Starting phenix.real_space_refine on Sat Aug 23 09:19:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ag8_11776/08_2025/7ag8_11776.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ag8_11776/08_2025/7ag8_11776.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ag8_11776/08_2025/7ag8_11776.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ag8_11776/08_2025/7ag8_11776.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ag8_11776/08_2025/7ag8_11776.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ag8_11776/08_2025/7ag8_11776.map" } resolution = 2.68 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= 0.001 sd= 0.086 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 Fe 2 7.16 5 S 38 5.16 5 C 6956 2.51 5 N 1867 2.21 5 O 2059 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 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: 10922 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5364 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 702, 5356 Classifications: {'peptide': 702} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 45, 'TRANS': 656} Chain breaks: 1 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Conformer: "B" Number of residues, atoms: 702, 5356 Classifications: {'peptide': 702} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 45, 'TRANS': 656} Chain breaks: 1 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 bond proxies already assigned to first conformer: 5495 Chain: "B" Number of atoms: 5472 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 715, 5464 Classifications: {'peptide': 715} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 46, 'TRANS': 668} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 49 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 715, 5464 Classifications: {'peptide': 715} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 46, 'TRANS': 668} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 49 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 5605 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.99, per 1000 atoms: 0.46 Number of scatterers: 10922 At special positions: 0 Unit cell: (84.66, 97.11, 124.5, 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) Fe 2 26.01 S 38 16.00 O 2059 8.00 N 1867 7.00 C 6956 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.95 Conformation dependent library (CDL) restraints added in 965.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2536 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 6 sheets defined 53.4% alpha, 3.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 28 through 32 Processing helix chain 'A' and resid 34 through 38 Processing helix chain 'A' and resid 44 through 48 removed outlier: 3.566A pdb=" N VAL A 47 " --> pdb=" O ASN A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 56 Processing helix chain 'A' and resid 63 through 69 removed outlier: 3.709A pdb=" N ALA A 69 " --> pdb=" O ALA A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 85 Processing helix chain 'A' and resid 93 through 97 removed outlier: 3.546A pdb=" N GLY A 96 " --> pdb=" O ALA A 93 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N HIS A 97 " --> pdb=" O ASP A 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 93 through 97' Processing helix chain 'A' and resid 98 through 111 Processing helix chain 'A' and resid 125 through 128 removed outlier: 3.542A pdb=" N ARG A 128 " --> pdb=" O GLY A 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 125 through 128' Processing helix chain 'A' and resid 129 through 134 removed outlier: 3.891A pdb=" N SER A 134 " --> pdb=" O ALA A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 148 removed outlier: 3.539A pdb=" N ALA A 144 " --> pdb=" O SER A 140 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU A 148 " --> pdb=" O ALA A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 156 removed outlier: 3.579A pdb=" N TYR A 155 " --> pdb=" O VAL A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 159 No H-bonds generated for 'chain 'A' and resid 157 through 159' Processing helix chain 'A' and resid 160 through 176 removed outlier: 3.691A pdb=" N VAL A 166 " --> pdb=" O ALA A 162 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY A 169 " --> pdb=" O ILE A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 238 Processing helix chain 'A' and resid 240 through 254 removed outlier: 3.921A pdb=" N VAL A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASP A 247 " --> pdb=" O ALA A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 270 Processing helix chain 'A' and resid 280 through 284 removed outlier: 3.602A pdb=" N LEU A 283 " --> pdb=" O PRO A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 291 Processing helix chain 'A' and resid 292 through 296 removed outlier: 3.539A pdb=" N GLN A 295 " --> pdb=" O PRO A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 312 removed outlier: 3.596A pdb=" N ASP A 311 " --> pdb=" O THR A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 337 Processing helix chain 'A' and resid 381 through 385 Processing helix chain 'A' and resid 387 through 400 removed outlier: 3.889A pdb=" N ARG A 392 " --> pdb=" O PRO A 388 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE A 393 " --> pdb=" O ILE A 389 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLU A 399 " --> pdb=" O ARG A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 416 removed outlier: 3.627A pdb=" N LEU A 404 " --> pdb=" O HIS A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 426 Processing helix chain 'A' and resid 436 through 440 Processing helix chain 'A' and resid 453 through 464 removed outlier: 3.593A pdb=" N ALA A 464 " --> pdb=" O SER A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 481 Processing helix chain 'A' and resid 495 through 498 removed outlier: 4.034A pdb=" N ARG A 498 " --> pdb=" O GLY A 495 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 495 through 498' Processing helix chain 'A' and resid 499 through 504 removed outlier: 3.625A pdb=" N GLY A 504 " --> pdb=" O GLN A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 531 removed outlier: 3.751A pdb=" N SER A 530 " --> pdb=" O GLU A 526 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA A 531 " --> pdb=" O SER A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 560 Processing helix chain 'A' and resid 580 through 585 Processing helix chain 'A' and resid 586 through 588 No H-bonds generated for 'chain 'A' and resid 586 through 588' Processing helix chain 'A' and resid 605 through 617 Processing helix chain 'A' and resid 620 through 635 removed outlier: 4.143A pdb=" N VAL A 633 " --> pdb=" O GLY A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 641 Processing helix chain 'A' and resid 655 through 662 Processing helix chain 'A' and resid 693 through 701 removed outlier: 4.286A pdb=" N PHE A 698 " --> pdb=" O VAL A 694 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N GLY A 699 " --> pdb=" O ASP A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 712 removed outlier: 3.686A pdb=" N LEU A 707 " --> pdb=" O GLU A 703 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL A 710 " --> pdb=" O ALA A 706 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N TYR A 711 " --> pdb=" O LEU A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 716 through 733 Processing helix chain 'B' and resid 44 through 50 removed outlier: 3.873A pdb=" N VAL B 47 " --> pdb=" O ASN B 44 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N HIS B 49 " --> pdb=" O LYS B 46 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLN B 50 " --> pdb=" O VAL B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 56 Processing helix chain 'B' and resid 63 through 69 Processing helix chain 'B' and resid 72 through 85 Processing helix chain 'B' and resid 93 through 97 Processing helix chain 'B' and resid 98 through 111 Processing helix chain 'B' and resid 135 through 139 Processing helix chain 'B' and resid 140 through 148 removed outlier: 3.663A pdb=" N ALA B 144 " --> pdb=" O SER B 140 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU B 148 " --> pdb=" O ALA B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 156 removed outlier: 3.716A pdb=" N LYS B 154 " --> pdb=" O PRO B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 159 No H-bonds generated for 'chain 'B' and resid 157 through 159' Processing helix chain 'B' and resid 160 through 176 removed outlier: 3.643A pdb=" N VAL B 166 " --> pdb=" O ALA B 162 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY B 169 " --> pdb=" O ILE B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 238 removed outlier: 3.508A pdb=" N GLY B 237 " --> pdb=" O GLY B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 254 Processing helix chain 'B' and resid 258 through 270 Processing helix chain 'B' and resid 280 through 284 Processing helix chain 'B' and resid 287 through 291 removed outlier: 3.513A pdb=" N ALA B 291 " --> pdb=" O PRO B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 296 Processing helix chain 'B' and resid 308 through 312 removed outlier: 3.810A pdb=" N ASP B 311 " --> pdb=" O THR B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 337 Processing helix chain 'B' and resid 356 through 359 Processing helix chain 'B' and resid 382 through 387 Processing helix chain 'B' and resid 387 through 399 removed outlier: 4.128A pdb=" N GLU B 399 " --> pdb=" O ARG B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 417 removed outlier: 3.574A pdb=" N LEU B 404 " --> pdb=" O HIS B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 421 removed outlier: 4.387A pdb=" N GLY B 421 " --> pdb=" O ARG B 418 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 418 through 421' Processing helix chain 'B' and resid 422 through 426 Processing helix chain 'B' and resid 436 through 440 Processing helix chain 'B' and resid 453 through 464 Processing helix chain 'B' and resid 468 through 481 Processing helix chain 'B' and resid 495 through 498 removed outlier: 3.904A pdb=" N ARG B 498 " --> pdb=" O GLY B 495 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 495 through 498' Processing helix chain 'B' and resid 499 through 504 removed outlier: 3.574A pdb=" N GLY B 504 " --> pdb=" O GLN B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 530 Processing helix chain 'B' and resid 539 through 560 Processing helix chain 'B' and resid 580 through 585 Processing helix chain 'B' and resid 586 through 588 No H-bonds generated for 'chain 'B' and resid 586 through 588' Processing helix chain 'B' and resid 593 through 596 Processing helix chain 'B' and resid 605 through 617 Processing helix chain 'B' and resid 620 through 634 removed outlier: 3.875A pdb=" N VAL B 633 " --> pdb=" O GLY B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 641 Processing helix chain 'B' and resid 656 through 662 Processing helix chain 'B' and resid 693 through 701 removed outlier: 4.542A pdb=" N PHE B 698 " --> pdb=" O VAL B 694 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLY B 699 " --> pdb=" O ASP B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 712 removed outlier: 3.529A pdb=" N ALA B 706 " --> pdb=" O SER B 702 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU B 707 " --> pdb=" O GLU B 703 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL B 710 " --> pdb=" O ALA B 706 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR B 711 " --> pdb=" O LEU B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 716 through 733 Processing sheet with id=AA1, first strand: chain 'A' and resid 341 through 345 Processing sheet with id=AA2, first strand: chain 'A' and resid 591 through 592 Processing sheet with id=AA3, first strand: chain 'A' and resid 667 through 670 Processing sheet with id=AA4, first strand: chain 'B' and resid 342 through 345 Processing sheet with id=AA5, first strand: chain 'B' and resid 591 through 592 Processing sheet with id=AA6, first strand: chain 'B' and resid 667 through 670 435 hydrogen bonds defined for protein. 1158 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: 1.85 Time building geometry restraints manager: 1.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.36: 3705 1.36 - 1.53: 7218 1.53 - 1.71: 233 1.71 - 1.88: 72 1.88 - 2.05: 8 Bond restraints: 11236 Sorted by residual: bond pdb=" C ALA B 130 " pdb=" N PRO B 131 " ideal model delta sigma weight residual 1.337 1.379 -0.042 1.11e-02 8.12e+03 1.45e+01 bond pdb=" C PRO B 89 " pdb=" O PRO B 89 " ideal model delta sigma weight residual 1.238 1.189 0.049 1.33e-02 5.65e+03 1.35e+01 bond pdb=" CA ALA A 93 " pdb=" CB ALA A 93 " ideal model delta sigma weight residual 1.530 1.476 0.054 1.48e-02 4.57e+03 1.32e+01 bond pdb=" C TYR B 98 " pdb=" O TYR B 98 " ideal model delta sigma weight residual 1.236 1.192 0.044 1.28e-02 6.10e+03 1.19e+01 bond pdb=" N ASN B 133 " pdb=" CA ASN B 133 " ideal model delta sigma weight residual 1.457 1.494 -0.036 1.29e-02 6.01e+03 7.89e+00 ... (remaining 11231 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 14940 1.64 - 3.28: 327 3.28 - 4.93: 69 4.93 - 6.57: 16 6.57 - 8.21: 7 Bond angle restraints: 15359 Sorted by residual: angle pdb=" C PRO B 89 " pdb=" CA PRO B 89 " pdb=" CB PRO B 89 " ideal model delta sigma weight residual 112.26 104.55 7.71 1.67e+00 3.59e-01 2.13e+01 angle pdb=" N ASN B 133 " pdb=" CA ASN B 133 " pdb=" CB ASN B 133 " ideal model delta sigma weight residual 110.49 117.88 -7.39 1.69e+00 3.50e-01 1.91e+01 angle pdb=" CA TRP A 91 " pdb=" C TRP A 91 " pdb=" N PRO A 92 " ideal model delta sigma weight residual 117.57 121.35 -3.78 8.70e-01 1.32e+00 1.88e+01 angle pdb=" CA TRP B 91 " pdb=" C TRP B 91 " pdb=" O TRP B 91 " ideal model delta sigma weight residual 121.34 117.37 3.97 9.40e-01 1.13e+00 1.78e+01 angle pdb=" N PRO B 89 " pdb=" CA PRO B 89 " pdb=" C PRO B 89 " ideal model delta sigma weight residual 113.81 119.72 -5.91 1.45e+00 4.76e-01 1.66e+01 ... (remaining 15354 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 5988 17.75 - 35.51: 425 35.51 - 53.26: 58 53.26 - 71.02: 24 71.02 - 88.77: 10 Dihedral angle restraints: 6505 sinusoidal: 2510 harmonic: 3995 Sorted by residual: dihedral pdb=" CA TYR B 28 " pdb=" C TYR B 28 " pdb=" N PRO B 29 " pdb=" CA PRO B 29 " ideal model delta harmonic sigma weight residual -180.00 -154.57 -25.43 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" CA PHE A 129 " pdb=" C PHE A 129 " pdb=" N ALA A 130 " pdb=" CA ALA A 130 " ideal model delta harmonic sigma weight residual -180.00 -158.65 -21.35 0 5.00e+00 4.00e-02 1.82e+01 dihedral pdb=" CA GLY B 451 " pdb=" C GLY B 451 " pdb=" N GLU B 452 " pdb=" CA GLU B 452 " ideal model delta harmonic sigma weight residual 180.00 159.40 20.60 0 5.00e+00 4.00e-02 1.70e+01 ... (remaining 6502 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1243 0.051 - 0.102: 315 0.102 - 0.152: 48 0.152 - 0.203: 2 0.203 - 0.254: 3 Chirality restraints: 1611 Sorted by residual: chirality pdb=" CA PRO A 92 " pdb=" N PRO A 92 " pdb=" C PRO A 92 " pdb=" CB PRO A 92 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CA TYR A 98 " pdb=" N TYR A 98 " pdb=" C TYR A 98 " pdb=" CB TYR A 98 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CA ASN B 133 " pdb=" N ASN B 133 " pdb=" C ASN B 133 " pdb=" CB ASN B 133 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.30e+00 ... (remaining 1608 not shown) Planarity restraints: 2023 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 130 " -0.052 5.00e-02 4.00e+02 7.81e-02 9.75e+00 pdb=" N PRO B 131 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO B 131 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 131 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 95 " 0.014 2.00e-02 2.50e+03 2.80e-02 7.86e+00 pdb=" C TYR A 95 " -0.049 2.00e-02 2.50e+03 pdb=" O TYR A 95 " 0.018 2.00e-02 2.50e+03 pdb=" N GLY A 96 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 133 " -0.011 2.00e-02 2.50e+03 2.30e-02 5.31e+00 pdb=" C ASN B 133 " 0.040 2.00e-02 2.50e+03 pdb=" O ASN B 133 " -0.015 2.00e-02 2.50e+03 pdb=" N SER B 134 " -0.014 2.00e-02 2.50e+03 ... (remaining 2020 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1830 2.76 - 3.29: 10441 3.29 - 3.83: 18701 3.83 - 4.36: 23160 4.36 - 4.90: 39543 Nonbonded interactions: 93675 Sorted by model distance: nonbonded pdb=" OH TYR B 337 " pdb=" OG1 THR B 394 " model vdw 2.220 3.040 nonbonded pdb=" OH TYR A 337 " pdb=" OG1 THR A 394 " model vdw 2.227 3.040 nonbonded pdb=" NZ LYS B 274 " pdb=" O THR B 275 " model vdw 2.285 3.120 nonbonded pdb=" NH1 ARG A 146 " pdb=" O MET A 296 " model vdw 2.295 3.120 nonbonded pdb=" O MET B 420 " pdb=" NH1 ARG B 425 " model vdw 2.305 3.120 ... (remaining 93670 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 26 through 45 or (resid 46 and (name N or name CA or name \ C or name O or name CB )) or resid 47 through 355 or (resid 356 and (name N or n \ ame CA or name C or name O or name CB )) or resid 357 through 417 or resid 419 t \ hrough 512 or (resid 513 and (name N or name CA or name C or name O or name CB ) \ ) or resid 514 through 714 or (resid 715 through 716 and (name N or name CA or n \ ame C or name O or name CB )) or resid 717 through 801)) selection = (chain 'B' and (resid 26 through 194 or (resid 195 and (name N or name CA or nam \ e C or name O or name CB )) or resid 196 through 202 or (resid 203 and (name N o \ r name CA or name C or name O or name CB )) or resid 204 through 205 or resid 22 \ 1 through 417 or resid 419 through 515 or (resid 516 and (name N or name CA or n \ ame C or name O or name CB )) or resid 517 through 556 or (resid 557 through 559 \ and (name N or name CA or name C or name O or name CB )) or resid 560 through 5 \ 89 or (resid 590 through 591 and (name N or name CA or name C or name O or name \ CB )) or resid 592 through 801)) } 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=0.00 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.790 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: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.730 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 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:7.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 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 : 0.008 0.460 11238 Z= 0.234 Angle : 0.647 8.212 15359 Z= 0.376 Chirality : 0.045 0.254 1611 Planarity : 0.005 0.078 2023 Dihedral : 13.126 88.772 3969 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.18 % Favored : 95.75 % Rotamer: Outliers : 0.37 % Allowed : 0.27 % Favored : 99.36 % 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: -0.60 (0.21), residues: 1413 helix: 0.56 (0.22), residues: 584 sheet: -0.45 (1.18), residues: 20 loop : -1.14 (0.20), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 736 TYR 0.015 0.001 TYR B 98 PHE 0.008 0.001 PHE A 167 TRP 0.038 0.001 TRP B 107 HIS 0.004 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00467 (11236) covalent geometry : angle 0.64707 (15359) hydrogen bonds : bond 0.18702 ( 435) hydrogen bonds : angle 5.54279 ( 1158) Misc. bond : bond 0.45042 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 99 time to evaluate : 0.472 Fit side-chains REVERT: A 82 GLU cc_start: 0.7071 (pp20) cc_final: 0.6859 (pp20) REVERT: A 94 ASP cc_start: 0.7954 (m-30) cc_final: 0.7748 (m-30) REVERT: A 225 MET cc_start: 0.4987 (pmm) cc_final: 0.3309 (ptm) REVERT: A 392 ARG cc_start: 0.6911 (ptp-110) cc_final: 0.6698 (mtm110) REVERT: B 304 TYR cc_start: 0.7422 (t80) cc_final: 0.6796 (t80) REVERT: B 663 ASP cc_start: 0.7672 (t0) cc_final: 0.7409 (t0) REVERT: B 703 GLU cc_start: 0.7261 (mt-10) cc_final: 0.6870 (mp0) outliers start: 1 outliers final: 1 residues processed: 100 average time/residue: 0.6707 time to fit residues: 72.1517 Evaluate side-chains 77 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 76 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 133 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.3980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN A 97 HIS ** A 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.122792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.096257 restraints weight = 34539.257| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 3.60 r_work: 0.3199 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3223 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3223 r_free = 0.3223 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3223 r_free = 0.3223 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| r_final: 0.3223 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.0873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.172 11238 Z= 0.116 Angle : 0.569 11.418 15359 Z= 0.280 Chirality : 0.042 0.149 1611 Planarity : 0.004 0.044 2023 Dihedral : 5.642 73.367 1549 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.25 % Favored : 95.68 % Rotamer: Outliers : 0.73 % Allowed : 4.67 % Favored : 94.60 % 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: -0.21 (0.21), residues: 1413 helix: 0.84 (0.21), residues: 584 sheet: -0.37 (0.94), residues: 30 loop : -0.88 (0.21), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 395 TYR 0.021 0.001 TYR B 155 PHE 0.007 0.001 PHE A 724 TRP 0.011 0.001 TRP A 341 HIS 0.003 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00269 (11236) covalent geometry : angle 0.56922 (15359) hydrogen bonds : bond 0.04010 ( 435) hydrogen bonds : angle 4.29533 ( 1158) Misc. bond : bond 0.15917 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 85 time to evaluate : 0.449 Fit side-chains REVERT: A 82 GLU cc_start: 0.7547 (pp20) cc_final: 0.7329 (pp20) REVERT: A 225 MET cc_start: 0.5131 (pmm) cc_final: 0.3423 (ptm) REVERT: A 392 ARG cc_start: 0.7210 (ptp-110) cc_final: 0.6976 (mtm110) REVERT: A 506 GLU cc_start: 0.8530 (tp30) cc_final: 0.8269 (tp30) REVERT: A 596 ASN cc_start: 0.8534 (t0) cc_final: 0.8298 (t0) REVERT: A 607 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.7342 (mp0) REVERT: B 133 ASN cc_start: 0.7645 (OUTLIER) cc_final: 0.7365 (p0) REVERT: B 304 TYR cc_start: 0.7672 (t80) cc_final: 0.6988 (t80) REVERT: B 703 GLU cc_start: 0.7741 (mt-10) cc_final: 0.7361 (mp0) outliers start: 5 outliers final: 1 residues processed: 89 average time/residue: 0.6349 time to fit residues: 61.2922 Evaluate side-chains 81 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 78 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 607 GLU Chi-restraints excluded: chain B residue 133 ASN Chi-restraints excluded: chain B residue 738 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 94 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 139 optimal weight: 1.9990 chunk 110 optimal weight: 0.6980 chunk 133 optimal weight: 0.0980 chunk 75 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 64 optimal weight: 6.9990 chunk 72 optimal weight: 0.9990 chunk 125 optimal weight: 0.5980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN ** A 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.123661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.097296 restraints weight = 30769.146| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 3.43 r_work: 0.3222 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3248 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3248 r_free = 0.3248 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3248 r_free = 0.3248 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| r_final: 0.3248 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.1122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.144 11238 Z= 0.110 Angle : 0.540 10.622 15359 Z= 0.262 Chirality : 0.042 0.132 1611 Planarity : 0.004 0.041 2023 Dihedral : 5.447 74.219 1549 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.54 % Favored : 96.39 % Rotamer: Outliers : 0.82 % Allowed : 5.49 % Favored : 93.68 % 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: 0.04 (0.22), residues: 1413 helix: 1.04 (0.21), residues: 584 sheet: 0.47 (1.04), residues: 20 loop : -0.74 (0.21), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 114 TYR 0.016 0.001 TYR B 155 PHE 0.008 0.001 PHE B 129 TRP 0.012 0.001 TRP A 191 HIS 0.004 0.001 HIS A 276 Details of bonding type rmsd covalent geometry : bond 0.00261 (11236) covalent geometry : angle 0.53980 (15359) hydrogen bonds : bond 0.03741 ( 435) hydrogen bonds : angle 4.05172 ( 1158) Misc. bond : bond 0.13055 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 79 time to evaluate : 0.402 Fit side-chains REVERT: A 225 MET cc_start: 0.5159 (pmm) cc_final: 0.3572 (ptm) REVERT: A 392 ARG cc_start: 0.7220 (ptp-110) cc_final: 0.6978 (mtm110) REVERT: A 474 SER cc_start: 0.7776 (t) cc_final: 0.7201 (m) REVERT: A 506 GLU cc_start: 0.8559 (tp30) cc_final: 0.8325 (tp30) REVERT: A 596 ASN cc_start: 0.8524 (t0) cc_final: 0.8292 (t0) REVERT: B 107 TRP cc_start: 0.7304 (OUTLIER) cc_final: 0.7013 (t60) REVERT: B 304 TYR cc_start: 0.7662 (t80) cc_final: 0.6953 (t80) REVERT: B 703 GLU cc_start: 0.7773 (mt-10) cc_final: 0.7386 (mp0) outliers start: 6 outliers final: 2 residues processed: 83 average time/residue: 0.5994 time to fit residues: 54.1507 Evaluate side-chains 79 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 76 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain B residue 107 TRP Chi-restraints excluded: chain B residue 738 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- 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: 50.63 > 50: distance: 120 - 136: 9.502 distance: 131 - 136: 6.241 distance: 132 - 160: 5.444 distance: 136 - 137: 5.179 distance: 137 - 138: 4.376 distance: 137 - 140: 8.425 distance: 138 - 139: 14.985 distance: 138 - 147: 9.573 distance: 139 - 167: 15.061 distance: 140 - 141: 6.498 distance: 141 - 142: 4.498 distance: 142 - 143: 7.392 distance: 143 - 144: 6.655 distance: 144 - 145: 5.612 distance: 144 - 146: 7.549 distance: 147 - 148: 7.781 distance: 148 - 149: 7.979 distance: 148 - 151: 11.763 distance: 149 - 150: 10.109 distance: 149 - 152: 6.179 distance: 152 - 153: 6.841 distance: 153 - 154: 6.383 distance: 153 - 156: 8.736 distance: 154 - 160: 3.702 distance: 156 - 157: 10.278 distance: 157 - 158: 9.537 distance: 157 - 159: 8.328 distance: 160 - 161: 5.721 distance: 161 - 162: 4.973 distance: 161 - 164: 8.083 distance: 162 - 163: 6.043 distance: 162 - 167: 5.169 distance: 163 - 195: 10.891 distance: 164 - 165: 9.163 distance: 164 - 166: 8.339 distance: 167 - 168: 4.894 distance: 168 - 169: 5.591 distance: 168 - 171: 7.688 distance: 169 - 170: 5.434 distance: 169 - 176: 3.971 distance: 171 - 172: 7.495 distance: 172 - 173: 6.809 distance: 173 - 174: 5.343 distance: 173 - 175: 6.557 distance: 176 - 177: 4.590 distance: 177 - 178: 8.341 distance: 177 - 180: 3.647 distance: 178 - 179: 3.161 distance: 178 - 183: 4.021 distance: 180 - 181: 7.518 distance: 180 - 182: 6.667 distance: 183 - 184: 7.805 distance: 184 - 185: 23.588 distance: 184 - 187: 13.424 distance: 185 - 186: 5.576 distance: 185 - 195: 34.617 distance: 187 - 188: 7.270 distance: 188 - 189: 8.508 distance: 188 - 190: 4.523 distance: 189 - 191: 9.817 distance: 190 - 192: 5.962 distance: 191 - 193: 4.226 distance: 192 - 193: 5.517 distance: 195 - 196: 13.845 distance: 196 - 197: 29.710 distance: 197 - 198: 8.983 distance: 197 - 199: 17.014 distance: 199 - 200: 21.203 distance: 200 - 201: 10.635 distance: 200 - 203: 9.866 distance: 201 - 202: 5.555 distance: 201 - 204: 6.853 distance: 204 - 205: 6.058 distance: 205 - 206: 4.702 distance: 205 - 208: 4.128 distance: 206 - 207: 8.272 distance: 206 - 212: 4.305 distance: 209 - 210: 4.223