Starting phenix.real_space_refine on Sat Aug 23 11:33:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ean_47837/08_2025/9ean_47837.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ean_47837/08_2025/9ean_47837.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ean_47837/08_2025/9ean_47837.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ean_47837/08_2025/9ean_47837.map" model { file = "/net/cci-nas-00/data/ceres_data/9ean_47837/08_2025/9ean_47837.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ean_47837/08_2025/9ean_47837.cif" } resolution = 2.4 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= 0.011 sd= 0.154 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: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 7603 2.51 5 N 1942 2.21 5 O 2205 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11798 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 515, 3953 Classifications: {'peptide': 515} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 44, 'TRANS': 468} Chain: "B" Number of atoms: 3963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 516, 3963 Classifications: {'peptide': 516} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 470} Chain: "C" Number of atoms: 3882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 3882 Classifications: {'peptide': 504} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 459} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.40, per 1000 atoms: 0.29 Number of scatterers: 11798 At special positions: 0 Unit cell: (119.9, 116.6, 122.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 48 16.00 O 2205 8.00 N 1942 7.00 C 7603 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: 0.92 Conformation dependent library (CDL) restraints added in 697.6 milliseconds Enol-peptide restraints added in 1.2 microseconds 3058 Ramachandran restraints generated. 1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2842 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 19 sheets defined 9.7% alpha, 36.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 37 through 42 removed outlier: 3.500A pdb=" N ALA A 41 " --> pdb=" O GLY A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 45 No H-bonds generated for 'chain 'A' and resid 43 through 45' Processing helix chain 'A' and resid 52 through 58 removed outlier: 3.926A pdb=" N ASN A 58 " --> pdb=" O ILE A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 88 Processing helix chain 'A' and resid 89 through 96 Processing helix chain 'A' and resid 97 through 99 No H-bonds generated for 'chain 'A' and resid 97 through 99' Processing helix chain 'A' and resid 139 through 144 removed outlier: 3.846A pdb=" N THR A 142 " --> pdb=" O ALA A 139 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N PHE A 144 " --> pdb=" O ILE A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 240 Processing helix chain 'B' and resid 41 through 45 Processing helix chain 'B' and resid 52 through 57 Processing helix chain 'B' and resid 85 through 88 removed outlier: 3.520A pdb=" N LEU B 88 " --> pdb=" O GLY B 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 85 through 88' Processing helix chain 'B' and resid 89 through 96 Processing helix chain 'B' and resid 97 through 99 No H-bonds generated for 'chain 'B' and resid 97 through 99' Processing helix chain 'B' and resid 140 through 144 Processing helix chain 'B' and resid 236 through 240 Processing helix chain 'B' and resid 454 through 465 Processing helix chain 'C' and resid 37 through 42 Processing helix chain 'C' and resid 43 through 45 No H-bonds generated for 'chain 'C' and resid 43 through 45' Processing helix chain 'C' and resid 52 through 58 removed outlier: 3.936A pdb=" N ASN C 58 " --> pdb=" O ILE C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 88 Processing helix chain 'C' and resid 89 through 96 Processing helix chain 'C' and resid 97 through 99 No H-bonds generated for 'chain 'C' and resid 97 through 99' Processing helix chain 'C' and resid 137 through 142 removed outlier: 3.933A pdb=" N THR C 142 " --> pdb=" O THR C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 240 Processing helix chain 'C' and resid 282 through 286 removed outlier: 3.788A pdb=" N VAL C 286 " --> pdb=" O GLY C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 465 Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 69 removed outlier: 12.796A pdb=" N GLN A 61 " --> pdb=" O PRO A 209 " (cutoff:3.500A) removed outlier: 10.927A pdb=" N SER A 207 " --> pdb=" O PRO A 63 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N GLY A 65 " --> pdb=" O LEU A 205 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N SER A 202 " --> pdb=" O ALA A 113 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N ASN A 105 " --> pdb=" O ALA A 210 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N ASP A 212 " --> pdb=" O VAL A 103 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N VAL A 103 " --> pdb=" O ASP A 212 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N ASN A 214 " --> pdb=" O GLY A 101 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N GLY A 101 " --> pdb=" O ASN A 214 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 60 through 69 removed outlier: 12.796A pdb=" N GLN A 61 " --> pdb=" O PRO A 209 " (cutoff:3.500A) removed outlier: 10.927A pdb=" N SER A 207 " --> pdb=" O PRO A 63 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N GLY A 65 " --> pdb=" O LEU A 205 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N SER A 202 " --> pdb=" O ALA A 113 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N ASN A 105 " --> pdb=" O ALA A 210 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N ASP A 212 " --> pdb=" O VAL A 103 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N VAL A 103 " --> pdb=" O ASP A 212 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N ASN A 214 " --> pdb=" O GLY A 101 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N GLY A 101 " --> pdb=" O ASN A 214 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 78 through 83 removed outlier: 7.273A pdb=" N ILE A 78 " --> pdb=" O LEU A 185 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N LEU A 185 " --> pdb=" O ILE A 78 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LYS A 121 " --> pdb=" O TYR A 186 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N ALA A 119 " --> pdb=" O PRO A 188 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 448 through 451 Processing sheet with id=AA5, first strand: chain 'A' and resid 448 through 451 removed outlier: 5.409A pdb=" N ILE A 497 " --> pdb=" O LEU A 430 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N SER A 500 " --> pdb=" O GLU A 488 " (cutoff:3.500A) removed outlier: 8.529A pdb=" N GLU A 488 " --> pdb=" O SER A 500 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE A 487 " --> pdb=" O TYR A 477 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ALA A 472 " --> pdb=" O TRP A 520 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N TRP A 520 " --> pdb=" O ALA A 472 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N LEU A 474 " --> pdb=" O VAL A 518 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 350 through 358 removed outlier: 6.964A pdb=" N SER A 332 " --> pdb=" O PHE A 401 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N PHE A 401 " --> pdb=" O SER A 332 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N GLU A 338 " --> pdb=" O PRO A 395 " (cutoff:3.500A) removed outlier: 8.879A pdb=" N GLN A 340 " --> pdb=" O ALA A 393 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N ALA A 393 " --> pdb=" O GLN A 340 " (cutoff:3.500A) removed outlier: 11.376A pdb=" N GLU A 342 " --> pdb=" O VAL A 391 " (cutoff:3.500A) removed outlier: 11.259A pdb=" N VAL A 391 " --> pdb=" O GLU A 342 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLY A 389 " --> pdb=" O ALA A 293 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ALA A 290 " --> pdb=" O ILE A 310 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 60 through 69 removed outlier: 6.809A pdb=" N LEU B 205 " --> pdb=" O CYS B 62 " (cutoff:3.500A) removed outlier: 9.922A pdb=" N LEU B 64 " --> pdb=" O GLY B 203 " (cutoff:3.500A) removed outlier: 10.131A pdb=" N GLY B 203 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 10.085A pdb=" N GLU B 66 " --> pdb=" O VAL B 201 " (cutoff:3.500A) removed outlier: 11.626A pdb=" N VAL B 201 " --> pdb=" O GLU B 66 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 78 through 83 removed outlier: 6.823A pdb=" N CYS B 183 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ASP B 81 " --> pdb=" O LEU B 181 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N LEU B 181 " --> pdb=" O ASP B 81 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LYS B 121 " --> pdb=" O TYR B 186 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ALA B 119 " --> pdb=" O PRO B 188 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 102 through 103 Processing sheet with id=AB1, first strand: chain 'B' and resid 447 through 451 removed outlier: 4.548A pdb=" N GLU B 447 " --> pdb=" O MET B 436 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N LEU B 252 " --> pdb=" O PHE B 509 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 289 through 298 removed outlier: 4.119A pdb=" N ALA B 290 " --> pdb=" O ILE B 310 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N PHE B 375 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N ILE B 358 " --> pdb=" O PHE B 375 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N GLN B 334 " --> pdb=" O GLY B 400 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N GLY B 400 " --> pdb=" O GLN B 334 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N GLU B 336 " --> pdb=" O ILE B 398 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N ILE B 398 " --> pdb=" O GLU B 336 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N GLU B 338 " --> pdb=" O ARG B 396 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N ARG B 396 " --> pdb=" O GLU B 338 " (cutoff:3.500A) removed outlier: 8.538A pdb=" N GLN B 340 " --> pdb=" O VAL B 394 " (cutoff:3.500A) removed outlier: 9.886A pdb=" N VAL B 394 " --> pdb=" O GLN B 340 " (cutoff:3.500A) removed outlier: 11.411A pdb=" N GLU B 342 " --> pdb=" O ARG B 392 " (cutoff:3.500A) removed outlier: 13.296A pdb=" N ARG B 392 " --> pdb=" O GLU B 342 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 427 through 429 removed outlier: 5.337A pdb=" N SER B 500 " --> pdb=" O GLU B 488 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N GLU B 488 " --> pdb=" O SER B 500 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N TYR B 477 " --> pdb=" O LEU B 486 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLU B 488 " --> pdb=" O LEU B 475 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU B 475 " --> pdb=" O GLU B 488 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N LYS B 490 " --> pdb=" O LEU B 473 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LEU B 473 " --> pdb=" O LYS B 490 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER B 519 " --> pdb=" O LEU B 474 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ARG B 476 " --> pdb=" O VAL B 517 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N VAL B 517 " --> pdb=" O ARG B 476 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ARG B 478 " --> pdb=" O PHE B 515 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N PHE B 515 " --> pdb=" O ARG B 478 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 60 through 69 removed outlier: 12.743A pdb=" N GLN C 61 " --> pdb=" O PRO C 209 " (cutoff:3.500A) removed outlier: 9.752A pdb=" N SER C 207 " --> pdb=" O PRO C 63 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N GLY C 65 " --> pdb=" O LEU C 205 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N SER C 202 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N ASN C 105 " --> pdb=" O ALA C 210 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N ASP C 212 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N VAL C 103 " --> pdb=" O ASP C 212 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N ASN C 214 " --> pdb=" O GLY C 101 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N GLY C 101 " --> pdb=" O ASN C 214 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 60 through 69 removed outlier: 12.743A pdb=" N GLN C 61 " --> pdb=" O PRO C 209 " (cutoff:3.500A) removed outlier: 9.752A pdb=" N SER C 207 " --> pdb=" O PRO C 63 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N GLY C 65 " --> pdb=" O LEU C 205 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N SER C 202 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N ASN C 105 " --> pdb=" O ALA C 210 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N ASP C 212 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N VAL C 103 " --> pdb=" O ASP C 212 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N ASN C 214 " --> pdb=" O GLY C 101 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N GLY C 101 " --> pdb=" O ASN C 214 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 78 through 83 removed outlier: 6.497A pdb=" N CYS C 183 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ASP C 81 " --> pdb=" O LEU C 181 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N LEU C 181 " --> pdb=" O ASP C 81 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N LYS C 121 " --> pdb=" O TYR C 186 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 448 through 451 removed outlier: 4.640A pdb=" N LEU C 252 " --> pdb=" O PHE C 509 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 289 through 296 removed outlier: 4.362A pdb=" N ALA C 290 " --> pdb=" O ILE C 310 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N PHE C 375 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N ILE C 358 " --> pdb=" O PHE C 375 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE C 337 " --> pdb=" O PHE C 355 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N SER C 332 " --> pdb=" O PHE C 401 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N PHE C 401 " --> pdb=" O SER C 332 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N SER C 397 " --> pdb=" O GLU C 336 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N GLU C 338 " --> pdb=" O PRO C 395 " (cutoff:3.500A) removed outlier: 8.832A pdb=" N GLN C 340 " --> pdb=" O ALA C 393 " (cutoff:3.500A) removed outlier: 8.432A pdb=" N ALA C 393 " --> pdb=" O GLN C 340 " (cutoff:3.500A) removed outlier: 11.310A pdb=" N GLU C 342 " --> pdb=" O VAL C 391 " (cutoff:3.500A) removed outlier: 10.962A pdb=" N VAL C 391 " --> pdb=" O GLU C 342 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE C 289 " --> pdb=" O ALA C 393 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 427 through 429 removed outlier: 7.018A pdb=" N TYR C 477 " --> pdb=" O LEU C 486 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 427 through 429 removed outlier: 3.856A pdb=" N ALA C 472 " --> pdb=" O VAL C 521 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER C 519 " --> pdb=" O LEU C 474 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ARG C 476 " --> pdb=" O VAL C 517 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N VAL C 517 " --> pdb=" O ARG C 476 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N ARG C 478 " --> pdb=" O PHE C 515 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N PHE C 515 " --> pdb=" O ARG C 478 " (cutoff:3.500A) 341 hydrogen bonds defined for protein. 843 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: 2.18 Time building geometry restraints manager: 1.29 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: 3365 1.33 - 1.45: 2116 1.45 - 1.58: 6571 1.58 - 1.70: 0 1.70 - 1.82: 72 Bond restraints: 12124 Sorted by residual: bond pdb=" C ASP B 231 " pdb=" N LEU B 232 " ideal model delta sigma weight residual 1.327 1.275 0.052 1.71e-02 3.42e+03 9.14e+00 bond pdb=" CB ASN B 192 " pdb=" CG ASN B 192 " ideal model delta sigma weight residual 1.516 1.473 0.043 2.50e-02 1.60e+03 2.98e+00 bond pdb=" CB ASN A 115 " pdb=" CG ASN A 115 " ideal model delta sigma weight residual 1.516 1.473 0.043 2.50e-02 1.60e+03 2.91e+00 bond pdb=" CB THR C 191 " pdb=" CG2 THR C 191 " ideal model delta sigma weight residual 1.521 1.468 0.053 3.30e-02 9.18e+02 2.59e+00 bond pdb=" CB PRO B 23 " pdb=" CG PRO B 23 " ideal model delta sigma weight residual 1.492 1.571 -0.079 5.00e-02 4.00e+02 2.51e+00 ... (remaining 12119 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.93: 16391 2.93 - 5.86: 213 5.86 - 8.78: 18 8.78 - 11.71: 1 11.71 - 14.64: 1 Bond angle restraints: 16624 Sorted by residual: angle pdb=" N GLY A 104 " pdb=" CA GLY A 104 " pdb=" C GLY A 104 " ideal model delta sigma weight residual 111.63 118.63 -7.00 1.15e+00 7.56e-01 3.71e+01 angle pdb=" N GLY B 104 " pdb=" CA GLY B 104 " pdb=" C GLY B 104 " ideal model delta sigma weight residual 111.63 117.98 -6.35 1.15e+00 7.56e-01 3.05e+01 angle pdb=" CA VAL C 216 " pdb=" C VAL C 216 " pdb=" N TYR C 217 " ideal model delta sigma weight residual 117.37 120.72 -3.35 7.40e-01 1.83e+00 2.05e+01 angle pdb=" C GLY C 347 " pdb=" N GLU C 348 " pdb=" CA GLU C 348 " ideal model delta sigma weight residual 121.54 130.13 -8.59 1.91e+00 2.74e-01 2.02e+01 angle pdb=" C PHE C 215 " pdb=" N VAL C 216 " pdb=" CA VAL C 216 " ideal model delta sigma weight residual 122.97 118.76 4.21 9.80e-01 1.04e+00 1.84e+01 ... (remaining 16619 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 6212 17.95 - 35.91: 698 35.91 - 53.86: 208 53.86 - 71.82: 53 71.82 - 89.77: 21 Dihedral angle restraints: 7192 sinusoidal: 2761 harmonic: 4431 Sorted by residual: dihedral pdb=" CA GLY B 195 " pdb=" C GLY B 195 " pdb=" N ASP B 196 " pdb=" CA ASP B 196 " ideal model delta harmonic sigma weight residual 180.00 152.13 27.87 0 5.00e+00 4.00e-02 3.11e+01 dihedral pdb=" CA GLY A 421 " pdb=" C GLY A 421 " pdb=" N PRO A 422 " pdb=" CA PRO A 422 " ideal model delta harmonic sigma weight residual 0.00 -27.43 27.43 0 5.00e+00 4.00e-02 3.01e+01 dihedral pdb=" CA SER B 17 " pdb=" C SER B 17 " pdb=" N GLY B 18 " pdb=" CA GLY B 18 " ideal model delta harmonic sigma weight residual -180.00 -153.96 -26.04 0 5.00e+00 4.00e-02 2.71e+01 ... (remaining 7189 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1272 0.048 - 0.095: 454 0.095 - 0.143: 152 0.143 - 0.191: 9 0.191 - 0.238: 4 Chirality restraints: 1891 Sorted by residual: chirality pdb=" CA PRO B 23 " pdb=" N PRO B 23 " pdb=" C PRO B 23 " pdb=" CB PRO B 23 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CA ASP B 196 " pdb=" N ASP B 196 " pdb=" C ASP B 196 " pdb=" CB ASP B 196 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CB VAL A 103 " pdb=" CA VAL A 103 " pdb=" CG1 VAL A 103 " pdb=" CG2 VAL A 103 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 1888 not shown) Planarity restraints: 2178 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 22 " -0.096 5.00e-02 4.00e+02 1.44e-01 3.33e+01 pdb=" N PRO B 23 " 0.250 5.00e-02 4.00e+02 pdb=" CA PRO B 23 " -0.079 5.00e-02 4.00e+02 pdb=" CD PRO B 23 " -0.074 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU B 471 " -0.015 2.00e-02 2.50e+03 3.02e-02 9.13e+00 pdb=" CD GLU B 471 " 0.052 2.00e-02 2.50e+03 pdb=" OE1 GLU B 471 " -0.019 2.00e-02 2.50e+03 pdb=" OE2 GLU B 471 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS B 62 " 0.040 5.00e-02 4.00e+02 6.06e-02 5.87e+00 pdb=" N PRO B 63 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO B 63 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 63 " 0.034 5.00e-02 4.00e+02 ... (remaining 2175 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 112 2.65 - 3.21: 9660 3.21 - 3.78: 16935 3.78 - 4.34: 23891 4.34 - 4.90: 39530 Nonbonded interactions: 90128 Sorted by model distance: nonbonded pdb=" ND2 ASN B 49 " pdb=" O VAL B 216 " model vdw 2.091 3.120 nonbonded pdb=" NH1 ARG C 244 " pdb=" OD2 ASP C 330 " model vdw 2.248 3.120 nonbonded pdb=" ND1 HIS B 270 " pdb=" OD1 ASP B 272 " model vdw 2.256 3.120 nonbonded pdb=" O ILE C 358 " pdb=" NE2 GLN C 367 " model vdw 2.262 3.120 nonbonded pdb=" O SER A 198 " pdb=" OG SER A 198 " model vdw 2.264 3.040 ... (remaining 90123 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 529 or (resid 530 and (name N or name CA or nam \ e C or name O or name CB or name CG2)))) selection = (chain 'B' and (resid 27 through 529 or (resid 530 and (name N or name CA or nam \ e C or name O or name CB or name CG2)))) selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 16.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.300 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: -0.0238 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 : 0.006 0.079 12124 Z= 0.251 Angle : 0.843 14.641 16624 Z= 0.466 Chirality : 0.053 0.238 1891 Planarity : 0.007 0.144 2178 Dihedral : 17.817 89.770 4350 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.49 % Favored : 94.31 % Rotamer: Outliers : 2.75 % Allowed : 26.91 % Favored : 70.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.24 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.84 (0.20), residues: 1529 helix: -0.54 (0.63), residues: 50 sheet: -0.10 (0.23), residues: 449 loop : -0.77 (0.18), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 152 TYR 0.032 0.003 TYR C 217 PHE 0.022 0.003 PHE A 289 TRP 0.015 0.002 TRP B 102 HIS 0.007 0.003 HIS B 270 Details of bonding type rmsd covalent geometry : bond 0.00576 (12124) covalent geometry : angle 0.84297 (16624) hydrogen bonds : bond 0.17408 ( 305) hydrogen bonds : angle 7.57402 ( 843) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3058 Ramachandran restraints generated. 1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3058 Ramachandran restraints generated. 1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 95 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 366 ASP cc_start: 0.1673 (p0) cc_final: 0.1230 (m-30) REVERT: C 95 LEU cc_start: 0.1607 (OUTLIER) cc_final: 0.1358 (mt) outliers start: 35 outliers final: 15 residues processed: 125 average time/residue: 0.4806 time to fit residues: 66.2756 Evaluate side-chains 64 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 48 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 270 HIS Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain B residue 512 ASP Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 374 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 60.3272 > 50: distance: 37 - 42: 25.611 distance: 42 - 43: 28.577 distance: 43 - 44: 31.401 distance: 44 - 45: 40.643 distance: 44 - 46: 8.934 distance: 46 - 47: 29.821 distance: 47 - 48: 34.561 distance: 47 - 50: 4.262 distance: 48 - 49: 25.259 distance: 48 - 55: 34.775 distance: 50 - 51: 21.684 distance: 51 - 52: 43.461 distance: 52 - 53: 30.825 distance: 52 - 54: 39.190 distance: 55 - 56: 50.751 distance: 56 - 57: 56.238 distance: 56 - 59: 6.995 distance: 57 - 58: 43.431 distance: 57 - 63: 19.030 distance: 59 - 60: 45.728 distance: 59 - 61: 52.562 distance: 60 - 62: 27.914 distance: 63 - 64: 18.089 distance: 63 - 203: 20.740 distance: 64 - 65: 21.448 distance: 64 - 67: 27.596 distance: 65 - 66: 37.397 distance: 65 - 71: 29.194 distance: 67 - 68: 29.761 distance: 68 - 69: 21.147 distance: 68 - 70: 18.022 distance: 71 - 72: 14.343 distance: 72 - 73: 20.803 distance: 72 - 75: 9.358 distance: 73 - 74: 29.754 distance: 73 - 82: 22.892 distance: 75 - 76: 11.304 distance: 76 - 77: 7.722 distance: 76 - 78: 5.632 distance: 77 - 79: 10.220 distance: 78 - 80: 10.255 distance: 79 - 81: 13.625 distance: 80 - 81: 11.150 distance: 82 - 83: 16.969 distance: 83 - 84: 31.686 distance: 83 - 86: 27.019 distance: 84 - 85: 43.035 distance: 84 - 90: 36.191 distance: 86 - 87: 34.867 distance: 87 - 88: 27.396 distance: 87 - 89: 22.868 distance: 90 - 91: 10.479 distance: 91 - 92: 7.572 distance: 91 - 94: 8.906 distance: 92 - 93: 21.659 distance: 92 - 98: 18.005 distance: 94 - 95: 11.258 distance: 95 - 96: 3.264 distance: 95 - 97: 9.510 distance: 98 - 99: 18.531 distance: 99 - 100: 20.398 distance: 99 - 102: 35.732 distance: 100 - 101: 47.692 distance: 100 - 103: 19.544 distance: 103 - 104: 12.868 distance: 104 - 105: 26.692 distance: 104 - 107: 16.099 distance: 105 - 106: 30.489 distance: 105 - 111: 18.785 distance: 107 - 108: 26.794 distance: 108 - 109: 15.036 distance: 108 - 110: 17.167 distance: 111 - 112: 43.148 distance: 112 - 113: 27.047 distance: 113 - 114: 6.311 distance: 113 - 115: 14.048 distance: 114 - 125: 9.868