Starting phenix.real_space_refine on Fri Feb 6 23:50:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ccr_30340/02_2026/7ccr_30340.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ccr_30340/02_2026/7ccr_30340.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ccr_30340/02_2026/7ccr_30340.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ccr_30340/02_2026/7ccr_30340.map" model { file = "/net/cci-nas-00/data/ceres_data/7ccr_30340/02_2026/7ccr_30340.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ccr_30340/02_2026/7ccr_30340.cif" } resolution = 4.9 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= 0.004 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 P 588 5.49 5 S 58 5.16 5 C 16892 2.51 5 N 5488 2.21 5 O 6696 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29722 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 784 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "B" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "C" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 787 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 5, 'TRANS': 96} Chain: "D" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 720 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "E" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 807 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "F" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 633 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "G" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 789 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "H" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 725 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3031 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2996 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "K" Number of atoms: 2962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2962 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 12, 'TRANS': 348} Chain breaks: 1 Restraints were copied for chains: L, M, N, O, P, Q, R, S, T, U, V Time building chain proxies: 7.87, per 1000 atoms: 0.26 Number of scatterers: 29722 At special positions: 0 Unit cell: (158, 165, 147, 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) S 58 16.00 P 588 15.00 O 6696 8.00 N 5488 7.00 C 16892 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.49 Conformation dependent library (CDL) restraints added in 941.6 milliseconds 4324 Ramachandran restraints generated. 2162 Oldfield, 0 Emsley, 2162 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4148 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 24 sheets defined 66.6% alpha, 5.1% beta 286 base pairs and 510 stacking pairs defined. Time for finding SS restraints: 4.96 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.744A pdb=" N LYS A 56 " --> pdb=" O ARG A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.505A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.564A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 removed outlier: 3.787A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.181A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.515A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 123 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 79 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.577A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.533A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.518A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.228A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 85 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 103 through 124 Processing helix chain 'K' and resid 161 through 176 Processing helix chain 'K' and resid 178 through 198 removed outlier: 4.253A pdb=" N ALA K 182 " --> pdb=" O ASP K 178 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLY K 184 " --> pdb=" O SER K 180 " (cutoff:3.500A) Processing helix chain 'K' and resid 200 through 204 removed outlier: 3.785A pdb=" N PHE K 203 " --> pdb=" O ASP K 200 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARG K 204 " --> pdb=" O SER K 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 200 through 204' Processing helix chain 'K' and resid 260 through 266 removed outlier: 3.570A pdb=" N GLN K 264 " --> pdb=" O ASN K 260 " (cutoff:3.500A) Processing helix chain 'K' and resid 272 through 289 removed outlier: 3.841A pdb=" N ASN K 289 " --> pdb=" O LYS K 285 " (cutoff:3.500A) Processing helix chain 'K' and resid 331 through 335 Processing helix chain 'K' and resid 345 through 354 Processing helix chain 'K' and resid 379 through 389 Processing helix chain 'K' and resid 405 through 424 Processing helix chain 'K' and resid 429 through 433 removed outlier: 3.597A pdb=" N LYS K 432 " --> pdb=" O HIS K 429 " (cutoff:3.500A) Processing helix chain 'K' and resid 434 through 449 removed outlier: 3.844A pdb=" N VAL K 438 " --> pdb=" O SER K 434 " (cutoff:3.500A) Processing helix chain 'K' and resid 452 through 458 removed outlier: 3.807A pdb=" N ASP K 456 " --> pdb=" O SER K 453 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N ARG K 457 " --> pdb=" O GLN K 454 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LYS K 458 " --> pdb=" O TRP K 455 " (cutoff:3.500A) Processing helix chain 'K' and resid 459 through 477 Processing helix chain 'K' and resid 497 through 513 Processing helix chain 'K' and resid 516 through 520 removed outlier: 4.176A pdb=" N ASP K 520 " --> pdb=" O PRO K 517 " (cutoff:3.500A) Processing helix chain 'L' and resid 44 through 57 removed outlier: 3.744A pdb=" N LYS L 56 " --> pdb=" O ARG L 52 " (cutoff:3.500A) Processing helix chain 'L' and resid 63 through 79 removed outlier: 3.505A pdb=" N PHE L 78 " --> pdb=" O ILE L 74 " (cutoff:3.500A) Processing helix chain 'L' and resid 85 through 114 Processing helix chain 'L' and resid 120 through 132 Processing helix chain 'M' and resid 30 through 42 Processing helix chain 'M' and resid 49 through 76 removed outlier: 3.564A pdb=" N GLU M 53 " --> pdb=" O LEU M 49 " (cutoff:3.500A) Processing helix chain 'M' and resid 82 through 94 removed outlier: 3.788A pdb=" N VAL M 86 " --> pdb=" O THR M 82 " (cutoff:3.500A) Processing helix chain 'N' and resid 17 through 22 Processing helix chain 'N' and resid 26 through 37 Processing helix chain 'N' and resid 45 through 73 removed outlier: 4.182A pdb=" N VAL N 49 " --> pdb=" O ALA N 45 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 90 removed outlier: 3.515A pdb=" N LEU N 83 " --> pdb=" O ILE N 79 " (cutoff:3.500A) Processing helix chain 'N' and resid 90 through 97 Processing helix chain 'O' and resid 37 through 49 Processing helix chain 'O' and resid 55 through 84 Processing helix chain 'O' and resid 90 through 102 Processing helix chain 'O' and resid 103 through 123 Processing helix chain 'P' and resid 44 through 57 Processing helix chain 'P' and resid 63 through 79 Processing helix chain 'P' and resid 85 through 114 Processing helix chain 'P' and resid 120 through 132 removed outlier: 3.578A pdb=" N ILE P 124 " --> pdb=" O MET P 120 " (cutoff:3.500A) Processing helix chain 'Q' and resid 25 through 29 Processing helix chain 'Q' and resid 30 through 41 Processing helix chain 'Q' and resid 49 through 76 removed outlier: 3.533A pdb=" N GLU Q 53 " --> pdb=" O LEU Q 49 " (cutoff:3.500A) Processing helix chain 'Q' and resid 82 through 94 removed outlier: 3.518A pdb=" N VAL Q 86 " --> pdb=" O THR Q 82 " (cutoff:3.500A) Processing helix chain 'R' and resid 16 through 22 Processing helix chain 'R' and resid 26 through 37 Processing helix chain 'R' and resid 45 through 73 removed outlier: 4.228A pdb=" N VAL R 49 " --> pdb=" O ALA R 45 " (cutoff:3.500A) Processing helix chain 'R' and resid 79 through 90 Processing helix chain 'R' and resid 90 through 97 Processing helix chain 'S' and resid 37 through 49 Processing helix chain 'S' and resid 55 through 85 Processing helix chain 'S' and resid 90 through 102 Processing helix chain 'S' and resid 103 through 124 Processing helix chain 'V' and resid 161 through 176 Processing helix chain 'V' and resid 178 through 198 removed outlier: 4.252A pdb=" N ALA V 182 " --> pdb=" O ASP V 178 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLY V 184 " --> pdb=" O SER V 180 " (cutoff:3.500A) Processing helix chain 'V' and resid 200 through 204 removed outlier: 3.784A pdb=" N PHE V 203 " --> pdb=" O ASP V 200 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARG V 204 " --> pdb=" O SER V 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 200 through 204' Processing helix chain 'V' and resid 260 through 266 removed outlier: 3.570A pdb=" N GLN V 264 " --> pdb=" O ASN V 260 " (cutoff:3.500A) Processing helix chain 'V' and resid 272 through 289 removed outlier: 3.841A pdb=" N ASN V 289 " --> pdb=" O LYS V 285 " (cutoff:3.500A) Processing helix chain 'V' and resid 331 through 335 Processing helix chain 'V' and resid 345 through 354 Processing helix chain 'V' and resid 379 through 389 Processing helix chain 'V' and resid 405 through 424 Processing helix chain 'V' and resid 429 through 433 removed outlier: 3.597A pdb=" N LYS V 432 " --> pdb=" O HIS V 429 " (cutoff:3.500A) Processing helix chain 'V' and resid 434 through 449 removed outlier: 3.843A pdb=" N VAL V 438 " --> pdb=" O SER V 434 " (cutoff:3.500A) Processing helix chain 'V' and resid 452 through 458 removed outlier: 3.808A pdb=" N ASP V 456 " --> pdb=" O SER V 453 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N ARG V 457 " --> pdb=" O GLN V 454 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LYS V 458 " --> pdb=" O TRP V 455 " (cutoff:3.500A) Processing helix chain 'V' and resid 459 through 477 Processing helix chain 'V' and resid 497 through 513 Processing helix chain 'V' and resid 516 through 520 removed outlier: 4.176A pdb=" N ASP V 520 " --> pdb=" O PRO V 517 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.048A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 5.952A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.424A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 removed outlier: 7.519A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.524A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.003A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'K' and resid 206 through 208 removed outlier: 5.865A pdb=" N PHE K 230 " --> pdb=" O ALA K 323 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N GLU K 325 " --> pdb=" O PHE K 230 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N LEU K 232 " --> pdb=" O GLU K 325 " (cutoff:3.500A) removed outlier: 9.335A pdb=" N LEU K 322 " --> pdb=" O PRO K 361 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N TYR K 358 " --> pdb=" O SER K 378 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 296 through 298 removed outlier: 3.602A pdb=" N ILE K 297 " --> pdb=" O LEU K 311 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU K 311 " --> pdb=" O ILE K 297 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 83 through 84 removed outlier: 7.048A pdb=" N ARG L 83 " --> pdb=" O VAL M 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'L' and resid 118 through 119 Processing sheet with id=AB6, first strand: chain 'M' and resid 96 through 98 removed outlier: 5.952A pdb=" N THR M 96 " --> pdb=" O THR R 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'N' and resid 42 through 43 removed outlier: 7.424A pdb=" N ARG N 42 " --> pdb=" O ILE O 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'N' and resid 77 through 78 Processing sheet with id=AB9, first strand: chain 'N' and resid 101 through 102 removed outlier: 7.519A pdb=" N THR N 101 " --> pdb=" O TYR Q 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'P' and resid 83 through 84 removed outlier: 6.525A pdb=" N ARG P 83 " --> pdb=" O VAL Q 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'P' and resid 118 through 119 Processing sheet with id=AC3, first strand: chain 'R' and resid 42 through 43 removed outlier: 7.003A pdb=" N ARG R 42 " --> pdb=" O ILE S 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'R' and resid 77 through 78 Processing sheet with id=AC5, first strand: chain 'V' and resid 206 through 208 removed outlier: 5.865A pdb=" N PHE V 230 " --> pdb=" O ALA V 323 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N GLU V 325 " --> pdb=" O PHE V 230 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N LEU V 232 " --> pdb=" O GLU V 325 " (cutoff:3.500A) removed outlier: 9.334A pdb=" N LEU V 322 " --> pdb=" O PRO V 361 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N TYR V 358 " --> pdb=" O SER V 378 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'V' and resid 296 through 298 removed outlier: 3.602A pdb=" N ILE V 297 " --> pdb=" O LEU V 311 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU V 311 " --> pdb=" O ILE V 297 " (cutoff:3.500A) 1092 hydrogen bonds defined for protein. 3222 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 728 hydrogen bonds 1448 hydrogen bond angles 0 basepair planarities 286 basepair parallelities 510 stacking parallelities Total time for adding SS restraints: 9.06 Time building geometry restraints manager: 3.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5214 1.33 - 1.45: 10194 1.45 - 1.57: 14790 1.57 - 1.69: 1172 1.69 - 1.81: 88 Bond restraints: 31458 Sorted by residual: bond pdb=" C3' DG T 20 " pdb=" O3' DG T 20 " ideal model delta sigma weight residual 1.422 1.485 -0.063 3.00e-02 1.11e+03 4.35e+00 bond pdb=" C3' DC U 6 " pdb=" O3' DC U 6 " ideal model delta sigma weight residual 1.422 1.360 0.062 3.00e-02 1.11e+03 4.32e+00 bond pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " ideal model delta sigma weight residual 1.422 1.484 -0.062 3.00e-02 1.11e+03 4.24e+00 bond pdb=" C3' DC J 6 " pdb=" O3' DC J 6 " ideal model delta sigma weight residual 1.422 1.360 0.062 3.00e-02 1.11e+03 4.23e+00 bond pdb=" CA LYS V 432 " pdb=" C LYS V 432 " ideal model delta sigma weight residual 1.523 1.548 -0.025 1.30e-02 5.92e+03 3.59e+00 ... (remaining 31453 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 42531 2.02 - 4.03: 2213 4.03 - 6.05: 156 6.05 - 8.07: 41 8.07 - 10.09: 13 Bond angle restraints: 44954 Sorted by residual: angle pdb=" N LYS V 432 " pdb=" CA LYS V 432 " pdb=" C LYS V 432 " ideal model delta sigma weight residual 111.28 119.14 -7.86 1.09e+00 8.42e-01 5.19e+01 angle pdb=" N LYS K 432 " pdb=" CA LYS K 432 " pdb=" C LYS K 432 " ideal model delta sigma weight residual 111.28 119.12 -7.84 1.09e+00 8.42e-01 5.17e+01 angle pdb=" N LEU V 430 " pdb=" CA LEU V 430 " pdb=" C LEU V 430 " ideal model delta sigma weight residual 111.28 118.24 -6.96 1.09e+00 8.42e-01 4.08e+01 angle pdb=" N LYS K 427 " pdb=" CA LYS K 427 " pdb=" C LYS K 427 " ideal model delta sigma weight residual 110.35 119.03 -8.68 1.36e+00 5.41e-01 4.07e+01 angle pdb=" N LEU K 430 " pdb=" CA LEU K 430 " pdb=" C LEU K 430 " ideal model delta sigma weight residual 111.28 118.22 -6.94 1.09e+00 8.42e-01 4.06e+01 ... (remaining 44949 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.34: 14566 32.34 - 64.68: 2832 64.68 - 97.02: 74 97.02 - 129.36: 2 129.36 - 161.70: 4 Dihedral angle restraints: 17478 sinusoidal: 11068 harmonic: 6410 Sorted by residual: dihedral pdb=" CA PRO O 103 " pdb=" C PRO O 103 " pdb=" N GLY O 104 " pdb=" CA GLY O 104 " ideal model delta harmonic sigma weight residual -180.00 -150.49 -29.51 0 5.00e+00 4.00e-02 3.48e+01 dihedral pdb=" CA PRO D 103 " pdb=" C PRO D 103 " pdb=" N GLY D 104 " pdb=" CA GLY D 104 " ideal model delta harmonic sigma weight residual 180.00 -150.50 -29.50 0 5.00e+00 4.00e-02 3.48e+01 dihedral pdb=" CA PRO K 361 " pdb=" C PRO K 361 " pdb=" N LYS K 362 " pdb=" CA LYS K 362 " ideal model delta harmonic sigma weight residual 180.00 153.23 26.77 0 5.00e+00 4.00e-02 2.87e+01 ... (remaining 17475 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 3815 0.061 - 0.123: 1041 0.123 - 0.184: 172 0.184 - 0.245: 26 0.245 - 0.307: 18 Chirality restraints: 5072 Sorted by residual: chirality pdb=" C1' DC T -27 " pdb=" O4' DC T -27 " pdb=" C2' DC T -27 " pdb=" N1 DC T -27 " both_signs ideal model delta sigma weight residual False 2.47 2.16 0.31 2.00e-01 2.50e+01 2.35e+00 chirality pdb=" C1' DC I -27 " pdb=" O4' DC I -27 " pdb=" C2' DC I -27 " pdb=" N1 DC I -27 " both_signs ideal model delta sigma weight residual False 2.47 2.16 0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" C1' DT U 13 " pdb=" O4' DT U 13 " pdb=" C2' DT U 13 " pdb=" N1 DT U 13 " both_signs ideal model delta sigma weight residual False 2.47 2.17 0.30 2.00e-01 2.50e+01 2.28e+00 ... (remaining 5069 not shown) Planarity restraints: 3660 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC U 56 " 0.045 2.00e-02 2.50e+03 3.32e-02 2.48e+01 pdb=" N1 DC U 56 " -0.076 2.00e-02 2.50e+03 pdb=" C2 DC U 56 " 0.040 2.00e-02 2.50e+03 pdb=" O2 DC U 56 " -0.019 2.00e-02 2.50e+03 pdb=" N3 DC U 56 " -0.005 2.00e-02 2.50e+03 pdb=" C4 DC U 56 " 0.005 2.00e-02 2.50e+03 pdb=" N4 DC U 56 " 0.012 2.00e-02 2.50e+03 pdb=" C5 DC U 56 " -0.007 2.00e-02 2.50e+03 pdb=" C6 DC U 56 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC J 56 " -0.045 2.00e-02 2.50e+03 3.31e-02 2.47e+01 pdb=" N1 DC J 56 " 0.075 2.00e-02 2.50e+03 pdb=" C2 DC J 56 " -0.040 2.00e-02 2.50e+03 pdb=" O2 DC J 56 " 0.019 2.00e-02 2.50e+03 pdb=" N3 DC J 56 " 0.005 2.00e-02 2.50e+03 pdb=" C4 DC J 56 " -0.005 2.00e-02 2.50e+03 pdb=" N4 DC J 56 " -0.011 2.00e-02 2.50e+03 pdb=" C5 DC J 56 " 0.007 2.00e-02 2.50e+03 pdb=" C6 DC J 56 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS V 425 " 0.025 2.00e-02 2.50e+03 4.91e-02 2.41e+01 pdb=" C LYS V 425 " -0.085 2.00e-02 2.50e+03 pdb=" O LYS V 425 " 0.032 2.00e-02 2.50e+03 pdb=" N ASP V 426 " 0.029 2.00e-02 2.50e+03 ... (remaining 3657 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.25: 4 2.25 - 2.92: 10890 2.92 - 3.58: 46988 3.58 - 4.24: 80363 4.24 - 4.90: 118794 Nonbonded interactions: 257039 Sorted by model distance: nonbonded pdb=" OP1 DA U 57 " pdb=" NZ LYS V 350 " model vdw 1.593 3.120 nonbonded pdb=" OP1 DA J 57 " pdb=" NZ LYS K 350 " model vdw 1.593 3.120 nonbonded pdb=" N2 DG T 21 " pdb=" O2 DC U -21 " model vdw 2.244 2.496 nonbonded pdb=" N2 DG I 21 " pdb=" O2 DC J -21 " model vdw 2.244 2.496 nonbonded pdb=" O LYS K 362 " pdb=" OG1 THR K 374 " model vdw 2.269 3.040 ... (remaining 257034 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'L' } ncs_group { reference = chain 'B' selection = chain 'M' } ncs_group { reference = chain 'C' selection = chain 'N' } ncs_group { reference = chain 'D' selection = chain 'O' } ncs_group { reference = chain 'E' selection = chain 'P' } ncs_group { reference = chain 'F' selection = chain 'Q' } ncs_group { reference = chain 'G' selection = chain 'R' } ncs_group { reference = chain 'H' selection = chain 'S' } ncs_group { reference = chain 'I' selection = chain 'T' } ncs_group { reference = chain 'J' selection = chain 'U' } ncs_group { reference = chain 'K' selection = chain 'V' } Set up NCS constraints Number of NCS constrained groups: 11 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'L' } pdb_interpretation.ncs_group { reference = chain 'B' selection = chain 'M' } pdb_interpretation.ncs_group { reference = chain 'C' selection = chain 'N' } pdb_interpretation.ncs_group { reference = chain 'D' selection = chain 'O' } pdb_interpretation.ncs_group { reference = chain 'E' selection = chain 'P' } pdb_interpretation.ncs_group { reference = chain 'F' selection = chain 'Q' } pdb_interpretation.ncs_group { reference = chain 'G' selection = chain 'R' } pdb_interpretation.ncs_group { reference = chain 'H' selection = chain 'S' } pdb_interpretation.ncs_group { reference = chain 'I' selection = chain 'T' } pdb_interpretation.ncs_group { reference = chain 'J' selection = chain 'U' } pdb_interpretation.ncs_group { reference = chain 'K' selection = chain 'V' } Set refine NCS operators NCS operators will be refined. 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 group one per residue 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: 2.570 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: 0.030 Extract box with map and model: 0.500 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 34.680 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.040 Load rotamer database and sin/cos tables:2.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6679 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 : 0.007 0.066 31458 Z= 0.339 Angle : 0.963 10.085 44954 Z= 0.579 Chirality : 0.058 0.307 5072 Planarity : 0.009 0.065 3660 Dihedral : 24.746 161.695 13330 Min Nonbonded Distance : 1.593 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 0.11 % Allowed : 1.37 % Favored : 98.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.64 (0.14), residues: 2162 helix: -1.31 (0.11), residues: 1342 sheet: -2.27 (0.44), residues: 90 loop : -2.26 (0.19), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 53 TYR 0.035 0.004 TYR M 88 PHE 0.027 0.003 PHE V 280 TRP 0.022 0.004 TRP V 343 HIS 0.021 0.003 HIS G 82 Details of bonding type rmsd covalent geometry : bond 0.00743 (31458) covalent geometry : angle 0.96329 (44954) hydrogen bonds : bond 0.12669 ( 1820) hydrogen bonds : angle 4.93169 ( 4670) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4324 Ramachandran restraints generated. 2162 Oldfield, 0 Emsley, 2162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4324 Ramachandran restraints generated. 2162 Oldfield, 0 Emsley, 2162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 83 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0583 time to fit residues: 1.5073 Evaluate side-chains 9 residues out of total 83 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 9 time to evaluate : 0.034 Evaluate side-chains 24 residues out of total 64 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.026 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 68 ASP cc_start: 0.7929 (m-30) cc_final: 0.7542 (m-30) outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0909 time to fit residues: 2.2880 Evaluate side-chains 12 residues out of total 64 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.026 Evaluate side-chains 22 residues out of total 81 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.031 Fit side-chains REVERT: C 64 GLU cc_start: 0.8385 (tt0) cc_final: 0.7167 (mm-30) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.0362 time to fit residues: 0.9158 Evaluate side-chains 8 residues out of total 81 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 8 time to evaluate : 0.032 Evaluate side-chains 34 residues out of total 79 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 62 MET cc_start: 0.9220 (mmm) cc_final: 0.8819 (mmm) REVERT: D 73 ILE cc_start: 0.9338 (mt) cc_final: 0.9095 (tp) REVERT: D 106 LEU cc_start: 0.8729 (tt) cc_final: 0.8467 (pp) outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.0966 time to fit residues: 3.4327 Evaluate side-chains 16 residues out of total 79 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.038 Evaluate side-chains 34 residues out of total 85 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.048 Fit side-chains revert: symmetry clash REVERT: E 62 ILE cc_start: 0.8744 (mt) cc_final: 0.8428 (mm) outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.0711 time to fit residues: 2.5967 Evaluate side-chains 13 residues out of total 85 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.048 Evaluate side-chains 36 residues out of total 65 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.026 Fit side-chains revert: symmetry clash REVERT: F 24 ASP cc_start: 0.8330 (t70) cc_final: 0.7819 (t0) REVERT: F 58 LEU cc_start: 0.9662 (tp) cc_final: 0.9364 (pp) REVERT: F 66 ILE cc_start: 0.9683 (mt) cc_final: 0.9284 (pt) outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.0936 time to fit residues: 3.4958 Evaluate side-chains 22 residues out of total 65 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.027 Evaluate side-chains 30 residues out of total 81 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.034 Fit side-chains REVERT: G 56 GLU cc_start: 0.8405 (tt0) cc_final: 0.7880 (mt-10) REVERT: G 95 LYS cc_start: 0.9290 (tttt) cc_final: 0.8835 (pptt) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.0534 time to fit residues: 1.7541 Evaluate side-chains 9 residues out of total 81 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 9 time to evaluate : 0.031 Evaluate side-chains 39 residues out of total 79 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 68 ASP cc_start: 0.9050 (t0) cc_final: 0.8457 (t0) REVERT: H 71 GLU cc_start: 0.8974 (mt-10) cc_final: 0.8714 (tp30) REVERT: H 72 ARG cc_start: 0.8769 (mtt180) cc_final: 0.8249 (mtt180) REVERT: H 93 GLU cc_start: 0.9002 (mp0) cc_final: 0.8801 (mp0) REVERT: H 100 LEU cc_start: 0.8874 (mt) cc_final: 0.8673 (tt) outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.0989 time to fit residues: 4.0153 Evaluate side-chains 25 residues out of total 79 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.029 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.031 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0404 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.030 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.030 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0393 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.027 Evaluate side-chains 38 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 37 time to evaluate : 0.080 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 276 MET cc_start: 0.9516 (mmm) cc_final: 0.9128 (tmm) REVERT: K 456 ASP cc_start: 0.8401 (t0) cc_final: 0.8145 (p0) outliers start: 1 outliers final: 0 residues processed: 38 average time/residue: 0.1138 time to fit residues: 4.9013 Evaluate side-chains 15 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 0.2980 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 0.8980 chunk 111 optimal weight: 0.0570 overall best weight: 1.2502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 24 GLN C 110 ASN Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 68 GLN P 93 GLN Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 110 ASN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 49 HIS H 109 HIS Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 192 HIS V 260 ASN ** V 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.071759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.061433 restraints weight = 7412.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.061704 restraints weight = 6855.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.061944 restraints weight = 6465.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.062368 restraints weight = 6097.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.062554 restraints weight = 5744.711| |-----------------------------------------------------------------------------| r_work (final): 0.3422 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.077030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.064759 restraints weight = 3848.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.066145 restraints weight = 2951.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.067206 restraints weight = 2375.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.067816 restraints weight = 1976.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.068760 restraints weight = 1728.258| |-----------------------------------------------------------------------------| r_work (final): 0.3502 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.059930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.049253 restraints weight = 7414.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.050081 restraints weight = 5686.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.050748 restraints weight = 4627.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.051272 restraints weight = 3924.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.051712 restraints weight = 3452.592| |-----------------------------------------------------------------------------| r_work (final): 0.3150 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.069134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.057026 restraints weight = 6291.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.058229 restraints weight = 4455.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.059179 restraints weight = 3436.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.059844 restraints weight = 2787.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.060370 restraints weight = 2373.906| |-----------------------------------------------------------------------------| r_work (final): 0.3316 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.067110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.055339 restraints weight = 6972.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.056318 restraints weight = 5424.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.057133 restraints weight = 4341.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.057813 restraints weight = 3568.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.058222 restraints weight = 3004.124| |-----------------------------------------------------------------------------| r_work (final): 0.3346 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.062798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.053397 restraints weight = 4845.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.054668 restraints weight = 3300.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.055604 restraints weight = 2379.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.056287 restraints weight = 1818.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.056844 restraints weight = 1487.636| |-----------------------------------------------------------------------------| r_work (final): 0.3314 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.062112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.051156 restraints weight = 5411.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.052424 restraints weight = 3890.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.053375 restraints weight = 2964.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.054221 restraints weight = 2373.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.054855 restraints weight = 1957.775| |-----------------------------------------------------------------------------| r_work (final): 0.3303 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.069004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.056318 restraints weight = 4827.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.057815 restraints weight = 3348.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.058961 restraints weight = 2542.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.059784 restraints weight = 2036.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.060558 restraints weight = 1714.457| |-----------------------------------------------------------------------------| r_work (final): 0.3426 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.106149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.097044 restraints weight = 35739.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.097775 restraints weight = 12576.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.097979 restraints weight = 7032.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.097976 restraints weight = 6020.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.097975 restraints weight = 6024.450| |-----------------------------------------------------------------------------| r_work (final): 0.3909 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.107939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.099946 restraints weight = 35164.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.100559 restraints weight = 12578.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.100746 restraints weight = 6983.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.100768 restraints weight = 5825.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.101185 restraints weight = 5668.167| |-----------------------------------------------------------------------------| r_work (final): 0.3947 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.071041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.062534 restraints weight = 57326.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.062635 restraints weight = 55058.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.062790 restraints weight = 53464.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.062790 restraints weight = 52043.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.062790 restraints weight = 52043.337| |-----------------------------------------------------------------------------| r_work (final): 0.4020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6168 moved from start: 0.3405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 31458 Z= 0.200 Angle : 0.722 11.555 44954 Z= 0.410 Chirality : 0.040 0.265 5072 Planarity : 0.007 0.084 3660 Dihedral : 29.854 161.231 8852 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 16.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.53 % Allowed : 2.74 % Favored : 96.73 % 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 are not related in a simple way. whole: -1.15 (0.16), residues: 2162 helix: -0.07 (0.12), residues: 1390 sheet: -2.01 (0.45), residues: 88 loop : -1.88 (0.22), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 79 TYR 0.059 0.003 TYR F 98 PHE 0.022 0.002 PHE E 104 TRP 0.012 0.002 TRP V 375 HIS 0.012 0.002 HIS M 75 Details of bonding type rmsd covalent geometry : bond 0.00444 (31458) covalent geometry : angle 0.72170 (44954) hydrogen bonds : bond 0.05250 ( 1820) hydrogen bonds : angle 4.24544 ( 4670) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 83 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.022 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.0426 time to fit residues: 0.8171 Evaluate side-chains 5 residues out of total 83 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.036 Evaluate side-chains 21 residues out of total 64 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 19 time to evaluate : 0.017 Fit side-chains revert: symmetry clash REVERT: M 64 ASN cc_start: 0.9418 (m-40) cc_final: 0.9054 (m110) REVERT: M 85 ASP cc_start: 0.8018 (m-30) cc_final: 0.7259 (m-30) outliers start: 2 outliers final: 0 residues processed: 20 average time/residue: 0.0829 time to fit residues: 1.7374 Evaluate side-chains 13 residues out of total 64 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.025 Evaluate side-chains 17 residues out of total 81 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.034 Fit side-chains REVERT: C 38 ASN cc_start: 0.8870 (m110) cc_final: 0.8345 (t0) REVERT: C 64 GLU cc_start: 0.8176 (tt0) cc_final: 0.7178 (mm-30) outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.0366 time to fit residues: 0.7280 Evaluate side-chains 7 residues out of total 81 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 7 time to evaluate : 0.033 Evaluate side-chains 22 residues out of total 79 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 21 time to evaluate : 0.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 71 GLU cc_start: 0.9080 (mm-30) cc_final: 0.8602 (mm-30) REVERT: D 73 ILE cc_start: 0.9367 (mt) cc_final: 0.9126 (tp) outliers start: 1 outliers final: 1 residues processed: 22 average time/residue: 0.0564 time to fit residues: 1.3581 Evaluate side-chains 18 residues out of total 79 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 17 time to evaluate : 0.031 Evaluate side-chains 22 residues out of total 85 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 21 time to evaluate : 0.037 Fit side-chains REVERT: P 54 TYR cc_start: 0.9398 (m-80) cc_final: 0.8568 (t80) REVERT: P 90 MET cc_start: 0.9395 (mmp) cc_final: 0.9125 (mmm) REVERT: P 94 GLU cc_start: 0.7984 (tt0) cc_final: 0.7472 (pt0) REVERT: P 97 GLU cc_start: 0.9376 (mm-30) cc_final: 0.8848 (mm-30) REVERT: P 105 GLU cc_start: 0.9299 (tm-30) cc_final: 0.9005 (tm-30) outliers start: 1 outliers final: 0 residues processed: 22 average time/residue: 0.0261 time to fit residues: 0.6868 Evaluate side-chains 13 residues out of total 85 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.035 Evaluate side-chains 27 residues out of total 65 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 26 time to evaluate : 0.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 100 PHE cc_start: 0.6796 (m-80) cc_final: 0.6323 (m-80) outliers start: 1 outliers final: 0 residues processed: 27 average time/residue: 0.0738 time to fit residues: 2.0963 Evaluate side-chains 20 residues out of total 65 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.026 Evaluate side-chains 18 residues out of total 81 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.032 Fit side-chains REVERT: R 56 GLU cc_start: 0.8557 (tt0) cc_final: 0.8346 (tt0) REVERT: R 90 ASP cc_start: 0.8275 (t70) cc_final: 0.7903 (t0) REVERT: R 95 LYS cc_start: 0.9116 (tttt) cc_final: 0.8755 (pptt) outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.0531 time to fit residues: 1.0555 Evaluate side-chains 9 residues out of total 81 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 9 time to evaluate : 0.022 Evaluate side-chains 27 residues out of total 79 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.030 Fit side-chains revert: symmetry clash REVERT: H 72 ARG cc_start: 0.9206 (mtt180) cc_final: 0.8902 (mtt180) outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.0815 time to fit residues: 2.3165 Evaluate side-chains 17 residues out of total 79 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.018 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.020 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0253 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.031 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.031 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0412 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.030 Evaluate side-chains 17 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.121 Fit side-chains revert: symmetry clash REVERT: V 413 MET cc_start: 0.0767 (ptm) cc_final: 0.0464 (ptm) REVERT: V 456 ASP cc_start: 0.7725 (t0) cc_final: 0.7412 (p0) outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.1057 time to fit residues: 2.1717 Evaluate side-chains 13 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 704, in refine_xyz self.minimization_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 794, in minimization_ncs weight = real_space_weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/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-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 394, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/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-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 126, in refine minimized = mmtbx.refinement.minimization_ncs_constraints.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 424, in __init__ minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/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-2.0-5952/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-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 456, in compute_functional_and_gradients t,g = self.target_and_grads_object.target_and_gradients( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 242, in target_and_gradients t_restraints, g_restraints = restraints_target_and_grads( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 110, in restraints_target_and_grads ef = restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/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-2.0-5952/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-2.0-5952/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: 64.1028 > 50: distance: 0 - 1: 11.898 distance: 0 - 2: 14.517 distance: 3 - 4: 24.560 distance: 4 - 5: 31.308 distance: 4 - 7: 16.993 distance: 5 - 6: 13.425 distance: 5 - 14: 22.980 distance: 6 - 40: 14.673 distance: 7 - 8: 33.605 distance: 8 - 9: 15.652 distance: 9 - 10: 39.958 distance: 10 - 11: 23.902 distance: 11 - 12: 24.519 distance: 11 - 13: 40.274 distance: 14 - 15: 14.621 distance: 15 - 16: 4.930 distance: 15 - 18: 17.614 distance: 16 - 17: 16.149 distance: 16 - 22: 42.532 distance: 17 - 49: 38.931 distance: 18 - 19: 12.585 distance: 19 - 20: 18.409 distance: 19 - 21: 43.924 distance: 22 - 23: 14.567 distance: 23 - 24: 33.063 distance: 23 - 26: 48.510 distance: 24 - 25: 50.464 distance: 24 - 29: 9.350 distance: 25 - 57: 42.221 distance: 26 - 27: 17.777 distance: 26 - 28: 21.452 distance: 29 - 30: 25.186 distance: 30 - 31: 13.884 distance: 30 - 33: 11.970 distance: 31 - 32: 17.743 distance: 31 - 40: 25.374 distance: 32 - 62: 43.260 distance: 33 - 34: 50.749 distance: 34 - 35: 45.971 distance: 35 - 36: 4.097 distance: 36 - 37: 8.938 distance: 37 - 38: 12.463 distance: 37 - 39: 11.428 distance: 40 - 41: 36.702 distance: 41 - 42: 24.610 distance: 41 - 44: 19.588 distance: 42 - 43: 17.159 distance: 42 - 49: 38.493 distance: 43 - 71: 49.016 distance: 44 - 45: 42.936 distance: 45 - 46: 49.157 distance: 46 - 47: 44.638 distance: 46 - 48: 61.726 distance: 49 - 50: 12.918 distance: 50 - 51: 22.949 distance: 50 - 53: 36.891 distance: 51 - 52: 34.211 distance: 51 - 57: 56.266 distance: 53 - 54: 30.288 distance: 53 - 55: 17.131 distance: 54 - 56: 34.347 distance: 57 - 58: 9.997 distance: 58 - 59: 23.726 distance: 58 - 61: 19.417 distance: 59 - 60: 10.187 distance: 59 - 62: 33.011 distance: 62 - 63: 32.839 distance: 63 - 64: 26.939 distance: 63 - 66: 25.584 distance: 64 - 65: 22.990 distance: 64 - 71: 23.953 distance: 66 - 67: 41.794 distance: 67 - 68: 41.035 distance: 68 - 69: 33.621 distance: 68 - 70: 30.416 distance: 71 - 72: 18.383 distance: 72 - 73: 17.129 distance: 72 - 75: 14.990 distance: 73 - 74: 22.375 distance: 73 - 79: 43.472 distance: 75 - 76: 20.903 distance: 76 - 77: 28.314 distance: 76 - 78: 46.078 distance: 79 - 80: 47.245 distance: 80 - 81: 27.244 distance: 80 - 83: 21.817 distance: 81 - 82: 41.936 distance: 83 - 84: 24.786 distance: 84 - 85: 8.516 distance: 84 - 86: 14.651 distance: 85 - 87: 6.413