Starting phenix.real_space_refine on Sat Aug 23 11:54:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xrb_38601/08_2025/8xrb_38601.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xrb_38601/08_2025/8xrb_38601.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8xrb_38601/08_2025/8xrb_38601.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xrb_38601/08_2025/8xrb_38601.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xrb_38601/08_2025/8xrb_38601.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xrb_38601/08_2025/8xrb_38601.map" } resolution = 2.49 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.025 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 72 5.16 5 C 7446 2.51 5 N 2035 2.21 5 O 2351 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 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: 11904 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 3930 Classifications: {'peptide': 497} Link IDs: {'PTRANS': 19, 'TRANS': 477} Chain: "B" Number of atoms: 3909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 3909 Classifications: {'peptide': 494} Link IDs: {'PTRANS': 19, 'TRANS': 474} Chain breaks: 1 Chain: "C" Number of atoms: 3883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3883 Classifications: {'peptide': 491} Link IDs: {'PTRANS': 19, 'TRANS': 471} Chain breaks: 1 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 2.98, per 1000 atoms: 0.25 Number of scatterers: 11904 At special positions: 0 Unit cell: (91.8, 86.7, 149.6, 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 72 16.00 O 2351 8.00 N 2035 7.00 C 7446 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 9 " - pdb=" SG CYS A 467 " distance=2.04 Simple disulfide: pdb=" SG CYS A 47 " - pdb=" SG CYS A 278 " distance=2.03 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 72 " distance=2.03 Simple disulfide: pdb=" SG CYS A 95 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 306 " distance=2.03 Simple disulfide: pdb=" SG CYS A 474 " - pdb=" SG CYS A 478 " distance=2.03 Simple disulfide: pdb=" SG CYS B 9 " - pdb=" SG CYS B 467 " distance=2.04 Simple disulfide: pdb=" SG CYS B 47 " - pdb=" SG CYS B 278 " distance=2.02 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 72 " distance=2.03 Simple disulfide: pdb=" SG CYS B 95 " - pdb=" SG CYS B 139 " distance=2.03 Simple disulfide: pdb=" SG CYS B 282 " - pdb=" SG CYS B 306 " distance=2.03 Simple disulfide: pdb=" SG CYS B 474 " - pdb=" SG CYS B 478 " distance=2.03 Simple disulfide: pdb=" SG CYS C 9 " - pdb=" SG CYS C 467 " distance=2.04 Simple disulfide: pdb=" SG CYS C 47 " - pdb=" SG CYS C 278 " distance=2.03 Simple disulfide: pdb=" SG CYS C 60 " - pdb=" SG CYS C 72 " distance=2.03 Simple disulfide: pdb=" SG CYS C 95 " - pdb=" SG CYS C 139 " distance=2.03 Simple disulfide: pdb=" SG CYS C 282 " - pdb=" SG CYS C 306 " distance=2.03 Simple disulfide: pdb=" SG CYS C 474 " - pdb=" SG CYS C 478 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A 701 " - " ASN A 28 " " NAG A 702 " - " ASN A 290 " " NAG A 703 " - " ASN A 16 " " NAG B 701 " - " ASN B 28 " " NAG B 702 " - " ASN B 290 " " NAG C 701 " - " ASN C 28 " " NAG C 702 " - " ASN C 290 " " NAG D 1 " - " ASN A 169 " " NAG E 1 " - " ASN B 169 " " NAG F 1 " - " ASN C 169 " Time building additional restraints: 1.02 Conformation dependent library (CDL) restraints added in 580.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2704 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 33 sheets defined 27.5% alpha, 22.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 61 through 68 Processing helix chain 'A' and resid 72 through 76 removed outlier: 3.716A pdb=" N LEU A 75 " --> pdb=" O CYS A 72 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU A 76 " --> pdb=" O ASP A 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 72 through 76' Processing helix chain 'A' and resid 102 through 111 Processing helix chain 'A' and resid 123 through 127 removed outlier: 3.959A pdb=" N TRP A 127 " --> pdb=" O LYS A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 196 Processing helix chain 'A' and resid 367 through 389 removed outlier: 3.940A pdb=" N THR A 371 " --> pdb=" O ASP A 367 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N MET A 389 " --> pdb=" O VAL A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 457 Processing helix chain 'A' and resid 475 through 485 Processing helix chain 'A' and resid 488 through 491 removed outlier: 3.723A pdb=" N LYS A 491 " --> pdb=" O ASP A 488 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 488 through 491' Processing helix chain 'A' and resid 492 through 502 removed outlier: 3.757A pdb=" N GLU A 502 " --> pdb=" O LEU A 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 68 Processing helix chain 'B' and resid 72 through 76 removed outlier: 3.589A pdb=" N LEU B 75 " --> pdb=" O CYS B 72 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU B 76 " --> pdb=" O ASP B 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 72 through 76' Processing helix chain 'B' and resid 102 through 111 Processing helix chain 'B' and resid 123 through 127 removed outlier: 3.565A pdb=" N TRP B 127 " --> pdb=" O LYS B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 195 Processing helix chain 'B' and resid 368 through 388 Processing helix chain 'B' and resid 404 through 457 Processing helix chain 'B' and resid 475 through 485 Processing helix chain 'B' and resid 492 through 502 removed outlier: 3.845A pdb=" N SER B 496 " --> pdb=" O TYR B 492 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU B 502 " --> pdb=" O LEU B 498 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 68 Processing helix chain 'C' and resid 69 through 76 removed outlier: 3.714A pdb=" N ASP C 73 " --> pdb=" O PRO C 70 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N ARG C 74 " --> pdb=" O GLU C 71 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU C 75 " --> pdb=" O CYS C 72 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU C 76 " --> pdb=" O ASP C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 111 Processing helix chain 'C' and resid 123 through 127 removed outlier: 3.640A pdb=" N TRP C 127 " --> pdb=" O LYS C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 196 Processing helix chain 'C' and resid 369 through 388 Processing helix chain 'C' and resid 404 through 456 Processing helix chain 'C' and resid 475 through 484 removed outlier: 3.507A pdb=" N MET C 479 " --> pdb=" O ASP C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 493 through 500 Processing sheet with id=AA1, first strand: chain 'A' and resid 362 through 363 removed outlier: 3.508A pdb=" N GLN A 7 " --> pdb=" O SER A 357 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ILE A 8 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N PHE A 468 " --> pdb=" O ILE A 8 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 11 through 12 removed outlier: 3.565A pdb=" N GLY A 11 " --> pdb=" O GLY A 353 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 20 through 21 Processing sheet with id=AA4, first strand: chain 'A' and resid 34 through 36 Processing sheet with id=AA5, first strand: chain 'A' and resid 38 through 39 Processing sheet with id=AA6, first strand: chain 'A' and resid 46 through 49 removed outlier: 6.249A pdb=" N LEU A 46 " --> pdb=" O GLU A 276 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N CYS A 278 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS A 48 " --> pdb=" O CYS A 278 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 55 through 56 removed outlier: 6.587A pdb=" N LEU A 55 " --> pdb=" O MET A 85 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILE A 84 " --> pdb=" O MET A 269 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 98 through 100 removed outlier: 5.607A pdb=" N ILE A 179 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N TYR A 256 " --> pdb=" O ILE A 179 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 98 through 100 removed outlier: 7.969A pdb=" N ILE A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 136 through 141 removed outlier: 7.898A pdb=" N ALA A 138 " --> pdb=" O ASN A 144 " (cutoff:3.500A) removed outlier: 10.235A pdb=" N ASN A 144 " --> pdb=" O ALA A 138 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 164 through 169 Processing sheet with id=AB3, first strand: chain 'A' and resid 288 through 289 removed outlier: 3.701A pdb=" N ILE A 289 " --> pdb=" O CYS A 282 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N CYS A 282 " --> pdb=" O ILE A 289 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 362 through 363 removed outlier: 3.648A pdb=" N GLY B 11 " --> pdb=" O GLY B 353 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN B 7 " --> pdb=" O SER B 357 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ILE B 8 " --> pdb=" O PHE B 468 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N PHE B 468 " --> pdb=" O ILE B 8 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 20 through 21 Processing sheet with id=AB6, first strand: chain 'B' and resid 34 through 36 Processing sheet with id=AB7, first strand: chain 'B' and resid 38 through 39 Processing sheet with id=AB8, first strand: chain 'B' and resid 55 through 56 removed outlier: 6.850A pdb=" N LEU B 55 " --> pdb=" O MET B 85 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ILE B 84 " --> pdb=" O MET B 269 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'B' and resid 98 through 100 removed outlier: 5.511A pdb=" N ILE B 179 " --> pdb=" O TYR B 256 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N TYR B 256 " --> pdb=" O ILE B 179 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 98 through 100 removed outlier: 8.095A pdb=" N ILE B 179 " --> pdb=" O PRO B 254 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 136 through 141 removed outlier: 7.603A pdb=" N ALA B 138 " --> pdb=" O ASN B 144 " (cutoff:3.500A) removed outlier: 10.093A pdb=" N ASN B 144 " --> pdb=" O ALA B 138 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 164 through 169 Processing sheet with id=AC4, first strand: chain 'B' and resid 288 through 289 removed outlier: 4.165A pdb=" N CYS B 282 " --> pdb=" O ILE B 289 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 362 through 363 removed outlier: 4.092A pdb=" N GLN C 7 " --> pdb=" O SER C 357 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE C 8 " --> pdb=" O PHE C 468 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N PHE C 468 " --> pdb=" O ILE C 8 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 19 through 21 removed outlier: 4.245A pdb=" N GLU C 19 " --> pdb=" O VAL C 31 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 34 through 36 Processing sheet with id=AC8, first strand: chain 'C' and resid 46 through 49 removed outlier: 6.097A pdb=" N LEU C 46 " --> pdb=" O GLU C 276 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N CYS C 278 " --> pdb=" O LEU C 46 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS C 48 " --> pdb=" O CYS C 278 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 55 through 56 removed outlier: 6.824A pdb=" N LEU C 55 " --> pdb=" O MET C 85 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ILE C 84 " --> pdb=" O MET C 269 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'C' and resid 98 through 100 removed outlier: 5.495A pdb=" N ILE C 179 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N TYR C 256 " --> pdb=" O ILE C 179 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 98 through 100 removed outlier: 7.973A pdb=" N ILE C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 136 through 141 removed outlier: 5.238A pdb=" N CYS C 139 " --> pdb=" O SER C 146 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 164 through 169 Processing sheet with id=AD5, first strand: chain 'C' and resid 288 through 289 removed outlier: 3.595A pdb=" N ILE C 289 " --> pdb=" O CYS C 282 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N CYS C 282 " --> pdb=" O ILE C 289 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 295 through 296 485 hydrogen bonds defined for protein. 1359 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: 2.21 Time building geometry restraints manager: 1.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 3938 1.35 - 1.47: 2871 1.47 - 1.59: 5240 1.59 - 1.72: 0 1.72 - 1.84: 108 Bond restraints: 12157 Sorted by residual: bond pdb=" C1 NAG B 701 " pdb=" O5 NAG B 701 " ideal model delta sigma weight residual 1.406 1.485 -0.079 2.00e-02 2.50e+03 1.57e+01 bond pdb=" C CYS C 306 " pdb=" N PRO C 307 " ideal model delta sigma weight residual 1.331 1.371 -0.039 1.21e-02 6.83e+03 1.05e+01 bond pdb=" CB CYS B 278 " pdb=" SG CYS B 278 " ideal model delta sigma weight residual 1.808 1.755 0.053 3.30e-02 9.18e+02 2.56e+00 bond pdb=" C1 NAG A 701 " pdb=" O5 NAG A 701 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.34e+00 bond pdb=" CA GLU C 305 " pdb=" CB GLU C 305 " ideal model delta sigma weight residual 1.530 1.553 -0.024 1.57e-02 4.06e+03 2.29e+00 ... (remaining 12152 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 16195 2.03 - 4.06: 217 4.06 - 6.09: 25 6.09 - 8.12: 4 8.12 - 10.15: 1 Bond angle restraints: 16442 Sorted by residual: angle pdb=" C ARG A 457 " pdb=" CA ARG A 457 " pdb=" CB ARG A 457 " ideal model delta sigma weight residual 117.23 109.77 7.46 1.36e+00 5.41e-01 3.01e+01 angle pdb=" N CYS B 47 " pdb=" CA CYS B 47 " pdb=" C CYS B 47 " ideal model delta sigma weight residual 108.24 114.76 -6.52 1.32e+00 5.74e-01 2.44e+01 angle pdb=" CA ARG A 457 " pdb=" C ARG A 457 " pdb=" N ASP A 458 " ideal model delta sigma weight residual 119.98 116.77 3.21 8.50e-01 1.38e+00 1.42e+01 angle pdb=" C ASP C 488 " pdb=" N TYR C 489 " pdb=" CA TYR C 489 " ideal model delta sigma weight residual 119.78 124.28 -4.50 1.24e+00 6.50e-01 1.31e+01 angle pdb=" N PRO C 307 " pdb=" CA PRO C 307 " pdb=" C PRO C 307 " ideal model delta sigma weight residual 111.33 116.38 -5.05 1.43e+00 4.89e-01 1.25e+01 ... (remaining 16437 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.38: 6537 24.38 - 48.76: 774 48.76 - 73.15: 142 73.15 - 97.53: 20 97.53 - 121.91: 3 Dihedral angle restraints: 7476 sinusoidal: 3238 harmonic: 4238 Sorted by residual: dihedral pdb=" CB CYS B 282 " pdb=" SG CYS B 282 " pdb=" SG CYS B 306 " pdb=" CB CYS B 306 " ideal model delta sinusoidal sigma weight residual 93.00 17.80 75.20 1 1.00e+01 1.00e-02 7.15e+01 dihedral pdb=" CB CYS A 95 " pdb=" SG CYS A 95 " pdb=" SG CYS A 139 " pdb=" CB CYS A 139 " ideal model delta sinusoidal sigma weight residual 93.00 18.58 74.42 1 1.00e+01 1.00e-02 7.02e+01 dihedral pdb=" CB CYS C 95 " pdb=" SG CYS C 95 " pdb=" SG CYS C 139 " pdb=" CB CYS C 139 " ideal model delta sinusoidal sigma weight residual 93.00 26.36 66.64 1 1.00e+01 1.00e-02 5.79e+01 ... (remaining 7473 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1351 0.044 - 0.089: 328 0.089 - 0.133: 120 0.133 - 0.178: 3 0.178 - 0.222: 1 Chirality restraints: 1803 Sorted by residual: chirality pdb=" C1 NAG B 701 " pdb=" ND2 ASN B 28 " pdb=" C2 NAG B 701 " pdb=" O5 NAG B 701 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA CYS B 47 " pdb=" N CYS B 47 " pdb=" C CYS B 47 " pdb=" CB CYS B 47 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.02e-01 chirality pdb=" CA ASP A 458 " pdb=" N ASP A 458 " pdb=" C ASP A 458 " pdb=" CB ASP A 458 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.30e-01 ... (remaining 1800 not shown) Planarity restraints: 2141 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP A 420 " 0.010 2.00e-02 2.50e+03 1.97e-02 3.90e+00 pdb=" CG ASP A 420 " -0.034 2.00e-02 2.50e+03 pdb=" OD1 ASP A 420 " 0.012 2.00e-02 2.50e+03 pdb=" OD2 ASP A 420 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 458 " 0.008 2.00e-02 2.50e+03 1.61e-02 2.59e+00 pdb=" C ASP C 458 " -0.028 2.00e-02 2.50e+03 pdb=" O ASP C 458 " 0.010 2.00e-02 2.50e+03 pdb=" N ASN C 459 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU C 293 " -0.025 5.00e-02 4.00e+02 3.84e-02 2.36e+00 pdb=" N PRO C 294 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO C 294 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 294 " -0.021 5.00e-02 4.00e+02 ... (remaining 2138 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 698 2.73 - 3.27: 10599 3.27 - 3.82: 18838 3.82 - 4.36: 22489 4.36 - 4.90: 39703 Nonbonded interactions: 92327 Sorted by model distance: nonbonded pdb=" OG1 THR A 131 " pdb=" O LYS A 156 " model vdw 2.189 3.040 nonbonded pdb=" OD1 ASN B 358 " pdb=" N ASP B 359 " model vdw 2.201 3.120 nonbonded pdb=" O SER C 142 " pdb=" OG SER C 142 " model vdw 2.244 3.040 nonbonded pdb=" NE2 GLN A 360 " pdb=" OD2 ASP A 476 " model vdw 2.245 3.120 nonbonded pdb=" OE2 GLU A 39 " pdb=" OG1 THR A 41 " model vdw 2.248 3.040 ... (remaining 92322 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 6 through 327 or resid 333 through 501 or resid 702)) selection = (chain 'B' and (resid 6 through 327 or resid 333 through 501 or resid 702)) selection = (chain 'C' and resid 6 through 701) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 12.730 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.020 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:6.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 12188 Z= 0.160 Angle : 0.583 10.150 16517 Z= 0.306 Chirality : 0.043 0.222 1803 Planarity : 0.004 0.038 2131 Dihedral : 19.636 121.908 4718 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 4.62 % Allowed : 31.43 % Favored : 63.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.03 (0.22), residues: 1472 helix: 2.64 (0.27), residues: 372 sheet: 0.16 (0.33), residues: 307 loop : -1.40 (0.20), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 91 TYR 0.011 0.001 TYR A 492 PHE 0.013 0.001 PHE C 440 TRP 0.012 0.001 TRP A 422 HIS 0.006 0.001 HIS B 356 Details of bonding type rmsd covalent geometry : bond 0.00339 (12157) covalent geometry : angle 0.56708 (16442) SS BOND : bond 0.00499 ( 18) SS BOND : angle 2.09234 ( 36) hydrogen bonds : bond 0.16476 ( 449) hydrogen bonds : angle 6.87541 ( 1359) link_BETA1-4 : bond 0.00360 ( 3) link_BETA1-4 : angle 0.80434 ( 9) link_NAG-ASN : bond 0.00370 ( 10) link_NAG-ASN : angle 2.34351 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 339 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 295 PHE cc_start: 0.8793 (m-80) cc_final: 0.8406 (m-80) REVERT: C 495 GLU cc_start: 0.6953 (tp30) cc_final: 0.6752 (tp30) outliers start: 60 outliers final: 52 residues processed: 387 average time/residue: 0.6267 time to fit residues: 260.4383 Evaluate side-chains 385 residues out of total 1298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 333 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLU Chi-restraints excluded: chain A residue 24 ILE Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 478 CYS Chi-restraints excluded: chain A residue 491 LYS Chi-restraints excluded: chain A residue 497 LYS Chi-restraints excluded: chain B residue 6 ASP Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain B residue 388 LYS Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 454 MET Chi-restraints excluded: chain B residue 459 ASN Chi-restraints excluded: chain B residue 468 PHE Chi-restraints excluded: chain B residue 497 LYS Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain C residue 401 SER Chi-restraints excluded: chain C residue 474 CYS Chi-restraints excluded: chain C residue 492 TYR Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain C residue 497 LYS 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: 72.1825 > 50: distance: 29 - 252: 37.294 distance: 32 - 249: 37.187 distance: 66 - 211: 37.258 distance: 69 - 208: 36.043 distance: 80 - 191: 36.987 distance: 83 - 188: 36.955 distance: 95 - 244: 33.451 distance: 98 - 241: 35.984 distance: 158 - 202: 33.547 distance: 161 - 199: 30.764 distance: 183 - 188: 34.879 distance: 189 - 190: 40.252 distance: 189 - 192: 70.585 distance: 190 - 191: 55.482 distance: 190 - 199: 58.242 distance: 192 - 193: 68.241 distance: 194 - 196: 52.576 distance: 195 - 197: 40.294 distance: 196 - 198: 57.191 distance: 197 - 198: 38.691 distance: 199 - 200: 58.645 distance: 200 - 201: 55.160 distance: 200 - 203: 41.472 distance: 201 - 202: 70.261 distance: 201 - 208: 69.087 distance: 203 - 204: 68.115 distance: 205 - 207: 57.638 distance: 208 - 209: 68.105 distance: 209 - 210: 40.236 distance: 209 - 212: 39.900 distance: 210 - 211: 57.061 distance: 215 - 216: 57.277 distance: 216 - 221: 39.166 distance: 218 - 219: 68.538 distance: 218 - 220: 55.557 distance: 222 - 223: 67.937 distance: 223 - 224: 40.259 distance: 223 - 225: 39.765 distance: 225 - 226: 56.525 distance: 226 - 227: 55.671 distance: 226 - 229: 56.163 distance: 227 - 228: 15.171 distance: 227 - 233: 43.098 distance: 229 - 230: 39.837 distance: 230 - 231: 56.224 distance: 230 - 232: 55.957 distance: 233 - 234: 27.861 distance: 234 - 235: 62.460 distance: 234 - 237: 56.228 distance: 235 - 236: 41.874 distance: 235 - 241: 41.509 distance: 237 - 238: 41.179 distance: 238 - 239: 38.966 distance: 238 - 240: 39.733 distance: 241 - 242: 56.017 distance: 242 - 243: 38.901 distance: 242 - 245: 13.561 distance: 243 - 249: 39.540 distance: 245 - 246: 26.354 distance: 245 - 247: 43.059 distance: 246 - 248: 39.901 distance: 249 - 250: 41.369 distance: 250 - 251: 39.023 distance: 251 - 252: 57.036 distance: 251 - 254: 56.336 distance: 254 - 255: 55.503 distance: 254 - 260: 69.850 distance: 255 - 256: 57.858 distance: 255 - 258: 40.020 distance: 256 - 257: 69.741 distance: 256 - 261: 33.340 distance: 259 - 260: 57.993