Starting phenix.real_space_refine on Fri Aug 22 20:51:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7e7s_31003/08_2025/7e7s_31003.cif Found real_map, /net/cci-nas-00/data/ceres_data/7e7s_31003/08_2025/7e7s_31003.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7e7s_31003/08_2025/7e7s_31003.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7e7s_31003/08_2025/7e7s_31003.map" model { file = "/net/cci-nas-00/data/ceres_data/7e7s_31003/08_2025/7e7s_31003.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7e7s_31003/08_2025/7e7s_31003.cif" } resolution = 3.3 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: 5 Type Number sf(0) Gaussians Ca 2 9.91 5 S 58 5.16 5 C 5027 2.51 5 N 1314 2.21 5 O 1483 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.00s 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: 7884 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1020, 7882 Classifications: {'peptide': 1020} Link IDs: {'PTRANS': 46, 'TRANS': 973} Chain breaks: 2 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.75, per 1000 atoms: 0.22 Number of scatterers: 7884 At special positions: 0 Unit cell: (78.435, 84.66, 150.645, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 2 19.99 S 58 16.00 O 1483 8.00 N 1314 7.00 C 5027 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 875 " - pdb=" SG CYS A 887 " 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 449.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1910 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 7 sheets defined 55.0% alpha, 14.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 3 through 7 removed outlier: 3.599A pdb=" N THR A 6 " --> pdb=" O ASN A 3 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LYS A 7 " --> pdb=" O ALA A 4 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3 through 7' Processing helix chain 'A' and resid 8 through 17 Processing helix chain 'A' and resid 25 through 36 removed outlier: 3.588A pdb=" N GLU A 34 " --> pdb=" O LYS A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 57 Processing helix chain 'A' and resid 59 through 76 Processing helix chain 'A' and resid 88 through 123 removed outlier: 3.509A pdb=" N PHE A 92 " --> pdb=" O PHE A 88 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE A 94 " --> pdb=" O GLU A 90 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ILE A 97 " --> pdb=" O VAL A 93 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU A 121 " --> pdb=" O GLU A 117 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLU A 123 " --> pdb=" O LEU A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 145 No H-bonds generated for 'chain 'A' and resid 143 through 145' Processing helix chain 'A' and resid 177 through 182 Processing helix chain 'A' and resid 226 through 230 removed outlier: 3.976A pdb=" N ASN A 229 " --> pdb=" O THR A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 274 Processing helix chain 'A' and resid 275 through 280 removed outlier: 3.748A pdb=" N HIS A 278 " --> pdb=" O ASN A 275 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ASN A 280 " --> pdb=" O GLY A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 285 Processing helix chain 'A' and resid 287 through 307 removed outlier: 3.631A pdb=" N PHE A 296 " --> pdb=" O ALA A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 329 Processing helix chain 'A' and resid 337 through 342 removed outlier: 3.690A pdb=" N THR A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 345 No H-bonds generated for 'chain 'A' and resid 343 through 345' Processing helix chain 'A' and resid 407 through 420 removed outlier: 3.745A pdb=" N VAL A 411 " --> pdb=" O TYR A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 453 Processing helix chain 'A' and resid 463 through 468 removed outlier: 4.106A pdb=" N ALA A 468 " --> pdb=" O LYS A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 478 Processing helix chain 'A' and resid 516 through 523 Processing helix chain 'A' and resid 537 through 554 removed outlier: 3.622A pdb=" N GLN A 542 " --> pdb=" O SER A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 586 removed outlier: 3.859A pdb=" N PHE A 583 " --> pdb=" O ASP A 579 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LYS A 585 " --> pdb=" O ALA A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 616 Processing helix chain 'A' and resid 627 through 639 Processing helix chain 'A' and resid 654 through 659 Processing helix chain 'A' and resid 661 through 672 removed outlier: 3.502A pdb=" N ASN A 671 " --> pdb=" O ASP A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 693 removed outlier: 3.868A pdb=" N LYS A 683 " --> pdb=" O GLU A 679 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER A 684 " --> pdb=" O PRO A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 705 No H-bonds generated for 'chain 'A' and resid 703 through 705' Processing helix chain 'A' and resid 706 through 713 Processing helix chain 'A' and resid 723 through 729 removed outlier: 3.639A pdb=" N LYS A 727 " --> pdb=" O THR A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 781 removed outlier: 3.705A pdb=" N VAL A 743 " --> pdb=" O PHE A 739 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLY A 769 " --> pdb=" O SER A 765 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE A 774 " --> pdb=" O GLU A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 800 removed outlier: 3.676A pdb=" N GLY A 800 " --> pdb=" O LEU A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 800 through 805 Processing helix chain 'A' and resid 806 through 809 Processing helix chain 'A' and resid 829 through 858 removed outlier: 3.557A pdb=" N TRP A 854 " --> pdb=" O ALA A 850 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE A 855 " --> pdb=" O ALA A 851 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ALA A 858 " --> pdb=" O TRP A 854 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 871 Processing helix chain 'A' and resid 872 through 875 Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 892 through 913 removed outlier: 4.425A pdb=" N MET A 896 " --> pdb=" O SER A 892 " (cutoff:3.500A) Processing helix chain 'A' and resid 914 through 916 No H-bonds generated for 'chain 'A' and resid 914 through 916' Processing helix chain 'A' and resid 925 through 928 Processing helix chain 'A' and resid 929 through 946 Processing helix chain 'A' and resid 952 through 957 Processing helix chain 'A' and resid 962 through 974 removed outlier: 3.621A pdb=" N MET A 968 " --> pdb=" O THR A 964 " (cutoff:3.500A) Processing helix chain 'A' and resid 974 through 990 removed outlier: 3.632A pdb=" N LEU A 978 " --> pdb=" O LEU A 974 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1030 Proline residue: A1024 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 126 through 129 Processing sheet with id=AA2, first strand: chain 'A' and resid 150 through 153 removed outlier: 6.861A pdb=" N MET A 220 " --> pdb=" O THR A 166 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ASP A 162 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ILE A 163 " --> pdb=" O LEU A 208 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU A 208 " --> pdb=" O ILE A 163 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 174 through 176 removed outlier: 6.552A pdb=" N ARG A 174 " --> pdb=" O ALA A 215 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN A 213 " --> pdb=" O ASP A 176 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 651 through 653 removed outlier: 8.069A pdb=" N PHE A 675 " --> pdb=" O VAL A 620 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N MET A 622 " --> pdb=" O PHE A 675 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N VAL A 347 " --> pdb=" O ALA A 698 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N THR A 700 " --> pdb=" O VAL A 347 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N CYS A 349 " --> pdb=" O THR A 700 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N THR A 697 " --> pdb=" O ILE A 715 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N ILE A 717 " --> pdb=" O THR A 697 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N MET A 699 " --> pdb=" O ILE A 717 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N MET A 719 " --> pdb=" O MET A 699 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU A 734 " --> pdb=" O ALA A 718 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 395 through 396 removed outlier: 7.446A pdb=" N THR A 376 " --> pdb=" O VAL A 372 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N VAL A 372 " --> pdb=" O THR A 376 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N SER A 378 " --> pdb=" O ASP A 370 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE A 368 " --> pdb=" O ASN A 380 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N CYS A 364 " --> pdb=" O ILE A 384 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N VAL A 363 " --> pdb=" O LEU A 599 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LEU A 599 " --> pdb=" O VAL A 363 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG A 365 " --> pdb=" O GLY A 597 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU A 369 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N VAL A 593 " --> pdb=" O LEU A 369 " (cutoff:3.500A) removed outlier: 14.034A pdb=" N ARG A 371 " --> pdb=" O THR A 591 " (cutoff:3.500A) removed outlier: 15.946A pdb=" N THR A 591 " --> pdb=" O ARG A 371 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N LEU A 563 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N CYS A 595 " --> pdb=" O LEU A 561 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LEU A 561 " --> pdb=" O CYS A 595 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N GLY A 597 " --> pdb=" O ARG A 559 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ARG A 559 " --> pdb=" O GLY A 597 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY A 515 " --> pdb=" O ALA A 562 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA A 564 " --> pdb=" O VAL A 513 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N THR A 499 " --> pdb=" O LYS A 481 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N LYS A 481 " --> pdb=" O THR A 499 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 395 through 396 removed outlier: 7.446A pdb=" N THR A 376 " --> pdb=" O VAL A 372 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N VAL A 372 " --> pdb=" O THR A 376 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N SER A 378 " --> pdb=" O ASP A 370 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE A 368 " --> pdb=" O ASN A 380 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N CYS A 364 " --> pdb=" O ILE A 384 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N VAL A 363 " --> pdb=" O LEU A 599 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LEU A 599 " --> pdb=" O VAL A 363 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG A 365 " --> pdb=" O GLY A 597 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU A 369 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N VAL A 593 " --> pdb=" O LEU A 369 " (cutoff:3.500A) removed outlier: 14.034A pdb=" N ARG A 371 " --> pdb=" O THR A 591 " (cutoff:3.500A) removed outlier: 15.946A pdb=" N THR A 591 " --> pdb=" O ARG A 371 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N CYS A 524 " --> pdb=" O LEU A 590 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N PHE A 592 " --> pdb=" O CYS A 524 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N HIS A 526 " --> pdb=" O PHE A 592 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N GLY A 594 " --> pdb=" O HIS A 526 " (cutoff:3.500A) removed outlier: 9.299A pdb=" N ARG A 528 " --> pdb=" O GLY A 594 " (cutoff:3.500A) removed outlier: 13.026A pdb=" N VAL A 596 " --> pdb=" O ARG A 528 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 424 through 428 413 hydrogen bonds defined for protein. 1185 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: 1.19 Time building geometry restraints manager: 0.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2577 1.34 - 1.46: 1658 1.46 - 1.58: 3706 1.58 - 1.69: 0 1.69 - 1.81: 90 Bond restraints: 8031 Sorted by residual: bond pdb=" CA VAL A 529 " pdb=" CB VAL A 529 " ideal model delta sigma weight residual 1.540 1.530 0.010 1.36e-02 5.41e+03 5.72e-01 bond pdb=" CG LEU A 806 " pdb=" CD1 LEU A 806 " ideal model delta sigma weight residual 1.521 1.498 0.023 3.30e-02 9.18e+02 4.87e-01 bond pdb=" N PRO A 819 " pdb=" CA PRO A 819 " ideal model delta sigma weight residual 1.457 1.466 -0.009 1.31e-02 5.83e+03 4.68e-01 bond pdb=" C PRO A 819 " pdb=" O PRO A 819 " ideal model delta sigma weight residual 1.246 1.240 0.005 8.50e-03 1.38e+04 4.18e-01 bond pdb=" CG PRO A 312 " pdb=" CD PRO A 312 " ideal model delta sigma weight residual 1.503 1.481 0.022 3.40e-02 8.65e+02 4.14e-01 ... (remaining 8026 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 10771 1.66 - 3.32: 94 3.32 - 4.98: 26 4.98 - 6.64: 7 6.64 - 8.30: 1 Bond angle restraints: 10899 Sorted by residual: angle pdb=" CB MET A 908 " pdb=" CG MET A 908 " pdb=" SD MET A 908 " ideal model delta sigma weight residual 112.70 121.00 -8.30 3.00e+00 1.11e-01 7.65e+00 angle pdb=" N ILE A 232 " pdb=" CA ILE A 232 " pdb=" C ILE A 232 " ideal model delta sigma weight residual 113.07 109.43 3.64 1.36e+00 5.41e-01 7.18e+00 angle pdb=" C VAL A 223 " pdb=" N VAL A 224 " pdb=" CA VAL A 224 " ideal model delta sigma weight residual 122.66 120.19 2.47 9.70e-01 1.06e+00 6.46e+00 angle pdb=" CB LYS A 541 " pdb=" CG LYS A 541 " pdb=" CD LYS A 541 " ideal model delta sigma weight residual 111.30 116.95 -5.65 2.30e+00 1.89e-01 6.04e+00 angle pdb=" N LEU A 952 " pdb=" CA LEU A 952 " pdb=" C LEU A 952 " ideal model delta sigma weight residual 109.81 115.21 -5.40 2.21e+00 2.05e-01 5.98e+00 ... (remaining 10894 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 4353 17.73 - 35.45: 426 35.45 - 53.18: 64 53.18 - 70.91: 17 70.91 - 88.63: 8 Dihedral angle restraints: 4868 sinusoidal: 1922 harmonic: 2946 Sorted by residual: dihedral pdb=" CA VAL A 949 " pdb=" C VAL A 949 " pdb=" N GLU A 950 " pdb=" CA GLU A 950 " ideal model delta harmonic sigma weight residual -180.00 -157.07 -22.93 0 5.00e+00 4.00e-02 2.10e+01 dihedral pdb=" CA ASP A1038 " pdb=" CB ASP A1038 " pdb=" CG ASP A1038 " pdb=" OD1 ASP A1038 " ideal model delta sinusoidal sigma weight residual -30.00 -88.97 58.97 1 2.00e+01 2.50e-03 1.16e+01 dihedral pdb=" CB GLU A 79 " pdb=" CG GLU A 79 " pdb=" CD GLU A 79 " pdb=" OE1 GLU A 79 " ideal model delta sinusoidal sigma weight residual 0.00 88.63 -88.63 1 3.00e+01 1.11e-03 1.04e+01 ... (remaining 4865 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 919 0.036 - 0.072: 256 0.072 - 0.108: 85 0.108 - 0.144: 18 0.144 - 0.180: 1 Chirality restraints: 1279 Sorted by residual: chirality pdb=" CB ILE A 150 " pdb=" CA ILE A 150 " pdb=" CG1 ILE A 150 " pdb=" CG2 ILE A 150 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 8.07e-01 chirality pdb=" CA ILE A 527 " pdb=" N ILE A 527 " pdb=" C ILE A 527 " pdb=" CB ILE A 527 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.37e-01 chirality pdb=" CA PRO A 788 " pdb=" N PRO A 788 " pdb=" C PRO A 788 " pdb=" CB PRO A 788 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 3.96e-01 ... (remaining 1276 not shown) Planarity restraints: 1389 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 400 " 0.035 5.00e-02 4.00e+02 5.36e-02 4.59e+00 pdb=" N PRO A 401 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 401 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 401 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 247 " -0.030 5.00e-02 4.00e+02 4.58e-02 3.35e+00 pdb=" N PRO A 248 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO A 248 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 248 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 892 " -0.025 5.00e-02 4.00e+02 3.87e-02 2.39e+00 pdb=" N PRO A 893 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 893 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 893 " -0.021 5.00e-02 4.00e+02 ... (remaining 1386 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 222 2.71 - 3.26: 8253 3.26 - 3.81: 12642 3.81 - 4.35: 15906 4.35 - 4.90: 26753 Nonbonded interactions: 63776 Sorted by model distance: nonbonded pdb=" ND2 ASN A 879 " pdb=" OD1 ASP A 881 " model vdw 2.166 3.120 nonbonded pdb=" O ILE A 307 " pdb=" OE1 GLU A 309 " model vdw 2.258 3.040 nonbonded pdb=" NH2 ARG A 619 " pdb=" O CYS A 669 " model vdw 2.264 3.120 nonbonded pdb=" O PHE A 209 " pdb=" OG1 THR A 212 " model vdw 2.284 3.040 nonbonded pdb=" OG SER A 38 " pdb=" O LYS A 143 " model vdw 2.296 3.040 ... (remaining 63771 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.300 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: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 7.920 Find NCS groups from input model: 0.130 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:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 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 : 0.003 0.031 8032 Z= 0.113 Angle : 0.496 8.299 10901 Z= 0.261 Chirality : 0.040 0.180 1279 Planarity : 0.004 0.054 1389 Dihedral : 14.410 88.632 2955 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % 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: -0.13 (0.26), residues: 1014 helix: 0.30 (0.23), residues: 482 sheet: -1.14 (0.48), residues: 109 loop : -0.03 (0.32), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 134 TYR 0.008 0.001 TYR A 842 PHE 0.014 0.001 PHE A1040 TRP 0.007 0.001 TRP A 272 HIS 0.001 0.000 HIS A 396 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 8031) covalent geometry : angle 0.49597 (10899) SS BOND : bond 0.00073 ( 1) SS BOND : angle 0.60668 ( 2) hydrogen bonds : bond 0.24706 ( 403) hydrogen bonds : angle 7.94273 ( 1185) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.299 Fit side-chains REVERT: A 126 MET cc_start: 0.7479 (mmm) cc_final: 0.7023 (tmm) REVERT: A 399 ASP cc_start: 0.6887 (t70) cc_final: 0.6640 (t70) REVERT: A 568 ASN cc_start: 0.7578 (t0) cc_final: 0.7082 (p0) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.0733 time to fit residues: 10.8544 Evaluate side-chains 81 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 9.9990 chunk 97 optimal weight: 0.5980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 6.9990 chunk 100 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 ASN A 403 ASN A 691 GLN A 913 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.184929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.115323 restraints weight = 8357.858| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.04 r_work: 0.2989 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.1168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8032 Z= 0.135 Angle : 0.538 7.143 10901 Z= 0.281 Chirality : 0.042 0.178 1279 Planarity : 0.004 0.048 1389 Dihedral : 3.869 22.242 1078 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.34 % Allowed : 6.30 % Favored : 93.36 % 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: 0.64 (0.27), residues: 1014 helix: 1.26 (0.23), residues: 501 sheet: -1.24 (0.46), residues: 105 loop : -0.02 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 619 TYR 0.017 0.001 TYR A 842 PHE 0.009 0.001 PHE A 367 TRP 0.006 0.001 TRP A 854 HIS 0.003 0.001 HIS A 566 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 8031) covalent geometry : angle 0.53833 (10899) SS BOND : bond 0.00056 ( 1) SS BOND : angle 0.39389 ( 2) hydrogen bonds : bond 0.05269 ( 403) hydrogen bonds : angle 5.17718 ( 1185) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 102 time to evaluate : 0.267 Fit side-chains REVERT: A 467 ARG cc_start: 0.7642 (tpp-160) cc_final: 0.7440 (tpp-160) REVERT: A 482 GLU cc_start: 0.6872 (mp0) cc_final: 0.6145 (mp0) REVERT: A 568 ASN cc_start: 0.7845 (t0) cc_final: 0.7365 (p0) REVERT: A 586 TYR cc_start: 0.6633 (m-10) cc_final: 0.6277 (m-10) REVERT: A 714 GLU cc_start: 0.8599 (mm-30) cc_final: 0.8379 (mm-30) outliers start: 3 outliers final: 2 residues processed: 104 average time/residue: 0.0833 time to fit residues: 12.1180 Evaluate side-chains 90 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 88 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 437 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 0 optimal weight: 30.0000 chunk 52 optimal weight: 10.0000 chunk 82 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 chunk 16 optimal weight: 9.9990 chunk 75 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 89 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- 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 = 0.4064 r_free = 0.4064 target = 0.183756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.111630 restraints weight = 8293.585| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 1.89 r_work: 0.3006 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8032 Z= 0.142 Angle : 0.519 5.933 10901 Z= 0.267 Chirality : 0.042 0.154 1279 Planarity : 0.004 0.046 1389 Dihedral : 3.879 24.073 1078 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.46 % Allowed : 10.42 % Favored : 89.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.80 (0.27), residues: 1014 helix: 1.47 (0.23), residues: 501 sheet: -0.89 (0.51), residues: 92 loop : -0.18 (0.31), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 134 TYR 0.017 0.001 TYR A 842 PHE 0.013 0.001 PHE A1040 TRP 0.009 0.001 TRP A 107 HIS 0.002 0.001 HIS A 566 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 8031) covalent geometry : angle 0.51862 (10899) SS BOND : bond 0.00121 ( 1) SS BOND : angle 0.46180 ( 2) hydrogen bonds : bond 0.04515 ( 403) hydrogen bonds : angle 4.82779 ( 1185) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 95 time to evaluate : 0.285 Fit side-chains REVERT: A 482 GLU cc_start: 0.6723 (mp0) cc_final: 0.6082 (mp0) REVERT: A 553 SER cc_start: 0.8142 (t) cc_final: 0.7819 (p) REVERT: A 568 ASN cc_start: 0.7826 (t0) cc_final: 0.7382 (p0) REVERT: A 585 LYS cc_start: 0.7942 (ptpp) cc_final: 0.7674 (pttp) REVERT: A 586 TYR cc_start: 0.6569 (m-10) cc_final: 0.6245 (m-80) REVERT: A 626 ASP cc_start: 0.7900 (t70) cc_final: 0.7659 (t0) REVERT: A 898 MET cc_start: 0.8994 (mmm) cc_final: 0.8757 (mmm) outliers start: 4 outliers final: 2 residues processed: 98 average time/residue: 0.0917 time to fit residues: 12.2721 Evaluate side-chains 93 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 91 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 663 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 22 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 chunk 21 optimal weight: 20.0000 chunk 75 optimal weight: 1.9990 chunk 101 optimal weight: 0.4980 chunk 62 optimal weight: 0.0870 chunk 14 optimal weight: 0.0050 chunk 80 optimal weight: 0.5980 chunk 36 optimal weight: 0.4980 chunk 24 optimal weight: 8.9990 chunk 34 optimal weight: 2.9990 overall best weight: 0.3372 ------------------------------------------------------------------------------- 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 = 0.4084 r_free = 0.4084 target = 0.185797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.113346 restraints weight = 8498.825| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 2.06 r_work: 0.3024 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8032 Z= 0.096 Angle : 0.485 6.507 10901 Z= 0.247 Chirality : 0.040 0.132 1279 Planarity : 0.004 0.046 1389 Dihedral : 3.738 22.422 1078 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.15 % Allowed : 11.68 % Favored : 87.17 % 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: 1.11 (0.27), residues: 1014 helix: 1.79 (0.24), residues: 501 sheet: -0.46 (0.59), residues: 74 loop : -0.22 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 549 TYR 0.013 0.001 TYR A 842 PHE 0.010 0.001 PHE A1040 TRP 0.007 0.001 TRP A 793 HIS 0.002 0.000 HIS A 566 Details of bonding type rmsd covalent geometry : bond 0.00207 ( 8031) covalent geometry : angle 0.48514 (10899) SS BOND : bond 0.00085 ( 1) SS BOND : angle 0.30879 ( 2) hydrogen bonds : bond 0.03638 ( 403) hydrogen bonds : angle 4.43945 ( 1185) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 100 time to evaluate : 0.220 Fit side-chains REVERT: A 479 MET cc_start: 0.7073 (tpt) cc_final: 0.6846 (tpt) REVERT: A 482 GLU cc_start: 0.6591 (mp0) cc_final: 0.6129 (mp0) REVERT: A 568 ASN cc_start: 0.7682 (t0) cc_final: 0.7307 (p0) REVERT: A 585 LYS cc_start: 0.7910 (ptpp) cc_final: 0.7631 (pttp) REVERT: A 586 TYR cc_start: 0.6655 (m-10) cc_final: 0.6417 (m-10) REVERT: A 763 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8561 (mp) outliers start: 10 outliers final: 5 residues processed: 103 average time/residue: 0.0722 time to fit residues: 10.2792 Evaluate side-chains 98 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 92 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 575 MET Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 978 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: 58.6108 > 50: distance: 77 - 94: 5.022 distance: 82 - 101: 31.065 distance: 86 - 109: 37.242 distance: 90 - 94: 6.379 distance: 91 - 116: 25.977 distance: 95 - 96: 14.572 distance: 95 - 98: 8.431 distance: 96 - 97: 11.608 distance: 96 - 101: 16.599 distance: 97 - 123: 7.566 distance: 98 - 99: 9.277 distance: 98 - 100: 3.329 distance: 101 - 102: 3.047 distance: 102 - 103: 34.724 distance: 103 - 104: 38.031 distance: 103 - 109: 30.296 distance: 104 - 131: 27.946 distance: 105 - 106: 10.061 distance: 106 - 107: 19.749 distance: 106 - 108: 10.069 distance: 109 - 110: 41.564 distance: 110 - 111: 9.760 distance: 110 - 113: 31.146 distance: 111 - 112: 13.944 distance: 111 - 116: 35.023 distance: 112 - 140: 35.078 distance: 113 - 114: 11.569 distance: 113 - 115: 3.089 distance: 116 - 117: 12.861 distance: 117 - 118: 11.976 distance: 117 - 120: 17.507 distance: 118 - 119: 12.753 distance: 118 - 123: 3.171 distance: 119 - 148: 7.692 distance: 120 - 121: 14.499 distance: 120 - 122: 11.317 distance: 125 - 126: 7.120 distance: 125 - 131: 4.359 distance: 126 - 154: 9.857 distance: 127 - 128: 7.401 distance: 127 - 129: 21.130 distance: 128 - 130: 11.251 distance: 131 - 132: 3.148 distance: 132 - 133: 4.502 distance: 132 - 135: 7.646 distance: 133 - 134: 7.049 distance: 133 - 140: 4.488 distance: 134 - 162: 16.505 distance: 135 - 136: 11.863 distance: 136 - 137: 8.740 distance: 137 - 138: 9.944 distance: 137 - 139: 3.545 distance: 140 - 141: 7.684 distance: 141 - 142: 7.580 distance: 142 - 143: 4.777 distance: 142 - 148: 4.801 distance: 143 - 167: 4.459 distance: 144 - 145: 7.635 distance: 145 - 146: 10.583 distance: 146 - 147: 9.975 distance: 149 - 150: 3.006 distance: 149 - 152: 5.881 distance: 150 - 151: 3.511 distance: 151 - 175: 7.506 distance: 152 - 153: 4.160 distance: 155 - 156: 4.957 distance: 156 - 157: 11.275 distance: 156 - 162: 4.962 distance: 158 - 159: 10.451 distance: 159 - 160: 6.998 distance: 159 - 161: 6.747 distance: 163 - 166: 5.750 distance: 164 - 165: 8.577