Starting phenix.real_space_refine on Fri Jul 3 11:25:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jhn_61488/07_2026/9jhn_61488.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jhn_61488/07_2026/9jhn_61488.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jhn_61488/07_2026/9jhn_61488.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jhn_61488/07_2026/9jhn_61488.map" model { file = "/net/cci-nas-00/data/ceres_data/9jhn_61488/07_2026/9jhn_61488.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jhn_61488/07_2026/9jhn_61488.cif" } resolution = 3.0 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= 0.007 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 4 7.51 5 P 70 5.49 5 S 40 5.16 5 C 8488 2.51 5 N 2230 2.21 5 O 2680 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s 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: 13512 Number of models: 1 Model: "" Number of chains: 5 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: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 359 Classifications: {'DNA': 17} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 16} Chain: "E" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 359 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} 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 Chain: "E" 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 Restraints were copied for chains: B, D, F Time building chain proxies: 6.05, per 1000 atoms: 0.45 Number of scatterers: 13512 At special positions: 0 Unit cell: (89.38, 118.9, 103.32, 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 4 24.99 S 40 16.00 P 70 15.00 O 2680 8.00 N 2230 7.00 C 8488 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: 1.08 Conformation dependent library (CDL) restraints added in 738.3 milliseconds 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2788 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 28 sheets defined 31.4% alpha, 17.2% beta 22 base pairs and 56 stacking pairs defined. Time for finding SS restraints: 1.88 Creating SS restraints... Processing helix chain 'A' and resid 43 through 54 Processing helix chain 'A' and resid 97 through 115 removed outlier: 4.078A pdb=" N LYS A 115 " --> pdb=" O LEU A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 195 removed outlier: 3.745A pdb=" N MET A 191 " --> pdb=" O ASN A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 241 Processing helix chain 'A' and resid 253 through 256 Processing helix chain 'A' and resid 281 through 289 Processing helix chain 'A' and resid 289 through 296 Processing helix chain 'A' and resid 296 through 301 removed outlier: 3.662A pdb=" N LYS A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 319 Processing helix chain 'A' and resid 336 through 341 removed outlier: 3.585A pdb=" N LEU A 339 " --> pdb=" O ASP A 336 " (cutoff:3.500A) 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 452 Processing helix chain 'A' and resid 474 through 485 Processing helix chain 'A' and resid 494 through 502 Processing helix chain 'A' and resid 506 through 523 removed outlier: 4.106A pdb=" N TYR A 510 " --> pdb=" O ASN A 506 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N TYR A 511 " --> pdb=" O THR A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 603 Processing helix chain 'A' and resid 620 through 630 Processing helix chain 'A' and resid 698 through 711 removed outlier: 3.567A pdb=" N ALA A 702 " --> pdb=" O ASP A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 735 Processing helix chain 'B' and resid 43 through 54 Processing helix chain 'B' and resid 97 through 115 removed outlier: 4.078A pdb=" N LYS B 115 " --> pdb=" O LEU B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 195 removed outlier: 3.744A pdb=" N MET B 191 " --> pdb=" O ASN B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 241 Processing helix chain 'B' and resid 253 through 256 Processing helix chain 'B' and resid 281 through 289 Processing helix chain 'B' and resid 289 through 296 Processing helix chain 'B' and resid 296 through 301 removed outlier: 3.662A pdb=" N LYS B 301 " --> pdb=" O GLU B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 319 Processing helix chain 'B' and resid 336 through 341 removed outlier: 3.586A pdb=" N LEU B 339 " --> pdb=" O ASP B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 369 Processing helix chain 'B' and resid 388 through 404 Processing helix chain 'B' and resid 439 through 452 Processing helix chain 'B' and resid 474 through 485 Processing helix chain 'B' and resid 494 through 502 Processing helix chain 'B' and resid 506 through 523 removed outlier: 4.105A pdb=" N TYR B 510 " --> pdb=" O ASN B 506 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N TYR B 511 " --> pdb=" O THR B 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 603 Processing helix chain 'B' and resid 620 through 630 Processing helix chain 'B' and resid 698 through 711 removed outlier: 3.566A pdb=" N ALA B 702 " --> pdb=" O ASP B 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 723 through 735 Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 12 Processing sheet with id=AA2, first strand: chain 'A' and resid 163 through 166 removed outlier: 4.697A pdb=" N VAL A 172 " --> pdb=" O GLY A 17 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 28 through 30 removed outlier: 7.347A pdb=" N GLN A 28 " --> pdb=" O VAL A 87 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 60 through 62 Processing sheet with id=AA5, first strand: chain 'A' and resid 117 through 118 Processing sheet with id=AA6, first strand: chain 'A' and resid 125 through 127 removed outlier: 3.732A pdb=" N LEU A 134 " --> pdb=" O ARG A 126 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 138 through 139 Processing sheet with id=AA8, first strand: chain 'A' and resid 268 through 271 removed outlier: 3.830A pdb=" N TYR A 271 " --> pdb=" O VAL A 260 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL A 260 " --> pdb=" O TYR A 271 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ILE A 259 " --> pdb=" O VAL A 219 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N VAL A 219 " --> pdb=" O ILE A 259 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ASN A 261 " --> pdb=" O GLU A 217 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL A 215 " --> pdb=" O ARG A 263 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU A 214 " --> pdb=" O VAL A 203 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 345 through 346 removed outlier: 6.679A pdb=" N ILE A 637 " --> pdb=" O SER A 693 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ILE A 609 " --> pdb=" O ASN A 636 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N ILE A 638 " --> pdb=" O ILE A 609 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N ILE A 611 " --> pdb=" O ILE A 638 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N VAL A 640 " --> pdb=" O ILE A 611 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ARG A 613 " --> pdb=" O VAL A 640 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N CYS A 539 " --> pdb=" O VAL A 610 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N HIS A 612 " --> pdb=" O CYS A 539 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N VAL A 541 " --> pdb=" O HIS A 612 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ALA A 614 " --> pdb=" O VAL A 541 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N LEU A 543 " --> pdb=" O ALA A 614 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ASP A 562 " --> pdb=" O LEU A 567 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N LEU A 567 " --> pdb=" O ASP A 562 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 358 through 359 removed outlier: 4.807A pdb=" N LEU A 352 " --> pdb=" O ILE A 359 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL A 529 " --> pdb=" O MET A 353 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 378 through 379 removed outlier: 6.775A pdb=" N VAL A 378 " --> pdb=" O GLU A 424 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 382 through 385 removed outlier: 5.976A pdb=" N VAL A 382 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N TYR A 435 " --> pdb=" O VAL A 382 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N TYR A 384 " --> pdb=" O TYR A 435 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 407 through 408 Processing sheet with id=AB5, first strand: chain 'A' and resid 462 through 463 Processing sheet with id=AB6, first strand: chain 'B' and resid 9 through 12 Processing sheet with id=AB7, first strand: chain 'B' and resid 163 through 166 removed outlier: 4.697A pdb=" N VAL B 172 " --> pdb=" O GLY B 17 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 30 removed outlier: 7.346A pdb=" N GLN B 28 " --> pdb=" O VAL B 87 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 60 through 62 Processing sheet with id=AC1, first strand: chain 'B' and resid 117 through 118 Processing sheet with id=AC2, first strand: chain 'B' and resid 125 through 127 removed outlier: 3.731A pdb=" N LEU B 134 " --> pdb=" O ARG B 126 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 138 through 139 Processing sheet with id=AC4, first strand: chain 'B' and resid 268 through 271 removed outlier: 3.829A pdb=" N TYR B 271 " --> pdb=" O VAL B 260 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL B 260 " --> pdb=" O TYR B 271 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ILE B 259 " --> pdb=" O VAL B 219 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N VAL B 219 " --> pdb=" O ILE B 259 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ASN B 261 " --> pdb=" O GLU B 217 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL B 215 " --> pdb=" O ARG B 263 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU B 214 " --> pdb=" O VAL B 203 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 345 through 346 removed outlier: 6.680A pdb=" N ILE B 637 " --> pdb=" O SER B 693 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ILE B 609 " --> pdb=" O ASN B 636 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N ILE B 638 " --> pdb=" O ILE B 609 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ILE B 611 " --> pdb=" O ILE B 638 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N VAL B 640 " --> pdb=" O ILE B 611 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ARG B 613 " --> pdb=" O VAL B 640 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N CYS B 539 " --> pdb=" O VAL B 610 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N HIS B 612 " --> pdb=" O CYS B 539 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N VAL B 541 " --> pdb=" O HIS B 612 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N ALA B 614 " --> pdb=" O VAL B 541 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N LEU B 543 " --> pdb=" O ALA B 614 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ASP B 562 " --> pdb=" O LEU B 567 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N LEU B 567 " --> pdb=" O ASP B 562 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 358 through 359 removed outlier: 4.806A pdb=" N LEU B 352 " --> pdb=" O ILE B 359 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL B 529 " --> pdb=" O MET B 353 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 378 through 379 removed outlier: 6.774A pdb=" N VAL B 378 " --> pdb=" O GLU B 424 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 382 through 385 removed outlier: 5.976A pdb=" N VAL B 382 " --> pdb=" O GLU B 433 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N TYR B 435 " --> pdb=" O VAL B 382 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N TYR B 384 " --> pdb=" O TYR B 435 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 407 through 408 Processing sheet with id=AD1, first strand: chain 'B' and resid 462 through 463 442 hydrogen bonds defined for protein. 1236 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 50 hydrogen bonds 100 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 56 stacking parallelities Total time for adding SS restraints: 2.60 Time building geometry restraints manager: 1.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2891 1.33 - 1.45: 3309 1.45 - 1.57: 7520 1.57 - 1.69: 136 1.69 - 1.81: 70 Bond restraints: 13926 Sorted by residual: bond pdb=" C3' DA D 7 " pdb=" O3' DA D 7 " ideal model delta sigma weight residual 1.435 1.380 0.055 1.30e-02 5.92e+03 1.81e+01 bond pdb=" C3' DA C 7 " pdb=" O3' DA C 7 " ideal model delta sigma weight residual 1.435 1.380 0.055 1.30e-02 5.92e+03 1.79e+01 bond pdb=" C3' DG D 8 " pdb=" O3' DG D 8 " ideal model delta sigma weight residual 1.435 1.383 0.052 1.30e-02 5.92e+03 1.62e+01 bond pdb=" C3' DG C 8 " pdb=" O3' DG C 8 " ideal model delta sigma weight residual 1.435 1.383 0.052 1.30e-02 5.92e+03 1.61e+01 bond pdb=" C3' DG D 5 " pdb=" O3' DG D 5 " ideal model delta sigma weight residual 1.435 1.387 0.048 1.30e-02 5.92e+03 1.37e+01 ... (remaining 13921 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 17834 1.87 - 3.73: 1081 3.73 - 5.60: 113 5.60 - 7.47: 31 7.47 - 9.34: 13 Bond angle restraints: 19072 Sorted by residual: angle pdb=" O4' DA C 17 " pdb=" C1' DA C 17 " pdb=" N9 DA C 17 " ideal model delta sigma weight residual 108.00 112.13 -4.13 7.00e-01 2.04e+00 3.49e+01 angle pdb=" O4' DA D 17 " pdb=" C1' DA D 17 " pdb=" N9 DA D 17 " ideal model delta sigma weight residual 108.00 112.10 -4.10 7.00e-01 2.04e+00 3.43e+01 angle pdb=" O4' DG D 4 " pdb=" C4' DG D 4 " pdb=" C3' DG D 4 " ideal model delta sigma weight residual 106.00 102.55 3.45 6.00e-01 2.78e+00 3.30e+01 angle pdb=" O4' DG C 4 " pdb=" C4' DG C 4 " pdb=" C3' DG C 4 " ideal model delta sigma weight residual 106.00 102.56 3.44 6.00e-01 2.78e+00 3.29e+01 angle pdb=" C LYS A 63 " pdb=" N ASP A 64 " pdb=" CA ASP A 64 " ideal model delta sigma weight residual 120.54 127.93 -7.39 1.35e+00 5.49e-01 3.00e+01 ... (remaining 19067 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.81: 7895 29.81 - 59.61: 352 59.61 - 89.42: 15 89.42 - 119.22: 0 119.22 - 149.03: 2 Dihedral angle restraints: 8264 sinusoidal: 3890 harmonic: 4374 Sorted by residual: 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 -143.69 -36.31 0 5.00e+00 4.00e-02 5.27e+01 dihedral pdb=" CA GLU B 470 " pdb=" C GLU B 470 " pdb=" N ILE B 471 " pdb=" CA ILE B 471 " ideal model delta harmonic sigma weight residual -180.00 -143.75 -36.25 0 5.00e+00 4.00e-02 5.26e+01 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 -148.14 -31.86 0 5.00e+00 4.00e-02 4.06e+01 ... (remaining 8261 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1670 0.075 - 0.150: 366 0.150 - 0.225: 42 0.225 - 0.300: 6 0.300 - 0.375: 4 Chirality restraints: 2088 Sorted by residual: chirality pdb=" CB ILE B 44 " pdb=" CA ILE B 44 " pdb=" CG1 ILE B 44 " pdb=" CG2 ILE B 44 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.37 2.00e-01 2.50e+01 3.51e+00 chirality pdb=" CB ILE A 44 " pdb=" CA ILE A 44 " pdb=" CG1 ILE A 44 " pdb=" CG2 ILE A 44 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.37 2.00e-01 2.50e+01 3.47e+00 chirality pdb=" CB ILE A 596 " pdb=" CA ILE A 596 " pdb=" CG1 ILE A 596 " pdb=" CG2 ILE A 596 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.45e+00 ... (remaining 2085 not shown) Planarity restraints: 2180 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 623 " -0.017 2.00e-02 2.50e+03 1.36e-02 4.60e+00 pdb=" CG TRP B 623 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 TRP B 623 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP B 623 " 0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP B 623 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 623 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 623 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 623 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 623 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP B 623 " -0.005 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 1.33e-02 4.42e+00 pdb=" CG TRP A 623 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 TRP A 623 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP A 623 " -0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP A 623 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 623 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 623 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 623 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 623 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP A 623 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 513 " -0.014 2.00e-02 2.50e+03 1.68e-02 4.24e+00 pdb=" CG HIS B 513 " 0.036 2.00e-02 2.50e+03 pdb=" ND1 HIS B 513 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 HIS B 513 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 HIS B 513 " 0.001 2.00e-02 2.50e+03 pdb=" NE2 HIS B 513 " -0.004 2.00e-02 2.50e+03 ... (remaining 2177 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.50: 84 2.50 - 3.10: 9004 3.10 - 3.70: 21376 3.70 - 4.30: 32705 4.30 - 4.90: 52409 Nonbonded interactions: 115578 Sorted by model distance: nonbonded pdb=" OP2 DT D 1 " pdb="MN MN D 801 " model vdw 1.895 3.060 nonbonded pdb=" OP2 DT C 1 " pdb="MN MN C 801 " model vdw 1.895 3.060 nonbonded pdb=" OP1 DT D 1 " pdb="MN MN D 801 " model vdw 1.923 3.060 nonbonded pdb=" OP1 DT C 1 " pdb="MN MN C 801 " model vdw 1.923 3.060 nonbonded pdb=" NZ LYS B 54 " pdb=" CD1 LEU B 79 " model vdw 1.944 3.540 ... (remaining 115573 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } 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: 3.790 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: 0.000 Extract box with map and model: 0.270 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 17.970 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.020 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:7.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 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 : 0.010 0.093 13926 Z= 0.551 Angle : 0.990 9.336 19072 Z= 0.628 Chirality : 0.064 0.375 2088 Planarity : 0.006 0.043 2180 Dihedral : 14.778 149.028 5476 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 0.15 % Allowed : 1.95 % Favored : 97.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -3.07 (0.18), residues: 1486 helix: -2.44 (0.18), residues: 444 sheet: -2.15 (0.24), residues: 342 loop : -1.52 (0.21), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 721 TYR 0.027 0.003 TYR A 511 PHE 0.025 0.004 PHE B 591 TRP 0.033 0.006 TRP B 623 HIS 0.020 0.004 HIS B 513 Details of bonding type rmsd/Z covalent geometry : bond 0.00978 / 0.55 (13926) covalent geometry : angle 0.98973 / 0.63 (19072) hydrogen bonds : bond 0.20092 / 12.98 ( 492) hydrogen bonds : angle 9.18993 / 6.47 ( 1336) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 200 time to evaluate : 0.531 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 outliers start: 2 outliers final: 2 residues processed: 202 average time/residue: 0.5191 time to fit residues: 115.3313 Evaluate side-chains 89 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 87 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 PHE Chi-restraints excluded: chain B residue 432 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 59.597 > 50: distance: 60 - 113: 23.932 distance: 63 - 110: 19.632 distance: 99 - 102: 23.136 distance: 102 - 103: 11.840 distance: 103 - 104: 12.961 distance: 103 - 106: 35.973 distance: 104 - 105: 34.156 distance: 104 - 110: 27.705 distance: 106 - 107: 20.463 distance: 107 - 108: 26.231 distance: 107 - 109: 19.839 distance: 110 - 111: 26.296 distance: 111 - 112: 51.745 distance: 111 - 114: 26.238 distance: 112 - 113: 30.819 distance: 112 - 119: 43.501 distance: 114 - 115: 46.401 distance: 115 - 116: 15.542 distance: 116 - 117: 25.265 distance: 117 - 118: 14.498 distance: 119 - 120: 11.680 distance: 119 - 125: 25.374 distance: 120 - 121: 34.783 distance: 120 - 123: 20.674 distance: 121 - 122: 28.742 distance: 121 - 126: 27.344 distance: 123 - 124: 5.172 distance: 124 - 125: 10.227 distance: 126 - 127: 50.754 distance: 127 - 128: 14.711 distance: 127 - 130: 42.405 distance: 128 - 129: 38.027 distance: 128 - 134: 18.596 distance: 130 - 131: 22.487 distance: 130 - 132: 38.179 distance: 131 - 133: 20.101 distance: 134 - 135: 18.603 distance: 135 - 136: 27.661 distance: 135 - 138: 28.968 distance: 136 - 137: 19.855 distance: 136 - 142: 18.271 distance: 138 - 139: 19.894 distance: 138 - 140: 35.157 distance: 139 - 141: 30.703 distance: 142 - 143: 43.708 distance: 143 - 144: 11.693 distance: 143 - 146: 35.570 distance: 144 - 145: 46.655 distance: 144 - 149: 16.575 distance: 145 - 181: 37.919 distance: 146 - 147: 38.765 distance: 146 - 148: 27.496 distance: 149 - 150: 20.601 distance: 150 - 151: 15.311 distance: 150 - 153: 45.437 distance: 151 - 152: 21.394 distance: 151 - 160: 12.002 distance: 152 - 189: 18.792 distance: 153 - 154: 32.764 distance: 154 - 155: 16.192 distance: 155 - 156: 6.431 distance: 156 - 157: 11.659 distance: 157 - 158: 11.634 distance: 157 - 159: 10.489 distance: 160 - 161: 18.214 distance: 161 - 164: 22.917 distance: 162 - 163: 10.011 distance: 162 - 169: 16.522 distance: 163 - 194: 18.173 distance: 164 - 165: 16.674 distance: 166 - 167: 4.404 distance: 169 - 170: 6.979 distance: 170 - 171: 7.013 distance: 170 - 173: 9.080 distance: 171 - 172: 9.063 distance: 171 - 181: 5.567 distance: 172 - 203: 17.209 distance: 173 - 174: 3.910 distance: 174 - 175: 7.821 distance: 174 - 176: 8.281 distance: 175 - 177: 3.269 distance: 176 - 178: 4.027 distance: 177 - 179: 11.764 distance: 178 - 179: 6.322 distance: 179 - 180: 10.088 distance: 181 - 182: 5.534 distance: 182 - 183: 9.964 distance: 182 - 185: 4.178 distance: 183 - 184: 5.180 distance: 183 - 189: 19.348 distance: 184 - 211: 23.071 distance: 185 - 186: 7.563 distance: 186 - 187: 14.690 distance: 186 - 188: 22.214 distance: 214 - 226: 3.048