Starting phenix.real_space_refine on Fri Aug 22 19:07:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x06_37970/08_2025/8x06_37970.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x06_37970/08_2025/8x06_37970.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8x06_37970/08_2025/8x06_37970.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x06_37970/08_2025/8x06_37970.map" model { file = "/net/cci-nas-00/data/ceres_data/8x06_37970/08_2025/8x06_37970.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x06_37970/08_2025/8x06_37970.cif" } resolution = 3.24 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 59 5.16 5 C 4514 2.51 5 N 1197 2.21 5 O 1283 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 47 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7053 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4320 Classifications: {'peptide': 536} Link IDs: {'PTRANS': 26, 'TRANS': 509} Chain breaks: 10 Chain: "C" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 359 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain breaks: 1 Chain: "D" Number of atoms: 261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 261 Classifications: {'peptide': 33} Link IDs: {'PTRANS': 1, 'TRANS': 31} Chain breaks: 2 Chain: "B" Number of atoms: 2113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 2113 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 10, 'TRANS': 243} Chain breaks: 10 Time building chain proxies: 1.84, per 1000 atoms: 0.26 Number of scatterers: 7053 At special positions: 0 Unit cell: (77.88, 92.4, 110.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 59 16.00 O 1283 8.00 N 1197 7.00 C 4514 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=20, symmetry=0 Simple disulfide: pdb=" SG CYS A 8 " - pdb=" SG CYS A 26 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 155 " distance=2.03 Simple disulfide: pdb=" SG CYS A 169 " - pdb=" SG CYS A 188 " distance=2.03 Simple disulfide: pdb=" SG CYS A 192 " - pdb=" SG CYS A 201 " distance=2.03 Simple disulfide: pdb=" SG CYS A 196 " - pdb=" SG CYS A 207 " distance=2.03 Simple disulfide: pdb=" SG CYS A 208 " - pdb=" SG CYS A 216 " distance=2.03 Simple disulfide: pdb=" SG CYS A 212 " - pdb=" SG CYS A 225 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 237 " distance=2.03 Simple disulfide: pdb=" SG CYS A 241 " - pdb=" SG CYS A 253 " distance=2.03 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 284 " distance=2.03 Simple disulfide: pdb=" SG CYS A 266 " - pdb=" SG CYS A 274 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 312 " - pdb=" SG CYS A 333 " distance=2.03 Simple disulfide: pdb=" SG CYS A 435 " - pdb=" SG CYS A 468 " distance=2.03 Simple disulfide: pdb=" SG CYS C 6 " - pdb=" SG CYS C 48 " distance=2.03 Simple disulfide: pdb=" SG CYS C 18 " - pdb=" SG CYS C 61 " distance=2.03 Simple disulfide: pdb=" SG CYS C 47 " - pdb=" SG CYS C 52 " distance=2.03 Simple disulfide: pdb=" SG CYS D 6 " - pdb=" SG CYS D 48 " distance=2.03 Simple disulfide: pdb=" SG CYS D 18 " - pdb=" SG CYS D 61 " distance=2.03 Simple disulfide: pdb=" SG CYS B 625 " - pdb=" SG CYS B 658 " 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: 0.54 Conformation dependent library (CDL) restraints added in 354.1 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1634 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 14 sheets defined 16.6% alpha, 12.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 17 through 24 removed outlier: 3.546A pdb=" N LEU A 20 " --> pdb=" O LEU A 17 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N HIS A 21 " --> pdb=" O THR A 18 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N GLU A 22 " --> pdb=" O ARG A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 46 Processing helix chain 'A' and resid 127 through 131 removed outlier: 3.544A pdb=" N THR A 130 " --> pdb=" O TYR A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 268 removed outlier: 3.663A pdb=" N CYS A 266 " --> pdb=" O LEU A 262 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASN A 268 " --> pdb=" O HIS A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 329 removed outlier: 3.597A pdb=" N ALA A 327 " --> pdb=" O SER A 323 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N GLU A 329 " --> pdb=" O THR A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 358 Processing helix chain 'A' and resid 394 through 396 No H-bonds generated for 'chain 'A' and resid 394 through 396' Processing helix chain 'A' and resid 435 through 447 removed outlier: 3.780A pdb=" N ILE A 439 " --> pdb=" O CYS A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 452 removed outlier: 3.535A pdb=" N GLN A 452 " --> pdb=" O LYS A 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 18 removed outlier: 3.717A pdb=" N VAL C 11 " --> pdb=" O GLY C 7 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU C 14 " --> pdb=" O LEU C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 48 Processing helix chain 'C' and resid 53 through 58 Processing helix chain 'C' and resid 59 through 61 No H-bonds generated for 'chain 'C' and resid 59 through 61' Processing helix chain 'D' and resid 9 through 15 Processing helix chain 'D' and resid 53 through 57 removed outlier: 3.819A pdb=" N ARG D 56 " --> pdb=" O ASP D 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 546 removed outlier: 4.052A pdb=" N ALA B 546 " --> pdb=" O ALA B 542 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 542 through 546' Processing helix chain 'B' and resid 625 through 631 removed outlier: 3.984A pdb=" N ILE B 629 " --> pdb=" O CYS B 625 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 634 No H-bonds generated for 'chain 'B' and resid 632 through 634' Processing helix chain 'B' and resid 882 through 904 Processing sheet with id=AA1, first strand: chain 'A' and resid 7 through 8 removed outlier: 3.668A pdb=" N ILE A 29 " --> pdb=" O MET A 56 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE A 57 " --> pdb=" O VAL A 81 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ILE A 82 " --> pdb=" O ASN A 111 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 33 through 38 removed outlier: 3.919A pdb=" N PHE A 64 " --> pdb=" O ILE A 35 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N VAL A 66 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LEU A 61 " --> pdb=" O VAL A 94 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N PHE A 96 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N LEU A 63 " --> pdb=" O PHE A 96 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N LEU A 93 " --> pdb=" O ARG A 118 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N GLU A 120 " --> pdb=" O LEU A 93 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ILE A 95 " --> pdb=" O GLU A 120 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TYR A 144 " --> pdb=" O VAL A 117 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE A 119 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 231 through 233 Processing sheet with id=AA4, first strand: chain 'A' and resid 245 through 246 Processing sheet with id=AA5, first strand: chain 'A' and resid 292 through 293 Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 313 removed outlier: 3.796A pdb=" N ASN A 337 " --> pdb=" O CYS A 312 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ILE A 336 " --> pdb=" O SER A 365 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ILE A 364 " --> pdb=" O ARG A 389 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 320 through 321 Processing sheet with id=AA8, first strand: chain 'A' and resid 368 through 370 removed outlier: 4.280A pdb=" N TYR A 398 " --> pdb=" O LYS A 425 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N PHE A 427 " --> pdb=" O TYR A 398 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N PHE A 400 " --> pdb=" O PHE A 427 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 484 through 487 removed outlier: 3.905A pdb=" N ILE A 485 " --> pdb=" O MET A 553 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N MET A 553 " --> pdb=" O ILE A 485 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU A 487 " --> pdb=" O TRP A 551 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 531 through 534 removed outlier: 3.640A pdb=" N PHE A 506 " --> pdb=" O PHE A 565 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N PHE A 565 " --> pdb=" O PHE A 506 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 525 through 526 removed outlier: 3.510A pdb=" N ILE B 526 " --> pdb=" O GLU B 553 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE B 554 " --> pdb=" O LEU B 577 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 558 through 560 Processing sheet with id=AB4, first strand: chain 'B' and resid 665 through 670 removed outlier: 3.550A pdb=" N ARG B 678 " --> pdb=" O SER B 666 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N ILE B 668 " --> pdb=" O LEU B 676 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N LEU B 676 " --> pdb=" O ILE B 668 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 722 through 724 removed outlier: 4.145A pdb=" N GLY B 692 " --> pdb=" O LEU B 759 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU B 759 " --> pdb=" O GLY B 692 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE B 755 " --> pdb=" O PHE B 696 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS B 698 " --> pdb=" O ALA B 753 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA B 753 " --> pdb=" O LYS B 698 " (cutoff:3.500A) 103 hydrogen bonds defined for protein. 258 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: 1.13 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: 1.23 - 1.35: 2264 1.35 - 1.46: 1718 1.46 - 1.58: 3148 1.58 - 1.70: 0 1.70 - 1.82: 73 Bond restraints: 7203 Sorted by residual: bond pdb=" CA LYS B 631 " pdb=" C LYS B 631 " ideal model delta sigma weight residual 1.523 1.570 -0.047 1.41e-02 5.03e+03 1.11e+01 bond pdb=" C PRO A 243 " pdb=" N PRO A 244 " ideal model delta sigma weight residual 1.335 1.361 -0.027 1.28e-02 6.10e+03 4.33e+00 bond pdb=" CB PRO A 307 " pdb=" CG PRO A 307 " ideal model delta sigma weight residual 1.492 1.542 -0.050 5.00e-02 4.00e+02 9.88e-01 bond pdb=" CB TRP B 604 " pdb=" CG TRP B 604 " ideal model delta sigma weight residual 1.498 1.524 -0.026 3.10e-02 1.04e+03 7.14e-01 bond pdb=" CA TYR D 60 " pdb=" CB TYR D 60 " ideal model delta sigma weight residual 1.524 1.535 -0.011 1.31e-02 5.83e+03 6.91e-01 ... (remaining 7198 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 9575 2.07 - 4.14: 128 4.14 - 6.21: 10 6.21 - 8.28: 2 8.28 - 10.35: 3 Bond angle restraints: 9718 Sorted by residual: angle pdb=" CB MET A 294 " pdb=" CG MET A 294 " pdb=" SD MET A 294 " ideal model delta sigma weight residual 112.70 122.46 -9.76 3.00e+00 1.11e-01 1.06e+01 angle pdb=" CA LEU B 550 " pdb=" CB LEU B 550 " pdb=" CG LEU B 550 " ideal model delta sigma weight residual 116.30 126.65 -10.35 3.50e+00 8.16e-02 8.75e+00 angle pdb=" CA LYS B 631 " pdb=" C LYS B 631 " pdb=" O LYS B 631 " ideal model delta sigma weight residual 119.28 122.83 -3.55 1.21e+00 6.83e-01 8.60e+00 angle pdb=" N GLY D 19 " pdb=" CA GLY D 19 " pdb=" C GLY D 19 " ideal model delta sigma weight residual 111.35 114.80 -3.45 1.20e+00 6.94e-01 8.27e+00 angle pdb=" CB ARG C 55 " pdb=" CG ARG C 55 " pdb=" CD ARG C 55 " ideal model delta sigma weight residual 111.30 117.54 -6.24 2.30e+00 1.89e-01 7.36e+00 ... (remaining 9713 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.10: 3560 17.10 - 34.20: 533 34.20 - 51.31: 188 51.31 - 68.41: 42 68.41 - 85.51: 19 Dihedral angle restraints: 4342 sinusoidal: 1827 harmonic: 2515 Sorted by residual: dihedral pdb=" CB CYS A 169 " pdb=" SG CYS A 169 " pdb=" SG CYS A 188 " pdb=" CB CYS A 188 " ideal model delta sinusoidal sigma weight residual -86.00 -171.51 85.51 1 1.00e+01 1.00e-02 8.85e+01 dihedral pdb=" CB CYS A 259 " pdb=" SG CYS A 259 " pdb=" SG CYS A 284 " pdb=" CB CYS A 284 " ideal model delta sinusoidal sigma weight residual -86.00 -164.02 78.02 1 1.00e+01 1.00e-02 7.61e+01 dihedral pdb=" CB CYS A 266 " pdb=" SG CYS A 266 " pdb=" SG CYS A 274 " pdb=" CB CYS A 274 " ideal model delta sinusoidal sigma weight residual 93.00 165.29 -72.29 1 1.00e+01 1.00e-02 6.68e+01 ... (remaining 4339 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 635 0.026 - 0.051: 249 0.051 - 0.077: 93 0.077 - 0.102: 44 0.102 - 0.128: 40 Chirality restraints: 1061 Sorted by residual: chirality pdb=" CA ILE A 585 " pdb=" N ILE A 585 " pdb=" C ILE A 585 " pdb=" CB ILE A 585 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.08e-01 chirality pdb=" CA ILE A 95 " pdb=" N ILE A 95 " pdb=" C ILE A 95 " pdb=" CB ILE A 95 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.91e-01 chirality pdb=" CA ILE A 370 " pdb=" N ILE A 370 " pdb=" C ILE A 370 " pdb=" CB ILE A 370 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.62e-01 ... (remaining 1058 not shown) Planarity restraints: 1233 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 306 " -0.042 5.00e-02 4.00e+02 6.30e-02 6.34e+00 pdb=" N PRO A 307 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO A 307 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 307 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 243 " 0.035 5.00e-02 4.00e+02 5.23e-02 4.38e+00 pdb=" N PRO A 244 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 244 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 244 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 316 " 0.007 2.00e-02 2.50e+03 1.38e-02 1.89e+00 pdb=" C GLU A 316 " -0.024 2.00e-02 2.50e+03 pdb=" O GLU A 316 " 0.009 2.00e-02 2.50e+03 pdb=" N GLY A 317 " 0.008 2.00e-02 2.50e+03 ... (remaining 1230 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1567 2.79 - 3.32: 5823 3.32 - 3.84: 10999 3.84 - 4.37: 12266 4.37 - 4.90: 21398 Nonbonded interactions: 52053 Sorted by model distance: nonbonded pdb=" O ILE A 29 " pdb=" OG1 THR A 58 " model vdw 2.261 3.040 nonbonded pdb=" OG1 THR A 41 " pdb=" O TYR A 67 " model vdw 2.262 3.040 nonbonded pdb=" O TYR B 697 " pdb=" OG1 THR B 720 " model vdw 2.288 3.040 nonbonded pdb=" O LYS B 747 " pdb=" OG1 THR B 750 " model vdw 2.293 3.040 nonbonded pdb=" O ILE A 336 " pdb=" OG SER A 365 " model vdw 2.306 3.040 ... (remaining 52048 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: 10.880 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: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.400 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 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 : 0.002 0.050 7223 Z= 0.123 Angle : 0.579 10.354 9758 Z= 0.323 Chirality : 0.040 0.128 1061 Planarity : 0.003 0.063 1233 Dihedral : 18.499 82.436 2648 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.25 % Allowed : 34.39 % Favored : 65.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.94 (0.30), residues: 816 helix: 0.05 (0.55), residues: 118 sheet: 0.45 (0.68), residues: 77 loop : -0.96 (0.25), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 55 TYR 0.012 0.001 TYR A 477 PHE 0.012 0.000 PHE B 696 TRP 0.020 0.001 TRP B 604 HIS 0.002 0.000 HIS A 100 Details of bonding type rmsd covalent geometry : bond 0.00220 ( 7203) covalent geometry : angle 0.58035 ( 9718) SS BOND : bond 0.00083 ( 20) SS BOND : angle 0.24514 ( 40) hydrogen bonds : bond 0.20241 ( 103) hydrogen bonds : angle 6.48183 ( 258) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 66 time to evaluate : 0.307 Fit side-chains revert: symmetry clash REVERT: A 487 LEU cc_start: 0.7393 (tp) cc_final: 0.6991 (pp) outliers start: 2 outliers final: 0 residues processed: 66 average time/residue: 0.0772 time to fit residues: 7.0750 Evaluate side-chains 65 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 49 optimal weight: 0.5980 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 10.0000 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 405 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 = 0.3827 r_free = 0.3827 target = 0.096596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.071326 restraints weight = 20544.205| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 3.86 r_work: 0.3132 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 7223 Z= 0.250 Angle : 0.643 9.047 9758 Z= 0.331 Chirality : 0.045 0.159 1061 Planarity : 0.005 0.048 1233 Dihedral : 4.031 16.087 931 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 5.48 % Allowed : 27.26 % Favored : 67.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.44 (0.29), residues: 816 helix: -0.48 (0.49), residues: 128 sheet: -0.84 (0.50), residues: 121 loop : -1.14 (0.26), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 42 TYR 0.020 0.002 TYR B 591 PHE 0.030 0.002 PHE B 696 TRP 0.013 0.001 TRP B 604 HIS 0.004 0.001 HIS A 21 Details of bonding type rmsd covalent geometry : bond 0.00566 ( 7203) covalent geometry : angle 0.64085 ( 9718) SS BOND : bond 0.00440 ( 20) SS BOND : angle 0.97726 ( 40) hydrogen bonds : bond 0.04634 ( 103) hydrogen bonds : angle 5.05371 ( 258) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 73 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 412 TRP cc_start: 0.9204 (OUTLIER) cc_final: 0.8482 (m-90) REVERT: C 55 ARG cc_start: 0.8884 (ttp80) cc_final: 0.8452 (tpt90) REVERT: B 621 ASN cc_start: 0.8172 (OUTLIER) cc_final: 0.7602 (p0) outliers start: 43 outliers final: 25 residues processed: 107 average time/residue: 0.0740 time to fit residues: 10.9272 Evaluate side-chains 95 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 68 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 PHE Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 241 CYS Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 412 TRP Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain D residue 21 ARG Chi-restraints excluded: chain B residue 523 CYS Chi-restraints excluded: chain B residue 621 ASN Chi-restraints excluded: chain B residue 647 ILE Chi-restraints excluded: chain B residue 676 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 775 ILE Chi-restraints excluded: chain B residue 905 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 16 optimal weight: 10.0000 chunk 47 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 36 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.096173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.070890 restraints weight = 20027.655| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 3.83 r_work: 0.3119 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.3617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7223 Z= 0.151 Angle : 0.516 9.415 9758 Z= 0.257 Chirality : 0.041 0.131 1061 Planarity : 0.004 0.064 1233 Dihedral : 3.735 14.750 931 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 3.69 % Allowed : 28.79 % Favored : 67.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.42 (0.29), residues: 816 helix: -0.14 (0.50), residues: 128 sheet: -0.47 (0.59), residues: 90 loop : -1.28 (0.25), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 55 TYR 0.012 0.001 TYR B 697 PHE 0.024 0.001 PHE B 696 TRP 0.010 0.001 TRP B 604 HIS 0.003 0.001 HIS B 619 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 7203) covalent geometry : angle 0.51554 ( 9718) SS BOND : bond 0.00704 ( 20) SS BOND : angle 0.65544 ( 40) hydrogen bonds : bond 0.03161 ( 103) hydrogen bonds : angle 4.93119 ( 258) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 75 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 412 TRP cc_start: 0.9139 (OUTLIER) cc_final: 0.7910 (m-90) outliers start: 29 outliers final: 16 residues processed: 97 average time/residue: 0.0795 time to fit residues: 10.6572 Evaluate side-chains 81 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 64 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 PHE Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 241 CYS Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 412 TRP Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain B residue 518 GLN Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 657 SER Chi-restraints excluded: chain B residue 676 LEU Chi-restraints excluded: chain B residue 705 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 20 optimal weight: 0.2980 chunk 57 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 51 optimal weight: 10.0000 chunk 38 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 33 optimal weight: 0.4980 chunk 2 optimal weight: 0.0570 chunk 46 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.096169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.070932 restraints weight = 20252.481| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 3.82 r_work: 0.3125 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.3773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 7223 Z= 0.100 Angle : 0.481 6.346 9758 Z= 0.239 Chirality : 0.041 0.172 1061 Planarity : 0.003 0.048 1233 Dihedral : 3.529 14.406 931 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 2.80 % Allowed : 29.30 % Favored : 67.90 % 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 aren not related in a simple way. whole: -1.40 (0.29), residues: 816 helix: -0.01 (0.51), residues: 128 sheet: -0.54 (0.58), residues: 90 loop : -1.28 (0.25), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 55 TYR 0.010 0.001 TYR B 591 PHE 0.019 0.001 PHE B 696 TRP 0.008 0.001 TRP B 604 HIS 0.002 0.000 HIS B 619 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 7203) covalent geometry : angle 0.48125 ( 9718) SS BOND : bond 0.00160 ( 20) SS BOND : angle 0.46963 ( 40) hydrogen bonds : bond 0.02477 ( 103) hydrogen bonds : angle 4.80372 ( 258) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 66 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 412 TRP cc_start: 0.9116 (OUTLIER) cc_final: 0.7979 (m-90) outliers start: 22 outliers final: 15 residues processed: 83 average time/residue: 0.0809 time to fit residues: 9.5241 Evaluate side-chains 81 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 241 CYS Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 412 TRP Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain B residue 516 SER Chi-restraints excluded: chain B residue 518 GLN Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 676 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 56.6628 > 50: distance: 33 - 114: 26.162 distance: 38 - 104: 6.747 distance: 57 - 74: 23.040 distance: 62 - 82: 15.170 distance: 68 - 74: 20.468 distance: 74 - 75: 29.158 distance: 75 - 76: 6.810 distance: 75 - 78: 34.024 distance: 76 - 77: 27.217 distance: 76 - 82: 30.808 distance: 78 - 79: 32.289 distance: 79 - 80: 38.151 distance: 79 - 81: 42.189 distance: 82 - 83: 17.610 distance: 83 - 84: 10.925 distance: 83 - 86: 22.082 distance: 84 - 85: 13.857 distance: 84 - 91: 41.411 distance: 86 - 87: 36.864 distance: 87 - 88: 31.997 distance: 88 - 89: 13.154 distance: 88 - 90: 23.412 distance: 91 - 92: 22.342 distance: 92 - 93: 34.050 distance: 92 - 95: 11.792 distance: 93 - 94: 10.186 distance: 93 - 99: 27.822 distance: 95 - 96: 7.875 distance: 96 - 97: 14.524 distance: 96 - 98: 8.318 distance: 99 - 100: 16.248 distance: 100 - 101: 21.732 distance: 100 - 103: 18.352 distance: 101 - 102: 16.010 distance: 101 - 105: 18.424 distance: 103 - 104: 26.389 distance: 105 - 106: 39.754 distance: 106 - 107: 7.113 distance: 106 - 109: 16.548 distance: 107 - 108: 26.290 distance: 107 - 111: 30.429 distance: 109 - 110: 41.102 distance: 111 - 112: 24.135 distance: 112 - 113: 36.840 distance: 112 - 115: 19.399 distance: 113 - 114: 38.282 distance: 113 - 118: 35.156 distance: 115 - 116: 31.992 distance: 115 - 117: 15.563 distance: 118 - 119: 14.177 distance: 119 - 120: 17.582 distance: 119 - 122: 20.809 distance: 120 - 121: 19.720 distance: 120 - 126: 37.375 distance: 122 - 123: 30.760 distance: 122 - 124: 24.911 distance: 123 - 125: 6.313 distance: 126 - 127: 15.838 distance: 127 - 128: 12.637 distance: 127 - 130: 15.607 distance: 128 - 129: 12.875 distance: 128 - 135: 11.674 distance: 130 - 131: 16.356 distance: 131 - 132: 5.930 distance: 135 - 136: 17.114 distance: 136 - 137: 35.000 distance: 137 - 138: 24.262 distance: 137 - 139: 33.557 distance: 139 - 140: 7.136 distance: 140 - 141: 6.731 distance: 140 - 143: 32.679 distance: 141 - 149: 21.609 distance: 143 - 144: 20.572 distance: 144 - 145: 10.198 distance: 144 - 146: 4.750 distance: 145 - 147: 8.131 distance: 146 - 148: 8.319 distance: 147 - 148: 7.438