 0.277 1072 Planarity : 0.007 0.053 1097 Dihedral : 16.103 126.480 2816 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.42 % 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: -3.78 (0.24), residues: 743 helix: -2.90 (0.23), residues: 224 sheet: -2.50 (0.42), residues: 122 loop : -2.24 (0.25), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.002 ARG A 721 TYR 0.034 0.004 TYR A 624 PHE 0.040 0.006 PHE A 154 TRP 0.040 0.008 TRP A 623 HIS 0.015 0.004 HIS A 513 Details of bonding type rmsd/Z covalent geometry : bond 0.01412 / 0.79 ( 7123) covalent geometry : angle 1.18513 / 0.74 ( 9783) hydrogen bonds : bond 0.22303 / 14.53 ( 243) hydrogen bonds : angle 9.19079 / 6.14 ( 676) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 ILE cc_start: 0.7405 (mt) cc_final: 0.7012 (mt) outliers start: 0 outliers final: 0 residues processed: 193 average time/residue: 0.0921 time to fit residues: 23.1579 Evaluate side-chains 129 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 85 ASN ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 288 ASN A 490 GLN A 574 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.068499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.053040 restraints weight = 26524.955| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 5.99 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 7123 Z= 0.222 Angle : 0.854 11.611 9783 Z= 0.458 Chirality : 0.053 0.375 1072 Planarity : 0.005 0.039 1097 Dihedral : 19.054 126.473 1277 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.59 % Allowed : 12.13 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.55 (0.27), residues: 743 helix: -1.55 (0.29), residues: 226 sheet: -2.35 (0.43), residues: 114 loop : -1.51 (0.27), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 56 TYR 0.033 0.002 TYR A 511 PHE 0.020 0.003 PHE A 738 TRP 0.019 0.003 TRP A 482 HIS 0.008 0.002 HIS A 513 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.22 ( 7123) covalent geometry : angle 0.85362 / 0.46 ( 9783) hydrogen bonds : bond 0.05754 / 3.67 ( 243) hydrogen bonds : angle 6.40636 / 4.45 ( 676) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 145 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 ASN cc_start: 0.9529 (m110) cc_final: 0.9256 (m-40) REVERT: A 98 MET cc_start: 0.9106 (mmt) cc_final: 0.8878 (mmp) REVERT: A 103 GLU cc_start: 0.9049 (OUTLIER) cc_final: 0.8674 (pm20) REVERT: A 131 LYS cc_start: 0.9119 (mmtt) cc_final: 0.8691 (mmtp) REVERT: A 191 MET cc_start: 0.9719 (mmm) cc_final: 0.9491 (mmm) REVERT: A 289 ASP cc_start: 0.8642 (t0) cc_final: 0.8171 (t0) REVERT: A 304 MET cc_start: 0.9434 (mmt) cc_final: 0.9058 (mmp) REVERT: A 353 MET cc_start: 0.8710 (ptt) cc_final: 0.8473 (ptt) REVERT: A 363 MET cc_start: 0.8993 (tpp) cc_final: 0.7981 (tpp) REVERT: A 444 LYS cc_start: 0.9666 (mttm) cc_final: 0.9352 (mmmt) REVERT: A 482 TRP cc_start: 0.8576 (m100) cc_final: 0.8331 (m100) REVERT: A 491 MET cc_start: 0.8726 (mtp) cc_final: 0.7883 (mtt) REVERT: A 495 LYS cc_start: 0.9724 (tttm) cc_final: 0.9472 (ttmm) REVERT: A 511 TYR cc_start: 0.9163 (m-80) cc_final: 0.8949 (m-80) REVERT: A 513 HIS cc_start: 0.9238 (m-70) cc_final: 0.8764 (m-70) REVERT: A 514 ASN cc_start: 0.9142 (m-40) cc_final: 0.8849 (t0) REVERT: A 647 LYS cc_start: 0.9289 (mmtm) cc_final: 0.8673 (mmmt) outliers start: 24 outliers final: 12 residues processed: 157 average time/residue: 0.0824 time to fit residues: 17.2733 Evaluate side-chains 137 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 124 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 274 HIS Chi-restraints excluded: chain A residue 528 TRP Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 733 CYS Chi-restraints excluded: chain A residue 739 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 76 optimal weight: 20.0000 chunk 6 optimal weight: 1.9990 chunk 7 optimal weight: 6.9990 chunk 29 optimal weight: 9.9990 chunk 51 optimal weight: 4.9990 chunk 33 optimal weight: 10.0000 chunk 1 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 71 optimal weight: 0.2980 chunk 19 optimal weight: 7.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 741 GLN ** 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 = 0.3291 r_free = 0.3291 target = 0.067129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.051882 restraints weight = 26677.120| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 5.85 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 7123 Z= 0.223 Angle : 0.759 11.434 9783 Z= 0.411 Chirality : 0.049 0.255 1072 Planarity : 0.004 0.025 1097 Dihedral : 19.039 128.907 1277 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 17.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.59 % Allowed : 14.82 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.89 (0.29), residues: 743 helix: -0.86 (0.32), residues: 225 sheet: -2.17 (0.44), residues: 124 loop : -1.07 (0.30), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 618 TYR 0.026 0.002 TYR A 306 PHE 0.031 0.003 PHE A 478 TRP 0.015 0.002 TRP A 623 HIS 0.006 0.002 HIS A 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.22 ( 7123) covalent geometry : angle 0.75882 / 0.41 ( 9783) hydrogen bonds : bond 0.05042 / 3.21 ( 243) hydrogen bonds : angle 6.07068 / 4.19 ( 676) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 126 time to evaluate : 0.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 MET cc_start: 0.9674 (mmt) cc_final: 0.8862 (tpp) REVERT: A 85 ASN cc_start: 0.9556 (m110) cc_final: 0.9299 (m-40) REVERT: A 98 MET cc_start: 0.9057 (mmt) cc_final: 0.8808 (mmp) REVERT: A 103 GLU cc_start: 0.8982 (OUTLIER) cc_final: 0.8730 (pm20) REVERT: A 131 LYS cc_start: 0.9010 (mmtt) cc_final: 0.8763 (mmtp) REVERT: A 191 MET cc_start: 0.9719 (mmm) cc_final: 0.9466 (mmm) REVERT: A 270 MET cc_start: 0.6847 (pmm) cc_final: 0.6646 (pmm) REVERT: A 289 ASP cc_start: 0.8756 (t0) cc_final: 0.8240 (t0) REVERT: A 295 GLU cc_start: 0.9025 (mt-10) cc_final: 0.8642 (pt0) REVERT: A 304 MET cc_start: 0.9384 (mmt) cc_final: 0.9131 (mmm) REVERT: A 363 MET cc_start: 0.9075 (tpp) cc_final: 0.8105 (tpp) REVERT: A 482 TRP cc_start: 0.8774 (m100) cc_final: 0.8521 (m100) REVERT: A 491 MET cc_start: 0.8947 (mtp) cc_final: 0.8579 (mtt) REVERT: A 495 LYS cc_start: 0.9725 (tttm) cc_final: 0.9483 (ttmm) REVERT: A 511 TYR cc_start: 0.9123 (m-80) cc_final: 0.8916 (m-80) REVERT: A 513 HIS cc_start: 0.9232 (m-70) cc_final: 0.8819 (m-70) REVERT: A 514 ASN cc_start: 0.9177 (m-40) cc_final: 0.8934 (t0) REVERT: A 531 LYS cc_start: 0.9655 (tmtt) cc_final: 0.9302 (ptmm) REVERT: A 536 ASP cc_start: 0.9267 (m-30) cc_final: 0.8887 (p0) REVERT: A 647 LYS cc_start: 0.9263 (mmtm) cc_final: 0.8495 (mmmm) outliers start: 24 outliers final: 13 residues processed: 140 average time/residue: 0.0781 time to fit residues: 14.9259 Evaluate side-chains 132 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 118 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 274 HIS Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 528 TRP Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 733 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 46 optimal weight: 4.9990 chunk 77 optimal weight: 10.0000 chunk 66 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 48 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 20 optimal weight: 10.0000 chunk 14 optimal weight: 7.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 741 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.068343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.053192 restraints weight = 26902.132| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 5.85 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.3719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7123 Z= 0.162 Angle : 0.714 9.132 9783 Z= 0.381 Chirality : 0.048 0.282 1072 Planarity : 0.003 0.035 1097 Dihedral : 18.899 128.372 1277 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 16.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 4.04 % Allowed : 15.12 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.53 (0.30), residues: 743 helix: -0.60 (0.32), residues: 226 sheet: -1.81 (0.44), residues: 127 loop : -0.87 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 158 TYR 0.023 0.002 TYR A 511 PHE 0.023 0.002 PHE A 432 TRP 0.012 0.002 TRP A 623 HIS 0.006 0.002 HIS A 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.16 ( 7123) covalent geometry : angle 0.71357 / 0.38 ( 9783) hydrogen bonds : bond 0.04469 / 2.88 ( 243) hydrogen bonds : angle 5.91479 / 4.08 ( 676) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 131 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 MET cc_start: 0.8989 (mmt) cc_final: 0.8736 (mmt) REVERT: A 30 LYS cc_start: 0.9652 (tmmt) cc_final: 0.9403 (tmmt) REVERT: A 51 MET cc_start: 0.9680 (mmt) cc_final: 0.8702 (tpp) REVERT: A 103 GLU cc_start: 0.9025 (OUTLIER) cc_final: 0.8727 (pm20) REVERT: A 132 GLU cc_start: 0.8376 (pm20) cc_final: 0.8017 (pm20) REVERT: A 191 MET cc_start: 0.9748 (mmm) cc_final: 0.9477 (mmm) REVERT: A 217 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.8220 (mp0) REVERT: A 270 MET cc_start: 0.6747 (pmm) cc_final: 0.6530 (pmm) REVERT: A 289 ASP cc_start: 0.8766 (t0) cc_final: 0.8258 (t0) REVERT: A 295 GLU cc_start: 0.9026 (mt-10) cc_final: 0.8637 (pt0) REVERT: A 302 MET cc_start: 0.8286 (mmm) cc_final: 0.7443 (mmm) REVERT: A 304 MET cc_start: 0.9348 (OUTLIER) cc_final: 0.9134 (mmm) REVERT: A 306 TYR cc_start: 0.8799 (t80) cc_final: 0.8478 (t80) REVERT: A 363 MET cc_start: 0.9068 (tpp) cc_final: 0.7976 (tpp) REVERT: A 491 MET cc_start: 0.8980 (mtp) cc_final: 0.8326 (mpp) REVERT: A 495 LYS cc_start: 0.9707 (tttm) cc_final: 0.9485 (ttmm) REVERT: A 513 HIS cc_start: 0.9243 (m-70) cc_final: 0.8630 (m-70) REVERT: A 531 LYS cc_start: 0.9649 (tmtt) cc_final: 0.9283 (ptmm) REVERT: A 533 MET cc_start: 0.8807 (tpt) cc_final: 0.8571 (tpt) REVERT: A 536 ASP cc_start: 0.9220 (m-30) cc_final: 0.8875 (p0) REVERT: A 591 PHE cc_start: 0.9381 (m-80) cc_final: 0.9083 (m-80) REVERT: A 647 LYS cc_start: 0.9267 (mmtm) cc_final: 0.8535 (mttm) outliers start: 27 outliers final: 13 residues processed: 148 average time/residue: 0.0727 time to fit residues: 14.7428 Evaluate side-chains 131 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 115 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 274 HIS Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 528 TRP Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 539 CYS Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 739 ILE Chi-restraints excluded: chain A residue 744 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- 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: 71.9499 > 50: distance: 4 - 9: 30.691 distance: 9 - 10: 31.514 distance: 10 - 11: 21.927 distance: 10 - 13: 25.636 distance: 11 - 18: 7.864 distance: 13 - 14: 38.974 distance: 14 - 15: 24.995 distance: 15 - 16: 33.030 distance: 15 - 17: 33.289 distance: 18 - 19: 32.649 distance: 18 - 145: 33.683 distance: 19 - 20: 68.854 distance: 20 - 22: 39.556 distance: 22 - 23: 8.687 distance: 22 - 173: 35.304 distance: 23 - 24: 5.565 distance: 23 - 26: 31.355 distance: 24 - 25: 29.505 distance: 24 - 30: 39.433 distance: 25 - 170: 34.376 distance: 26 - 27: 47.969 distance: 26 - 28: 43.149 distance: 27 - 29: 47.797 distance: 31 - 32: 57.554 distance: 32 - 33: 33.369 distance: 32 - 34: 51.681 distance: 36 - 37: 39.961 distance: 38 - 39: 37.529 distance: 40 - 41: 70.203 distance: 41 - 42: 23.073 distance: 41 - 44: 38.946 distance: 42 - 43: 32.896 distance: 42 - 47: 42.547 distance: 44 - 45: 39.633 distance: 44 - 46: 40.091 distance: 47 - 48: 40.381 distance: 48 - 49: 68.938 distance: 48 - 51: 43.412 distance: 49 - 55: 13.419 distance: 51 - 52: 13.111 distance: 52 - 53: 57.577 distance: 52 - 54: 39.494 distance: 55 - 56: 28.697 distance: 55 - 61: 57.743 distance: 56 - 57: 25.893 distance: 56 - 59: 39.794 distance: 57 - 58: 14.137 distance: 57 - 62: 12.232 distance: 60 - 61: 40.131 distance: 62 - 63: 37.106 distance: 63 - 64: 69.317 distance: 63 - 66: 41.104 distance: 64 - 70: 33.294 distance: 66 - 67: 24.491 distance: 67 - 68: 41.786 distance: 68 - 69: 48.954 distance: 70 - 71: 40.631 distance: 71 - 72: 18.211 distance: 71 - 74: 35.510 distance: 72 - 78: 35.025 distance: 74 - 75: 37.047 distance: 75 - 76: 37.113 distance: 75 - 77: 29.330