Starting phenix.real_space_refine on Sun Aug 24 05:25:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ru0_24692/08_2025/7ru0_24692.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ru0_24692/08_2025/7ru0_24692.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ru0_24692/08_2025/7ru0_24692.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ru0_24692/08_2025/7ru0_24692.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ru0_24692/08_2025/7ru0_24692.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ru0_24692/08_2025/7ru0_24692.map" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 6008 atoms to isotropic. 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 4 5.49 5 S 28 5.16 5 C 8044 2.51 5 N 2040 2.21 5 O 2168 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s 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: 12284 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 3049 Classifications: {'peptide': 384} Link IDs: {'PTRANS': 23, 'TRANS': 360} Chain breaks: 2 Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Restraints were copied for chains: B, C, D Time building chain proxies: 2.91, per 1000 atoms: 0.24 Number of scatterers: 12284 At special positions: 0 Unit cell: (111.282, 110.191, 113.464, 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 28 16.00 P 4 15.00 O 2168 8.00 N 2040 7.00 C 8044 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.04 Conformation dependent library (CDL) restraints added in 704.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2912 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 8 sheets defined 59.6% alpha, 3.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 11 through 36 Proline residue: A 31 - end of helix Processing helix chain 'A' and resid 43 through 56 removed outlier: 3.568A pdb=" N ALA A 50 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 89 removed outlier: 3.574A pdb=" N LEU A 89 " --> pdb=" O LEU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 112 removed outlier: 4.256A pdb=" N LEU A 106 " --> pdb=" O PRO A 103 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LEU A 107 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL A 110 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG A 111 " --> pdb=" O SER A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 122 removed outlier: 4.167A pdb=" N SER A 117 " --> pdb=" O LEU A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 158 removed outlier: 3.639A pdb=" N GLY A 142 " --> pdb=" O LEU A 138 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N PHE A 143 " --> pdb=" O SER A 139 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU A 158 " --> pdb=" O GLY A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 182 Processing helix chain 'A' and resid 193 through 223 removed outlier: 3.551A pdb=" N SER A 223 " --> pdb=" O ALA A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 246 removed outlier: 3.502A pdb=" N GLU A 234 " --> pdb=" O LEU A 230 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL A 239 " --> pdb=" O ARG A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 254 Processing helix chain 'A' and resid 256 through 266 Processing helix chain 'A' and resid 272 through 277 Processing helix chain 'A' and resid 280 through 292 Processing helix chain 'A' and resid 307 through 314 removed outlier: 3.731A pdb=" N ILE A 314 " --> pdb=" O ILE A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 402 removed outlier: 3.658A pdb=" N SER A 402 " --> pdb=" O ASP A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 417 removed outlier: 4.029A pdb=" N LEU A 414 " --> pdb=" O GLN A 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 36 Proline residue: B 31 - end of helix Processing helix chain 'B' and resid 43 through 56 removed outlier: 3.568A pdb=" N ALA B 50 " --> pdb=" O LEU B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 89 removed outlier: 3.574A pdb=" N LEU B 89 " --> pdb=" O LEU B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 112 removed outlier: 4.256A pdb=" N LEU B 106 " --> pdb=" O PRO B 103 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LEU B 107 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL B 110 " --> pdb=" O LEU B 107 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG B 111 " --> pdb=" O SER B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 122 removed outlier: 4.168A pdb=" N SER B 117 " --> pdb=" O LEU B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 158 removed outlier: 3.640A pdb=" N GLY B 142 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N PHE B 143 " --> pdb=" O SER B 139 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU B 158 " --> pdb=" O GLY B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 182 Processing helix chain 'B' and resid 193 through 223 removed outlier: 3.551A pdb=" N SER B 223 " --> pdb=" O ALA B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 246 removed outlier: 3.502A pdb=" N GLU B 234 " --> pdb=" O LEU B 230 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL B 239 " --> pdb=" O ARG B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 254 Processing helix chain 'B' and resid 256 through 266 Processing helix chain 'B' and resid 272 through 277 Processing helix chain 'B' and resid 280 through 292 Processing helix chain 'B' and resid 307 through 314 removed outlier: 3.730A pdb=" N ILE B 314 " --> pdb=" O ILE B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 402 removed outlier: 3.658A pdb=" N SER B 402 " --> pdb=" O ASP B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 417 removed outlier: 4.029A pdb=" N LEU B 414 " --> pdb=" O GLN B 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 36 Proline residue: C 31 - end of helix Processing helix chain 'C' and resid 43 through 56 removed outlier: 3.569A pdb=" N ALA C 50 " --> pdb=" O LEU C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 89 removed outlier: 3.574A pdb=" N LEU C 89 " --> pdb=" O LEU C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 112 removed outlier: 4.256A pdb=" N LEU C 106 " --> pdb=" O PRO C 103 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LEU C 107 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL C 110 " --> pdb=" O LEU C 107 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG C 111 " --> pdb=" O SER C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 122 removed outlier: 4.168A pdb=" N SER C 117 " --> pdb=" O LEU C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 158 removed outlier: 3.639A pdb=" N GLY C 142 " --> pdb=" O LEU C 138 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N PHE C 143 " --> pdb=" O SER C 139 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU C 158 " --> pdb=" O GLY C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 182 Processing helix chain 'C' and resid 193 through 223 removed outlier: 3.551A pdb=" N SER C 223 " --> pdb=" O ALA C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 246 removed outlier: 3.502A pdb=" N GLU C 234 " --> pdb=" O LEU C 230 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL C 239 " --> pdb=" O ARG C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 254 Processing helix chain 'C' and resid 256 through 266 Processing helix chain 'C' and resid 272 through 277 Processing helix chain 'C' and resid 280 through 292 Processing helix chain 'C' and resid 307 through 314 removed outlier: 3.731A pdb=" N ILE C 314 " --> pdb=" O ILE C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 402 removed outlier: 3.658A pdb=" N SER C 402 " --> pdb=" O ASP C 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 417 removed outlier: 4.028A pdb=" N LEU C 414 " --> pdb=" O GLN C 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 36 Proline residue: D 31 - end of helix Processing helix chain 'D' and resid 43 through 56 removed outlier: 3.568A pdb=" N ALA D 50 " --> pdb=" O LEU D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 89 removed outlier: 3.574A pdb=" N LEU D 89 " --> pdb=" O LEU D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 112 removed outlier: 4.256A pdb=" N LEU D 106 " --> pdb=" O PRO D 103 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LEU D 107 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL D 110 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG D 111 " --> pdb=" O SER D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 122 removed outlier: 4.168A pdb=" N SER D 117 " --> pdb=" O LEU D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 158 removed outlier: 3.640A pdb=" N GLY D 142 " --> pdb=" O LEU D 138 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N PHE D 143 " --> pdb=" O SER D 139 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU D 158 " --> pdb=" O GLY D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 182 Processing helix chain 'D' and resid 193 through 223 removed outlier: 3.550A pdb=" N SER D 223 " --> pdb=" O ALA D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 246 removed outlier: 3.502A pdb=" N GLU D 234 " --> pdb=" O LEU D 230 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL D 239 " --> pdb=" O ARG D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 254 Processing helix chain 'D' and resid 256 through 266 Processing helix chain 'D' and resid 272 through 277 Processing helix chain 'D' and resid 280 through 292 Processing helix chain 'D' and resid 307 through 314 removed outlier: 3.730A pdb=" N ILE D 314 " --> pdb=" O ILE D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 402 removed outlier: 3.658A pdb=" N SER D 402 " --> pdb=" O ASP D 398 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 417 removed outlier: 4.029A pdb=" N LEU D 414 " --> pdb=" O GLN D 410 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 319 through 322 removed outlier: 8.525A pdb=" N ASP A 388 " --> pdb=" O ASN A 342 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ASN A 342 " --> pdb=" O ASP A 388 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N PHE A 340 " --> pdb=" O TYR A 390 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 346 through 348 Processing sheet with id=AA3, first strand: chain 'B' and resid 319 through 322 removed outlier: 8.525A pdb=" N ASP B 388 " --> pdb=" O ASN B 342 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ASN B 342 " --> pdb=" O ASP B 388 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N PHE B 340 " --> pdb=" O TYR B 390 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 346 through 348 Processing sheet with id=AA5, first strand: chain 'C' and resid 319 through 322 removed outlier: 8.524A pdb=" N ASP C 388 " --> pdb=" O ASN C 342 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ASN C 342 " --> pdb=" O ASP C 388 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N PHE C 340 " --> pdb=" O TYR C 390 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 346 through 348 Processing sheet with id=AA7, first strand: chain 'D' and resid 319 through 322 removed outlier: 8.525A pdb=" N ASP D 388 " --> pdb=" O ASN D 342 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ASN D 342 " --> pdb=" O ASP D 388 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N PHE D 340 " --> pdb=" O TYR D 390 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 346 through 348 632 hydrogen bonds defined for protein. 1788 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: 1.93 Time building geometry restraints manager: 1.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3718 1.34 - 1.46: 1954 1.46 - 1.57: 6840 1.57 - 1.69: 8 1.69 - 1.81: 48 Bond restraints: 12568 Sorted by residual: bond pdb=" C SER B 157 " pdb=" N LEU B 158 " ideal model delta sigma weight residual 1.332 1.223 0.109 1.31e-02 5.83e+03 6.91e+01 bond pdb=" C SER A 157 " pdb=" N LEU A 158 " ideal model delta sigma weight residual 1.332 1.223 0.109 1.31e-02 5.83e+03 6.86e+01 bond pdb=" C SER D 157 " pdb=" N LEU D 158 " ideal model delta sigma weight residual 1.332 1.223 0.108 1.31e-02 5.83e+03 6.83e+01 bond pdb=" C SER C 157 " pdb=" N LEU C 158 " ideal model delta sigma weight residual 1.332 1.224 0.108 1.31e-02 5.83e+03 6.78e+01 bond pdb=" C LEU C 283 " pdb=" N ARG C 284 " ideal model delta sigma weight residual 1.335 1.243 0.092 1.38e-02 5.25e+03 4.44e+01 ... (remaining 12563 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 16105 2.02 - 4.03: 782 4.03 - 6.05: 125 6.05 - 8.07: 84 8.07 - 10.08: 44 Bond angle restraints: 17140 Sorted by residual: angle pdb=" O SER C 157 " pdb=" C SER C 157 " pdb=" N LEU C 158 " ideal model delta sigma weight residual 122.07 115.71 6.36 1.03e+00 9.43e-01 3.82e+01 angle pdb=" O SER B 157 " pdb=" C SER B 157 " pdb=" N LEU B 158 " ideal model delta sigma weight residual 122.07 115.71 6.36 1.03e+00 9.43e-01 3.82e+01 angle pdb=" O SER A 157 " pdb=" C SER A 157 " pdb=" N LEU A 158 " ideal model delta sigma weight residual 122.07 115.71 6.36 1.03e+00 9.43e-01 3.81e+01 angle pdb=" O SER D 157 " pdb=" C SER D 157 " pdb=" N LEU D 158 " ideal model delta sigma weight residual 122.07 115.71 6.36 1.03e+00 9.43e-01 3.81e+01 angle pdb=" N ARG B 284 " pdb=" CA ARG B 284 " pdb=" C ARG B 284 " ideal model delta sigma weight residual 111.82 105.17 6.65 1.16e+00 7.43e-01 3.29e+01 ... (remaining 17135 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.68: 7308 28.68 - 57.36: 208 57.36 - 86.03: 28 86.03 - 114.71: 0 114.71 - 143.39: 8 Dihedral angle restraints: 7552 sinusoidal: 3044 harmonic: 4508 Sorted by residual: dihedral pdb=" C5' CMP C 501 " pdb=" O5' CMP C 501 " pdb=" P CMP C 501 " pdb=" O1P CMP C 501 " ideal model delta sinusoidal sigma weight residual 60.00 -179.61 -120.39 1 2.00e+01 2.50e-03 3.61e+01 dihedral pdb=" C5' CMP D 501 " pdb=" O5' CMP D 501 " pdb=" P CMP D 501 " pdb=" O1P CMP D 501 " ideal model delta sinusoidal sigma weight residual 60.00 -179.63 -120.37 1 2.00e+01 2.50e-03 3.61e+01 dihedral pdb=" C5' CMP A 501 " pdb=" O5' CMP A 501 " pdb=" P CMP A 501 " pdb=" O1P CMP A 501 " ideal model delta sinusoidal sigma weight residual 60.00 -179.63 -120.37 1 2.00e+01 2.50e-03 3.61e+01 ... (remaining 7549 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1496 0.059 - 0.118: 448 0.118 - 0.177: 101 0.177 - 0.236: 3 0.236 - 0.295: 4 Chirality restraints: 2052 Sorted by residual: chirality pdb=" CA LYS D 298 " pdb=" N LYS D 298 " pdb=" C LYS D 298 " pdb=" CB LYS D 298 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" CA LYS B 298 " pdb=" N LYS B 298 " pdb=" C LYS B 298 " pdb=" CB LYS B 298 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" CA LYS C 298 " pdb=" N LYS C 298 " pdb=" C LYS C 298 " pdb=" CB LYS C 298 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.17e+00 ... (remaining 2049 not shown) Planarity restraints: 2100 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS A 232 " 0.016 2.00e-02 2.50e+03 3.17e-02 1.01e+01 pdb=" C HIS A 232 " -0.055 2.00e-02 2.50e+03 pdb=" O HIS A 232 " 0.020 2.00e-02 2.50e+03 pdb=" N ARG A 233 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS C 232 " -0.016 2.00e-02 2.50e+03 3.17e-02 1.00e+01 pdb=" C HIS C 232 " 0.055 2.00e-02 2.50e+03 pdb=" O HIS C 232 " -0.020 2.00e-02 2.50e+03 pdb=" N ARG C 233 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS D 232 " -0.016 2.00e-02 2.50e+03 3.15e-02 9.93e+00 pdb=" C HIS D 232 " 0.055 2.00e-02 2.50e+03 pdb=" O HIS D 232 " -0.020 2.00e-02 2.50e+03 pdb=" N ARG D 233 " -0.018 2.00e-02 2.50e+03 ... (remaining 2097 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 386 2.70 - 3.25: 12358 3.25 - 3.80: 19248 3.80 - 4.35: 23937 4.35 - 4.90: 37952 Nonbonded interactions: 93881 Sorted by model distance: nonbonded pdb=" O LEU B 158 " pdb=" CD1 LEU B 158 " model vdw 2.146 3.460 nonbonded pdb=" O LEU C 158 " pdb=" CD1 LEU C 158 " model vdw 2.147 3.460 nonbonded pdb=" O LEU D 158 " pdb=" CD1 LEU D 158 " model vdw 2.147 3.460 nonbonded pdb=" O LEU A 158 " pdb=" CD1 LEU A 158 " model vdw 2.148 3.460 nonbonded pdb=" O GLY C 293 " pdb=" NZ LYS C 298 " model vdw 2.202 3.120 ... (remaining 93876 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 12.710 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4769 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 : 0.005 0.109 12568 Z= 0.313 Angle : 1.125 10.082 17140 Z= 0.583 Chirality : 0.057 0.295 2052 Planarity : 0.007 0.049 2100 Dihedral : 14.475 143.388 4640 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % 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: -3.06 (0.20), residues: 1512 helix: -1.65 (0.15), residues: 908 sheet: -0.84 (0.58), residues: 88 loop : -2.70 (0.27), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 391 TYR 0.023 0.002 TYR A 404 PHE 0.016 0.002 PHE C 309 TRP 0.013 0.002 TRP C 264 HIS 0.024 0.003 HIS B 232 Details of bonding type rmsd covalent geometry : bond 0.00508 (12568) covalent geometry : angle 1.12538 (17140) hydrogen bonds : bond 0.16374 ( 632) hydrogen bonds : angle 6.53623 ( 1788) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 379 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 LEU cc_start: 0.8709 (mt) cc_final: 0.7996 (mt) REVERT: A 104 LEU cc_start: 0.7719 (pp) cc_final: 0.6954 (mm) REVERT: A 224 LYS cc_start: 0.1293 (tmtt) cc_final: 0.0869 (ttmt) REVERT: A 235 ARG cc_start: 0.6404 (mtp180) cc_final: 0.5637 (mmt180) REVERT: A 261 ASP cc_start: 0.7496 (m-30) cc_final: 0.7021 (m-30) REVERT: A 353 GLU cc_start: 0.8267 (tp30) cc_final: 0.8042 (tm-30) REVERT: A 390 TYR cc_start: 0.6292 (m-80) cc_final: 0.5535 (m-80) REVERT: B 40 PHE cc_start: 0.7031 (t80) cc_final: 0.6792 (t80) REVERT: B 100 LEU cc_start: 0.8651 (mt) cc_final: 0.8304 (mt) REVERT: B 312 ASP cc_start: 0.6036 (m-30) cc_final: 0.5721 (p0) REVERT: B 313 ILE cc_start: 0.6768 (pt) cc_final: 0.6559 (pt) REVERT: B 329 ILE cc_start: 0.5495 (pt) cc_final: 0.5118 (pt) REVERT: B 339 TYR cc_start: 0.4402 (m-10) cc_final: 0.3798 (m-80) REVERT: B 414 LEU cc_start: 0.6641 (tt) cc_final: 0.6232 (mm) REVERT: C 29 ARG cc_start: 0.6152 (tmt170) cc_final: 0.4951 (mpt180) REVERT: C 39 LEU cc_start: 0.7503 (mm) cc_final: 0.7277 (mp) REVERT: C 81 ARG cc_start: 0.0610 (ptt180) cc_final: 0.0184 (ptt180) REVERT: C 261 ASP cc_start: 0.7545 (m-30) cc_final: 0.6868 (m-30) REVERT: C 390 TYR cc_start: 0.5832 (m-80) cc_final: 0.5351 (m-80) REVERT: D 29 ARG cc_start: 0.6304 (tmt170) cc_final: 0.5128 (mpt180) REVERT: D 40 PHE cc_start: 0.7359 (t80) cc_final: 0.7134 (t80) REVERT: D 81 ARG cc_start: 0.0895 (ptt180) cc_final: 0.0589 (ptt180) REVERT: D 100 LEU cc_start: 0.8646 (mt) cc_final: 0.8257 (mt) REVERT: D 104 LEU cc_start: 0.7700 (pp) cc_final: 0.7010 (mm) REVERT: D 235 ARG cc_start: 0.6488 (mtp180) cc_final: 0.5768 (mmt180) REVERT: D 261 ASP cc_start: 0.7688 (m-30) cc_final: 0.7018 (m-30) REVERT: D 390 TYR cc_start: 0.6500 (m-80) cc_final: 0.5929 (m-80) outliers start: 0 outliers final: 0 residues processed: 379 average time/residue: 0.1357 time to fit residues: 70.0515 Evaluate side-chains 211 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 211 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 0.0980 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 9.9990 overall best weight: 1.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 HIS A 196 GLN A 217 ASN B 196 GLN B 217 ASN ** B 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 GLN C 196 GLN C 217 ASN C 410 GLN D 196 GLN D 217 ASN D 410 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4670 r_free = 0.4670 target = 0.252305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.227494 restraints weight = 141642.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.235184 restraints weight = 72351.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.231910 restraints weight = 65148.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.232152 restraints weight = 56376.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.231495 restraints weight = 53698.014| |-----------------------------------------------------------------------------| r_work (final): 0.4218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6081 moved from start: 0.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 12568 Z= 0.218 Angle : 0.894 10.214 17140 Z= 0.436 Chirality : 0.048 0.144 2052 Planarity : 0.007 0.055 2100 Dihedral : 12.276 176.858 1752 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 0.38 % Allowed : 8.99 % Favored : 90.62 % 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: -2.09 (0.21), residues: 1512 helix: -0.90 (0.17), residues: 924 sheet: -0.54 (0.57), residues: 88 loop : -2.27 (0.29), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 399 TYR 0.023 0.002 TYR D 357 PHE 0.018 0.002 PHE C 242 TRP 0.022 0.002 TRP B 264 HIS 0.013 0.002 HIS D 232 Details of bonding type rmsd covalent geometry : bond 0.00497 (12568) covalent geometry : angle 0.89392 (17140) hydrogen bonds : bond 0.04851 ( 632) hydrogen bonds : angle 5.22142 ( 1788) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 230 time to evaluate : 0.469 Fit side-chains revert: symmetry clash REVERT: A 104 LEU cc_start: 0.7057 (pp) cc_final: 0.5757 (mm) REVERT: A 218 ILE cc_start: 0.3513 (OUTLIER) cc_final: 0.2758 (tp) REVERT: A 261 ASP cc_start: 0.7001 (m-30) cc_final: 0.6783 (m-30) REVERT: A 368 GLU cc_start: 0.5868 (pm20) cc_final: 0.5136 (pm20) REVERT: B 410 GLN cc_start: 0.7074 (tp40) cc_final: 0.6860 (tp-100) REVERT: C 218 ILE cc_start: 0.3161 (OUTLIER) cc_final: 0.2532 (tp) REVERT: C 232 HIS cc_start: 0.5162 (t-90) cc_final: 0.4740 (t70) REVERT: D 203 ILE cc_start: 0.8210 (tp) cc_final: 0.7985 (tp) REVERT: D 218 ILE cc_start: 0.3118 (OUTLIER) cc_final: 0.2397 (tp) REVERT: D 261 ASP cc_start: 0.6814 (m-30) cc_final: 0.6587 (m-30) REVERT: D 339 TYR cc_start: 0.4578 (m-10) cc_final: 0.3968 (m-80) outliers start: 5 outliers final: 1 residues processed: 234 average time/residue: 0.1027 time to fit residues: 35.7900 Evaluate side-chains 198 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 194 time to evaluate : 0.511 ------------------------------------------------------------------------------- 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-2.0-5787/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: 68.0433 > 50: distance: 11 - 16: 29.189 distance: 16 - 17: 44.102 distance: 17 - 18: 19.149 distance: 18 - 19: 16.596 distance: 18 - 20: 21.767 distance: 20 - 21: 28.996 distance: 21 - 22: 9.733 distance: 21 - 24: 5.327 distance: 22 - 23: 36.509 distance: 22 - 28: 23.677 distance: 24 - 25: 14.929 distance: 25 - 26: 32.053 distance: 25 - 27: 38.059 distance: 28 - 29: 26.261 distance: 29 - 30: 23.683 distance: 29 - 32: 50.667 distance: 30 - 31: 28.666 distance: 30 - 35: 32.139 distance: 32 - 33: 43.310 distance: 32 - 34: 33.369 distance: 35 - 36: 31.935 distance: 36 - 37: 36.419 distance: 36 - 39: 37.067 distance: 37 - 38: 37.447 distance: 37 - 43: 42.214 distance: 39 - 40: 39.635 distance: 39 - 41: 39.721 distance: 40 - 42: 14.469 distance: 43 - 44: 27.498 distance: 44 - 45: 11.887 distance: 44 - 47: 7.434 distance: 45 - 46: 20.633 distance: 45 - 52: 33.335 distance: 47 - 48: 22.343 distance: 48 - 49: 18.300 distance: 49 - 50: 9.395 distance: 49 - 51: 14.440 distance: 52 - 53: 6.892 distance: 53 - 54: 19.489 distance: 53 - 56: 38.810 distance: 54 - 55: 21.543 distance: 54 - 61: 42.391 distance: 56 - 57: 24.901 distance: 57 - 58: 29.682 distance: 58 - 59: 43.189 distance: 59 - 60: 44.873 distance: 61 - 62: 52.242 distance: 62 - 63: 51.650 distance: 62 - 65: 42.721 distance: 63 - 64: 38.589 distance: 63 - 68: 58.375 distance: 65 - 66: 40.350 distance: 65 - 67: 43.844 distance: 68 - 69: 47.220 distance: 68 - 74: 29.588 distance: 69 - 70: 52.791 distance: 69 - 72: 58.430 distance: 70 - 71: 21.435 distance: 70 - 75: 15.444 distance: 72 - 73: 42.746 distance: 73 - 74: 19.543 distance: 75 - 76: 19.727 distance: 76 - 77: 25.406 distance: 76 - 79: 28.467 distance: 77 - 78: 50.634 distance: 77 - 83: 43.479 distance: 79 - 80: 7.191 distance: 80 - 81: 22.598 distance: 80 - 82: 19.982 distance: 83 - 84: 19.474 distance: 84 - 85: 26.825 distance: 84 - 87: 11.686 distance: 85 - 86: 25.093 distance: 85 - 94: 29.770 distance: 87 - 88: 21.075 distance: 88 - 89: 10.138 distance: 88 - 90: 13.250 distance: 89 - 91: 11.846 distance: 90 - 92: 22.971 distance: 91 - 93: 9.762 distance: 92 - 93: 18.634