Starting phenix.real_space_refine on Wed Feb 4 10:39:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e4d_47506/02_2026/9e4d_47506.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e4d_47506/02_2026/9e4d_47506.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9e4d_47506/02_2026/9e4d_47506.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e4d_47506/02_2026/9e4d_47506.map" model { file = "/net/cci-nas-00/data/ceres_data/9e4d_47506/02_2026/9e4d_47506.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e4d_47506/02_2026/9e4d_47506.cif" } resolution = 3.19 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= 0.012 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 87 5.16 5 C 6330 2.51 5 N 1632 2.21 5 O 1866 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9915 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3305 Classifications: {'peptide': 413} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 394} Chain: "B" Number of atoms: 3305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3305 Classifications: {'peptide': 413} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 394} Chain: "C" Number of atoms: 3305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3305 Classifications: {'peptide': 413} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 394} Time building chain proxies: 2.20, per 1000 atoms: 0.22 Number of scatterers: 9915 At special positions: 0 Unit cell: (92.84, 98.748, 131.664, 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 87 16.00 O 1866 8.00 N 1632 7.00 C 6330 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 93 " - pdb=" SG CYS A 194 " distance=2.03 Simple disulfide: pdb=" SG CYS A 172 " - pdb=" SG CYS A 179 " distance=2.03 Simple disulfide: pdb=" SG CYS A 290 " - pdb=" SG CYS A 367 " distance=2.03 Simple disulfide: pdb=" SG CYS A 310 " - pdb=" SG CYS A 363 " distance=2.03 Simple disulfide: pdb=" SG CYS A 314 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 323 " - pdb=" SG CYS A 345 " distance=2.03 Simple disulfide: pdb=" SG CYS A 325 " - pdb=" SG CYS A 337 " distance=2.03 Simple disulfide: pdb=" SG CYS B 93 " - pdb=" SG CYS B 194 " distance=2.02 Simple disulfide: pdb=" SG CYS B 172 " - pdb=" SG CYS B 179 " distance=2.03 Simple disulfide: pdb=" SG CYS B 290 " - pdb=" SG CYS B 367 " distance=2.03 Simple disulfide: pdb=" SG CYS B 310 " - pdb=" SG CYS B 363 " distance=2.03 Simple disulfide: pdb=" SG CYS B 314 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 323 " - pdb=" SG CYS B 345 " distance=2.03 Simple disulfide: pdb=" SG CYS B 325 " - pdb=" SG CYS B 337 " distance=2.03 Simple disulfide: pdb=" SG CYS C 93 " - pdb=" SG CYS C 194 " distance=2.02 Simple disulfide: pdb=" SG CYS C 172 " - pdb=" SG CYS C 179 " distance=2.03 Simple disulfide: pdb=" SG CYS C 290 " - pdb=" SG CYS C 367 " distance=2.03 Simple disulfide: pdb=" SG CYS C 310 " - pdb=" SG CYS C 363 " distance=2.03 Simple disulfide: pdb=" SG CYS C 314 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 323 " - pdb=" SG CYS C 345 " distance=2.03 Simple disulfide: pdb=" SG CYS C 325 " - pdb=" SG CYS C 337 " 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 Time building additional restraints: 0.81 Conformation dependent library (CDL) restraints added in 535.1 milliseconds 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2322 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 12 sheets defined 42.1% alpha, 21.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 40 through 70 removed outlier: 3.574A pdb=" N LEU A 45 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU A 54 " --> pdb=" O PHE A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 112 Processing helix chain 'A' and resid 131 through 143 removed outlier: 3.517A pdb=" N ASN A 143 " --> pdb=" O GLN A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 162 Processing helix chain 'A' and resid 164 through 169 Processing helix chain 'A' and resid 180 through 182 No H-bonds generated for 'chain 'A' and resid 180 through 182' Processing helix chain 'A' and resid 199 through 203 removed outlier: 4.111A pdb=" N ASP A 202 " --> pdb=" O SER A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 216 Processing helix chain 'A' and resid 225 through 229 Processing helix chain 'A' and resid 292 through 297 removed outlier: 3.772A pdb=" N ASP A 296 " --> pdb=" O VAL A 293 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N SER A 297 " --> pdb=" O THR A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 324 Processing helix chain 'A' and resid 338 through 345 Processing helix chain 'A' and resid 345 through 355 Processing helix chain 'A' and resid 386 through 394 Processing helix chain 'A' and resid 397 through 404 removed outlier: 3.500A pdb=" N GLY A 402 " --> pdb=" O GLU A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 452 removed outlier: 3.836A pdb=" N LEU A 432 " --> pdb=" O ILE A 428 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLY A 433 " --> pdb=" O ALA A 429 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP A 434 " --> pdb=" O GLY A 430 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY A 437 " --> pdb=" O GLY A 433 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLN A 438 " --> pdb=" O ASP A 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 71 removed outlier: 3.715A pdb=" N CYS B 59 " --> pdb=" O ALA B 55 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL B 60 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TYR B 71 " --> pdb=" O TYR B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 112 Processing helix chain 'B' and resid 126 through 130 removed outlier: 3.521A pdb=" N ALA B 130 " --> pdb=" O THR B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 142 Processing helix chain 'B' and resid 153 through 162 Processing helix chain 'B' and resid 164 through 168 Processing helix chain 'B' and resid 180 through 182 No H-bonds generated for 'chain 'B' and resid 180 through 182' Processing helix chain 'B' and resid 199 through 203 removed outlier: 3.815A pdb=" N ASP B 202 " --> pdb=" O SER B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 229 Processing helix chain 'B' and resid 257 through 262 Processing helix chain 'B' and resid 292 through 297 removed outlier: 3.575A pdb=" N ASP B 296 " --> pdb=" O VAL B 293 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N SER B 297 " --> pdb=" O THR B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 324 Processing helix chain 'B' and resid 338 through 345 removed outlier: 3.533A pdb=" N LYS B 343 " --> pdb=" O PRO B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 355 Processing helix chain 'B' and resid 386 through 394 Processing helix chain 'B' and resid 397 through 404 removed outlier: 3.601A pdb=" N GLY B 402 " --> pdb=" O GLU B 398 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU B 403 " --> pdb=" O GLN B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 452 removed outlier: 3.504A pdb=" N LEU B 432 " --> pdb=" O ILE B 428 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY B 433 " --> pdb=" O ALA B 429 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLY B 437 " --> pdb=" O GLY B 433 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLN B 438 " --> pdb=" O ASP B 434 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLU B 452 " --> pdb=" O LEU B 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 70 removed outlier: 3.948A pdb=" N VAL C 60 " --> pdb=" O VAL C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 112 Processing helix chain 'C' and resid 126 through 130 removed outlier: 4.063A pdb=" N ALA C 130 " --> pdb=" O THR C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 142 Processing helix chain 'C' and resid 153 through 162 Processing helix chain 'C' and resid 164 through 168 Processing helix chain 'C' and resid 180 through 182 No H-bonds generated for 'chain 'C' and resid 180 through 182' Processing helix chain 'C' and resid 199 through 203 removed outlier: 4.127A pdb=" N ASP C 202 " --> pdb=" O SER C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 229 Processing helix chain 'C' and resid 257 through 262 removed outlier: 3.617A pdb=" N GLY C 262 " --> pdb=" O ILE C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 324 Processing helix chain 'C' and resid 338 through 345 removed outlier: 3.596A pdb=" N LYS C 343 " --> pdb=" O PRO C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 355 Processing helix chain 'C' and resid 386 through 394 Processing helix chain 'C' and resid 397 through 403 removed outlier: 3.619A pdb=" N GLY C 402 " --> pdb=" O GLU C 398 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU C 403 " --> pdb=" O GLN C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 427 through 452 removed outlier: 3.666A pdb=" N LEU C 441 " --> pdb=" O GLY C 437 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 73 through 80 removed outlier: 3.625A pdb=" N GLU A 421 " --> pdb=" O LYS A 76 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 177 through 178 removed outlier: 4.208A pdb=" N PHE A 269 " --> pdb=" O ILE A 405 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL A 407 " --> pdb=" O PHE A 269 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 85 through 86 Processing sheet with id=AA4, first strand: chain 'A' and resid 184 through 189 removed outlier: 6.668A pdb=" N LYS A 193 " --> pdb=" O ASN A 94 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N ASN A 94 " --> pdb=" O LYS A 193 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 73 through 80 removed outlier: 3.533A pdb=" N GLU B 421 " --> pdb=" O LYS B 76 " (cutoff:3.500A) removed outlier: 9.412A pdb=" N GLU B 418 " --> pdb=" O CYS B 275 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLU B 277 " --> pdb=" O GLU B 418 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N ILE B 420 " --> pdb=" O GLU B 277 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ARG B 279 " --> pdb=" O ILE B 420 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N GLN B 422 " --> pdb=" O ARG B 279 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILE B 281 " --> pdb=" O GLN B 422 " (cutoff:3.500A) removed outlier: 8.694A pdb=" N LYS B 424 " --> pdb=" O ILE B 281 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 169 through 174 removed outlier: 5.745A pdb=" N LEU B 169 " --> pdb=" O ASP B 223 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ASP B 223 " --> pdb=" O LEU B 169 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N PHE B 269 " --> pdb=" O ILE B 405 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL B 407 " --> pdb=" O PHE B 269 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 85 through 86 Processing sheet with id=AA8, first strand: chain 'B' and resid 184 through 189 removed outlier: 6.926A pdb=" N LYS B 193 " --> pdb=" O ASN B 94 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N ASN B 94 " --> pdb=" O LYS B 193 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 73 through 80 removed outlier: 3.559A pdb=" N GLU C 421 " --> pdb=" O LYS C 76 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 169 through 174 removed outlier: 5.689A pdb=" N LEU C 169 " --> pdb=" O ASP C 223 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ASP C 223 " --> pdb=" O LEU C 169 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N PHE C 269 " --> pdb=" O ILE C 405 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 85 through 86 Processing sheet with id=AB3, first strand: chain 'C' and resid 184 through 189 removed outlier: 6.773A pdb=" N LYS C 193 " --> pdb=" O ASN C 94 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N ASN C 94 " --> pdb=" O LYS C 193 " (cutoff:3.500A) 479 hydrogen bonds defined for protein. 1326 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: 1.60 Time building geometry restraints manager: 1.12 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: 3237 1.34 - 1.46: 2358 1.46 - 1.58: 4428 1.58 - 1.70: 0 1.70 - 1.82: 120 Bond restraints: 10143 Sorted by residual: bond pdb=" CG1 ILE A 258 " pdb=" CD1 ILE A 258 " ideal model delta sigma weight residual 1.513 1.473 0.040 3.90e-02 6.57e+02 1.07e+00 bond pdb=" CA VAL C 178 " pdb=" CB VAL C 178 " ideal model delta sigma weight residual 1.527 1.537 -0.011 1.31e-02 5.83e+03 6.44e-01 bond pdb=" CA VAL A 186 " pdb=" CB VAL A 186 " ideal model delta sigma weight residual 1.540 1.530 0.010 1.36e-02 5.41e+03 5.21e-01 bond pdb=" CB CYS C 314 " pdb=" SG CYS C 314 " ideal model delta sigma weight residual 1.808 1.784 0.024 3.30e-02 9.18e+02 5.10e-01 bond pdb=" CB CYS C 93 " pdb=" SG CYS C 93 " ideal model delta sigma weight residual 1.808 1.785 0.023 3.30e-02 9.18e+02 4.95e-01 ... (remaining 10138 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.21: 13426 1.21 - 2.42: 214 2.42 - 3.63: 60 3.63 - 4.84: 8 4.84 - 6.06: 5 Bond angle restraints: 13713 Sorted by residual: angle pdb=" N VAL C 178 " pdb=" CA VAL C 178 " pdb=" C VAL C 178 " ideal model delta sigma weight residual 106.55 109.89 -3.34 1.45e+00 4.76e-01 5.29e+00 angle pdb=" N LEU C 169 " pdb=" CA LEU C 169 " pdb=" C LEU C 169 " ideal model delta sigma weight residual 108.17 111.29 -3.12 1.85e+00 2.92e-01 2.85e+00 angle pdb=" CA LEU C 369 " pdb=" CB LEU C 369 " pdb=" CG LEU C 369 " ideal model delta sigma weight residual 116.30 121.86 -5.56 3.50e+00 8.16e-02 2.53e+00 angle pdb=" C PHE A 257 " pdb=" N ILE A 258 " pdb=" CA ILE A 258 " ideal model delta sigma weight residual 121.97 124.81 -2.84 1.80e+00 3.09e-01 2.48e+00 angle pdb=" N ILE A 124 " pdb=" CA ILE A 124 " pdb=" CB ILE A 124 " ideal model delta sigma weight residual 110.08 111.50 -1.42 9.30e-01 1.16e+00 2.34e+00 ... (remaining 13708 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.49: 5393 16.49 - 32.99: 610 32.99 - 49.48: 113 49.48 - 65.98: 29 65.98 - 82.47: 8 Dihedral angle restraints: 6153 sinusoidal: 2535 harmonic: 3618 Sorted by residual: dihedral pdb=" CB CYS A 172 " pdb=" SG CYS A 172 " pdb=" SG CYS A 179 " pdb=" CB CYS A 179 " ideal model delta sinusoidal sigma weight residual -86.00 -37.37 -48.63 1 1.00e+01 1.00e-02 3.26e+01 dihedral pdb=" CB CYS B 310 " pdb=" SG CYS B 310 " pdb=" SG CYS B 363 " pdb=" CB CYS B 363 " ideal model delta sinusoidal sigma weight residual -86.00 -131.39 45.39 1 1.00e+01 1.00e-02 2.86e+01 dihedral pdb=" CB CYS B 314 " pdb=" SG CYS B 314 " pdb=" SG CYS B 361 " pdb=" CB CYS B 361 " ideal model delta sinusoidal sigma weight residual 93.00 50.15 42.85 1 1.00e+01 1.00e-02 2.56e+01 ... (remaining 6150 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 890 0.029 - 0.058: 411 0.058 - 0.086: 105 0.086 - 0.115: 66 0.115 - 0.144: 4 Chirality restraints: 1476 Sorted by residual: chirality pdb=" CA ILE A 410 " pdb=" N ILE A 410 " pdb=" C ILE A 410 " pdb=" CB ILE A 410 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.19e-01 chirality pdb=" CA ILE B 410 " pdb=" N ILE B 410 " pdb=" C ILE B 410 " pdb=" CB ILE B 410 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.82e-01 chirality pdb=" CA ILE C 410 " pdb=" N ILE C 410 " pdb=" C ILE C 410 " pdb=" CB ILE C 410 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.59e-01 ... (remaining 1473 not shown) Planarity restraints: 1788 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 342 " 0.009 2.00e-02 2.50e+03 7.21e-03 1.04e+00 pdb=" CG TYR C 342 " -0.017 2.00e-02 2.50e+03 pdb=" CD1 TYR C 342 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR C 342 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR C 342 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR C 342 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR C 342 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR C 342 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 342 " 0.007 2.00e-02 2.50e+03 6.77e-03 9.17e-01 pdb=" CG TYR B 342 " -0.016 2.00e-02 2.50e+03 pdb=" CD1 TYR B 342 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR B 342 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR B 342 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR B 342 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR B 342 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 342 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 338 " -0.016 5.00e-02 4.00e+02 2.39e-02 9.17e-01 pdb=" N PRO A 339 " 0.041 5.00e-02 4.00e+02 pdb=" CA PRO A 339 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 339 " -0.013 5.00e-02 4.00e+02 ... (remaining 1785 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 460 2.73 - 3.27: 10096 3.27 - 3.81: 16672 3.81 - 4.36: 20424 4.36 - 4.90: 35162 Nonbonded interactions: 82814 Sorted by model distance: nonbonded pdb=" OH TYR C 426 " pdb=" OD2 ASP C 434 " model vdw 2.181 3.040 nonbonded pdb=" O PHE C 87 " pdb=" ND2 ASN C 198 " model vdw 2.246 3.120 nonbonded pdb=" O LEU A 77 " pdb=" OG1 THR C 75 " model vdw 2.271 3.040 nonbonded pdb=" NH1 ARG A 326 " pdb=" O MET A 330 " model vdw 2.276 3.120 nonbonded pdb=" OD2 ASP A 313 " pdb=" NH2 ARG A 317 " model vdw 2.307 3.120 ... (remaining 82809 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' 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: 0.000 Normalize map: mean=0, sd=1: 4.410 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: 0.020 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.710 Find NCS groups from input model: 0.170 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:1.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 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 0.040 10164 Z= 0.142 Angle : 0.448 6.055 13755 Z= 0.228 Chirality : 0.038 0.144 1476 Planarity : 0.002 0.024 1788 Dihedral : 14.131 82.475 3768 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.25), residues: 1233 helix: 1.49 (0.27), residues: 385 sheet: -0.46 (0.31), residues: 286 loop : 0.65 (0.27), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 43 TYR 0.017 0.001 TYR C 342 PHE 0.010 0.001 PHE C 257 TRP 0.005 0.001 TRP B 46 HIS 0.002 0.000 HIS A 173 Details of bonding type rmsd covalent geometry : bond 0.00331 (10143) covalent geometry : angle 0.44355 (13713) SS BOND : bond 0.00310 ( 21) SS BOND : angle 1.23177 ( 42) hydrogen bonds : bond 0.21454 ( 479) hydrogen bonds : angle 8.78813 ( 1326) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 ARG cc_start: 0.8298 (mmt180) cc_final: 0.8088 (mmm160) REVERT: A 426 TYR cc_start: 0.7451 (t80) cc_final: 0.7160 (t80) REVERT: B 64 ARG cc_start: 0.8176 (mmp-170) cc_final: 0.7751 (mmt-90) REVERT: B 66 GLN cc_start: 0.8914 (tp40) cc_final: 0.8341 (tm-30) REVERT: B 68 TYR cc_start: 0.9257 (t80) cc_final: 0.8941 (t80) REVERT: B 73 HIS cc_start: 0.9023 (p90) cc_final: 0.8589 (p-80) REVERT: C 70 HIS cc_start: 0.9204 (m90) cc_final: 0.8523 (m-70) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.1398 time to fit residues: 23.3752 Evaluate side-chains 68 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/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-2.0-5952/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/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-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.6328 > 50: distance: 27 - 33: 29.610 distance: 33 - 34: 47.263 distance: 34 - 35: 42.459 distance: 34 - 37: 46.531 distance: 35 - 36: 38.565 distance: 35 - 44: 26.928 distance: 37 - 38: 28.220 distance: 38 - 39: 36.639 distance: 39 - 40: 9.571 distance: 40 - 41: 18.434 distance: 41 - 42: 14.598 distance: 41 - 43: 40.671 distance: 44 - 45: 52.505 distance: 44 - 151: 33.468 distance: 45 - 46: 40.580 distance: 47 - 148: 33.814 distance: 49 - 50: 39.355 distance: 52 - 53: 8.056 distance: 53 - 54: 16.317 distance: 53 - 56: 33.656 distance: 54 - 55: 51.548 distance: 54 - 60: 52.702 distance: 56 - 57: 3.268 distance: 57 - 59: 41.633 distance: 61 - 64: 3.317 distance: 62 - 72: 57.102 distance: 64 - 65: 25.000 distance: 65 - 66: 7.690 distance: 65 - 67: 23.182 distance: 66 - 68: 32.619 distance: 68 - 70: 28.878 distance: 72 - 73: 39.832 distance: 73 - 74: 3.837 distance: 73 - 76: 39.609 distance: 74 - 75: 52.701 distance: 74 - 80: 4.469 distance: 76 - 77: 56.509 distance: 77 - 78: 65.578 distance: 77 - 79: 39.260 distance: 80 - 86: 40.075 distance: 81 - 82: 56.075 distance: 81 - 84: 39.405 distance: 82 - 87: 40.595 distance: 87 - 88: 51.827 distance: 87 - 93: 54.149 distance: 88 - 89: 39.852 distance: 88 - 91: 39.237 distance: 89 - 90: 40.382 distance: 89 - 94: 40.879 distance: 91 - 92: 41.359 distance: 94 - 100: 56.084 distance: 95 - 96: 50.040 distance: 95 - 98: 56.208 distance: 96 - 97: 28.865 distance: 96 - 101: 26.700 distance: 98 - 99: 31.685 distance: 99 - 100: 41.600 distance: 101 - 102: 34.267 distance: 102 - 103: 38.360 distance: 102 - 105: 45.672 distance: 103 - 115: 48.413 distance: 105 - 106: 15.738 distance: 106 - 107: 18.346 distance: 106 - 108: 22.370 distance: 107 - 109: 34.442 distance: 109 - 110: 46.287 distance: 110 - 112: 36.896 distance: 111 - 113: 16.232 distance: 112 - 114: 34.858 distance: 113 - 114: 15.163 distance: 115 - 116: 49.257 distance: 116 - 117: 25.022 distance: 117 - 118: 13.532 distance: 117 - 119: 28.211