Starting phenix.real_space_refine on Fri Aug 22 20:00:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6oy9_20222/08_2025/6oy9_20222.cif Found real_map, /net/cci-nas-00/data/ceres_data/6oy9_20222/08_2025/6oy9_20222.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6oy9_20222/08_2025/6oy9_20222.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6oy9_20222/08_2025/6oy9_20222.map" model { file = "/net/cci-nas-00/data/ceres_data/6oy9_20222/08_2025/6oy9_20222.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6oy9_20222/08_2025/6oy9_20222.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.436 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 63 5.16 5 C 4810 2.51 5 N 1249 2.21 5 O 1397 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 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: 7519 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1809 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 2, 'TRANS': 220} Chain breaks: 1 Chain: "B" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2607 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "G" Number of atoms: 494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 494 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 3, 'TRANS': 56} Chain: "R" Number of atoms: 2589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2589 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 307} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "R" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'RET': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 2.10, per 1000 atoms: 0.28 Number of scatterers: 7519 At special positions: 0 Unit cell: (73.1, 124.7, 122.12, 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 63 16.00 O 1397 8.00 N 1249 7.00 C 4810 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 110 " - pdb=" SG CYS R 187 " 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.64 Conformation dependent library (CDL) restraints added in 403.3 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1774 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 9 sheets defined 40.0% alpha, 12.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 6 through 27 Processing helix chain 'A' and resid 41 through 48 Processing helix chain 'A' and resid 203 through 212 removed outlier: 3.691A pdb=" N LYS A 206 " --> pdb=" O GLU A 203 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N TRP A 207 " --> pdb=" O ARG A 204 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N ILE A 208 " --> pdb=" O LYS A 205 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N HIS A 209 " --> pdb=" O LYS A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 251 removed outlier: 3.596A pdb=" N GLU A 241 " --> pdb=" O ASN A 237 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N SER A 248 " --> pdb=" O HIS A 244 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ILE A 249 " --> pdb=" O LEU A 245 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N CYS A 250 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASN A 251 " --> pdb=" O ASN A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 271 Processing helix chain 'A' and resid 272 through 274 No H-bonds generated for 'chain 'A' and resid 272 through 274' Processing helix chain 'A' and resid 291 through 305 removed outlier: 3.556A pdb=" N ALA A 295 " --> pdb=" O THR A 291 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ASN A 297 " --> pdb=" O GLU A 293 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS A 300 " --> pdb=" O GLY A 296 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL A 301 " --> pdb=" O ASN A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 336 Processing helix chain 'A' and resid 339 through 348 removed outlier: 3.930A pdb=" N LEU A 344 " --> pdb=" O ILE A 340 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LYS A 345 " --> pdb=" O LYS A 341 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASP A 346 " --> pdb=" O GLU A 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 23 removed outlier: 3.523A pdb=" N LEU B 7 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLN B 13 " --> pdb=" O GLN B 9 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU B 14 " --> pdb=" O GLU B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.883A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 26 removed outlier: 4.316A pdb=" N LEU G 15 " --> pdb=" O GLU G 11 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N LYS G 16 " --> pdb=" O LYS G 12 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL G 26 " --> pdb=" O LEU G 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 32 through 48 removed outlier: 3.957A pdb=" N ARG G 47 " --> pdb=" O TYR G 43 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 51 No H-bonds generated for 'chain 'G' and resid 49 through 51' Processing helix chain 'R' and resid 33 through 65 removed outlier: 3.561A pdb=" N PHE R 37 " --> pdb=" O GLU R 33 " (cutoff:3.500A) Proline residue: R 53 - end of helix removed outlier: 3.973A pdb=" N HIS R 65 " --> pdb=" O VAL R 61 " (cutoff:3.500A) Processing helix chain 'R' and resid 73 through 89 removed outlier: 3.687A pdb=" N ASP R 83 " --> pdb=" O LEU R 79 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LEU R 84 " --> pdb=" O ALA R 80 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N PHE R 85 " --> pdb=" O VAL R 81 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N MET R 86 " --> pdb=" O ALA R 82 " (cutoff:3.500A) Processing helix chain 'R' and resid 91 through 100 Processing helix chain 'R' and resid 106 through 141 removed outlier: 4.139A pdb=" N PHE R 115 " --> pdb=" O ASN R 111 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N GLY R 120 " --> pdb=" O PHE R 116 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N GLY R 121 " --> pdb=" O ALA R 117 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS R 141 " --> pdb=" O VAL R 137 " (cutoff:3.500A) Processing helix chain 'R' and resid 150 through 167 Processing helix chain 'R' and resid 195 through 198 removed outlier: 3.666A pdb=" N THR R 198 " --> pdb=" O HIS R 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 195 through 198' Processing helix chain 'R' and resid 199 through 211 removed outlier: 3.666A pdb=" N PHE R 203 " --> pdb=" O ASN R 199 " (cutoff:3.500A) Processing helix chain 'R' and resid 212 through 235 Processing helix chain 'R' and resid 240 through 266 removed outlier: 3.724A pdb=" N GLN R 244 " --> pdb=" O SER R 240 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LYS R 248 " --> pdb=" O GLN R 244 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ILE R 255 " --> pdb=" O THR R 251 " (cutoff:3.500A) Processing helix chain 'R' and resid 266 through 278 Processing helix chain 'R' and resid 286 through 288 No H-bonds generated for 'chain 'R' and resid 286 through 288' Processing helix chain 'R' and resid 289 through 297 Processing helix chain 'R' and resid 298 through 300 No H-bonds generated for 'chain 'R' and resid 298 through 300' Processing helix chain 'R' and resid 313 through 318 Processing sheet with id=AA1, first strand: chain 'A' and resid 192 through 195 removed outlier: 3.570A pdb=" N ARG A 193 " --> pdb=" O VAL A 30 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU A 34 " --> pdb=" O PHE A 195 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N ILE A 218 " --> pdb=" O LYS A 31 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU A 33 " --> pdb=" O ILE A 218 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ILE A 217 " --> pdb=" O ILE A 261 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 50 removed outlier: 4.110A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA B 328 " --> pdb=" O GLY B 319 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY B 319 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.154A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N MET B 61 " --> pdb=" O LEU B 71 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N LEU B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE B 81 " --> pdb=" O HIS B 91 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 103 through 104 Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.878A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER B 160 " --> pdb=" O CYS B 148 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 192 removed outlier: 3.989A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY B 202 " --> pdb=" O SER B 189 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER B 191 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL B 200 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU B 210 " --> pdb=" O GLN B 220 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.611A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 7.117A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'R' and resid 4 through 5 286 hydrogen bonds defined for protein. 825 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: 1.10 Time building geometry restraints manager: 0.88 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: 2300 1.34 - 1.45: 1462 1.45 - 1.57: 3827 1.57 - 1.69: 0 1.69 - 1.81: 94 Bond restraints: 7683 Sorted by residual: bond pdb=" C7 RET R 401 " pdb=" C8 RET R 401 " ideal model delta sigma weight residual 1.349 1.298 0.051 2.00e-02 2.50e+03 6.44e+00 bond pdb=" CA LEU B 336 " pdb=" CB LEU B 336 " ideal model delta sigma weight residual 1.525 1.492 0.033 1.47e-02 4.63e+03 5.06e+00 bond pdb=" CB PHE B 234 " pdb=" CG PHE B 234 " ideal model delta sigma weight residual 1.502 1.451 0.051 2.30e-02 1.89e+03 4.95e+00 bond pdb=" CB TRP B 99 " pdb=" CG TRP B 99 " ideal model delta sigma weight residual 1.498 1.431 0.067 3.10e-02 1.04e+03 4.61e+00 bond pdb=" C PHE B 199 " pdb=" N VAL B 200 " ideal model delta sigma weight residual 1.327 1.269 0.058 2.97e-02 1.13e+03 3.84e+00 ... (remaining 7678 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.49: 10216 3.49 - 6.98: 159 6.98 - 10.47: 16 10.47 - 13.96: 3 13.96 - 17.45: 1 Bond angle restraints: 10395 Sorted by residual: angle pdb=" CA LEU G 32 " pdb=" CB LEU G 32 " pdb=" CG LEU G 32 " ideal model delta sigma weight residual 116.30 133.75 -17.45 3.50e+00 8.16e-02 2.48e+01 angle pdb=" C VAL R 300 " pdb=" N TYR R 301 " pdb=" CA TYR R 301 " ideal model delta sigma weight residual 122.38 114.17 8.21 1.81e+00 3.05e-01 2.06e+01 angle pdb=" C GLU R 25 " pdb=" N ALA R 26 " pdb=" CA ALA R 26 " ideal model delta sigma weight residual 121.80 132.53 -10.73 2.44e+00 1.68e-01 1.93e+01 angle pdb=" CA PRO R 291 " pdb=" N PRO R 291 " pdb=" CD PRO R 291 " ideal model delta sigma weight residual 112.00 106.52 5.48 1.40e+00 5.10e-01 1.53e+01 angle pdb=" C CYS R 322 " pdb=" N CYS R 323 " pdb=" CA CYS R 323 " ideal model delta sigma weight residual 122.08 127.41 -5.33 1.47e+00 4.63e-01 1.31e+01 ... (remaining 10390 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.99: 3915 16.99 - 33.98: 526 33.98 - 50.98: 95 50.98 - 67.97: 13 67.97 - 84.96: 5 Dihedral angle restraints: 4554 sinusoidal: 1805 harmonic: 2749 Sorted by residual: dihedral pdb=" CB CYS R 110 " pdb=" SG CYS R 110 " pdb=" SG CYS R 187 " pdb=" CB CYS R 187 " ideal model delta sinusoidal sigma weight residual -86.00 -139.86 53.86 1 1.00e+01 1.00e-02 3.94e+01 dihedral pdb=" CA LYS A 275 " pdb=" C LYS A 275 " pdb=" N LYS A 276 " pdb=" CA LYS A 276 " ideal model delta harmonic sigma weight residual -180.00 -153.10 -26.90 0 5.00e+00 4.00e-02 2.89e+01 dihedral pdb=" CA ASP B 118 " pdb=" C ASP B 118 " pdb=" N ASN B 119 " pdb=" CA ASN B 119 " ideal model delta harmonic sigma weight residual -180.00 -154.61 -25.39 0 5.00e+00 4.00e-02 2.58e+01 ... (remaining 4551 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 1050 0.112 - 0.224: 105 0.224 - 0.336: 1 0.336 - 0.448: 0 0.448 - 0.561: 1 Chirality restraints: 1157 Sorted by residual: chirality pdb=" CB ILE R 214 " pdb=" CA ILE R 214 " pdb=" CG1 ILE R 214 " pdb=" CG2 ILE R 214 " both_signs ideal model delta sigma weight residual False 2.64 2.08 0.56 2.00e-01 2.50e+01 7.86e+00 chirality pdb=" CB VAL B 320 " pdb=" CA VAL B 320 " pdb=" CG1 VAL B 320 " pdb=" CG2 VAL B 320 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CB ILE B 43 " pdb=" CA ILE B 43 " pdb=" CG1 ILE B 43 " pdb=" CG2 ILE B 43 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 1154 not shown) Planarity restraints: 1326 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR R 70 " 0.072 5.00e-02 4.00e+02 1.08e-01 1.88e+01 pdb=" N PRO R 71 " -0.187 5.00e-02 4.00e+02 pdb=" CA PRO R 71 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO R 71 " 0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO R 170 " 0.068 5.00e-02 4.00e+02 1.00e-01 1.61e+01 pdb=" N PRO R 171 " -0.174 5.00e-02 4.00e+02 pdb=" CA PRO R 171 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO R 171 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 82 " 0.021 2.00e-02 2.50e+03 2.05e-02 1.06e+01 pdb=" CG TRP B 82 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 TRP B 82 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP B 82 " -0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP B 82 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 82 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 82 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 82 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 82 " 0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP B 82 " -0.002 2.00e-02 2.50e+03 ... (remaining 1323 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 2147 2.80 - 3.32: 6890 3.32 - 3.85: 11894 3.85 - 4.37: 12456 4.37 - 4.90: 21424 Nonbonded interactions: 54811 Sorted by model distance: nonbonded pdb=" O SER B 84 " pdb=" OG SER B 84 " model vdw 2.269 3.040 nonbonded pdb=" O ALA B 56 " pdb=" OG SER B 334 " model vdw 2.284 3.040 nonbonded pdb=" OG1 THR B 321 " pdb=" OD1 ASP B 323 " model vdw 2.291 3.040 nonbonded pdb=" OG SER R 22 " pdb=" OE1 GLU R 25 " model vdw 2.302 3.040 nonbonded pdb=" O SER R 298 " pdb=" OG SER R 298 " model vdw 2.304 3.040 ... (remaining 54806 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.900 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.880 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 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 : 0.009 0.138 7685 Z= 0.436 Angle : 1.097 17.446 10397 Z= 0.589 Chirality : 0.065 0.561 1157 Planarity : 0.008 0.108 1326 Dihedral : 15.304 84.962 2777 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.66 % Favored : 89.34 % Rotamer: Outliers : 0.24 % Allowed : 17.56 % Favored : 82.20 % 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: -4.69 (0.21), residues: 938 helix: -2.38 (0.22), residues: 348 sheet: -3.07 (0.36), residues: 135 loop : -3.78 (0.21), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 30 TYR 0.038 0.004 TYR R 96 PHE 0.022 0.003 PHE B 241 TRP 0.054 0.004 TRP B 82 HIS 0.009 0.002 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00917 ( 7683) covalent geometry : angle 1.09717 (10395) SS BOND : bond 0.00148 ( 1) SS BOND : angle 0.22454 ( 2) hydrogen bonds : bond 0.15729 ( 286) hydrogen bonds : angle 6.00769 ( 825) Misc. bond : bond 0.13822 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 152 time to evaluate : 0.306 Fit side-chains revert: symmetry clash REVERT: A 28 ARG cc_start: 0.8678 (ptp-170) cc_final: 0.8397 (ptp90) REVERT: A 49 MET cc_start: 0.8944 (tpp) cc_final: 0.8415 (mmm) REVERT: A 193 ARG cc_start: 0.8934 (ttm110) cc_final: 0.8649 (mtp85) REVERT: A 238 ARG cc_start: 0.8755 (ttm170) cc_final: 0.8474 (ttp-170) REVERT: A 306 LEU cc_start: 0.9248 (tp) cc_final: 0.8920 (tp) REVERT: B 215 GLU cc_start: 0.8265 (mm-30) cc_final: 0.7994 (mm-30) REVERT: B 260 GLU cc_start: 0.8122 (mp0) cc_final: 0.7888 (mp0) REVERT: B 271 CYS cc_start: 0.7359 (p) cc_final: 0.6616 (p) REVERT: B 290 ASP cc_start: 0.7761 (m-30) cc_final: 0.7186 (m-30) REVERT: B 325 MET cc_start: 0.8172 (mmt) cc_final: 0.7877 (mmm) REVERT: G 12 LYS cc_start: 0.7789 (mttt) cc_final: 0.7407 (mmmt) REVERT: R 44 MET cc_start: 0.8920 (tpp) cc_final: 0.8666 (tpp) REVERT: R 69 ARG cc_start: 0.8324 (ttp-170) cc_final: 0.7844 (ttm-80) REVERT: R 179 ILE cc_start: 0.8710 (mt) cc_final: 0.8494 (tp) REVERT: R 190 ASP cc_start: 0.7536 (p0) cc_final: 0.7011 (p0) REVERT: R 200 ASN cc_start: 0.7987 (t0) cc_final: 0.6630 (t0) REVERT: R 231 LYS cc_start: 0.8897 (tppt) cc_final: 0.8596 (tmtt) outliers start: 2 outliers final: 2 residues processed: 154 average time/residue: 0.1134 time to fit residues: 22.6367 Evaluate side-chains 116 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 114 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 176 SER Chi-restraints excluded: chain R residue 198 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 10.0000 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 GLN B 293 ASN B 311 HIS R 100 HIS R 238 GLN R 278 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.114219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.089704 restraints weight = 16086.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.092505 restraints weight = 9087.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.094401 restraints weight = 6299.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.095653 restraints weight = 4945.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.096363 restraints weight = 4220.136| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7685 Z= 0.126 Angle : 0.667 15.076 10397 Z= 0.343 Chirality : 0.042 0.250 1157 Planarity : 0.005 0.083 1326 Dihedral : 6.028 44.078 1027 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 2.44 % Allowed : 20.37 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.09 (0.25), residues: 938 helix: -0.45 (0.27), residues: 352 sheet: -2.40 (0.40), residues: 139 loop : -3.36 (0.24), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 309 TYR 0.028 0.002 TYR R 96 PHE 0.026 0.001 PHE B 235 TRP 0.021 0.002 TRP R 35 HIS 0.004 0.001 HIS B 311 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 7683) covalent geometry : angle 0.66718 (10395) SS BOND : bond 0.00136 ( 1) SS BOND : angle 0.29951 ( 2) hydrogen bonds : bond 0.04776 ( 286) hydrogen bonds : angle 4.57592 ( 825) Misc. bond : bond 0.00011 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 160 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 ARG cc_start: 0.8634 (ptp-170) cc_final: 0.8419 (ptp90) REVERT: A 194 MET cc_start: 0.9039 (ptp) cc_final: 0.8837 (ptp) REVERT: A 238 ARG cc_start: 0.8705 (ttm170) cc_final: 0.8063 (mmp-170) REVERT: A 306 LEU cc_start: 0.9118 (tp) cc_final: 0.8748 (tp) REVERT: B 10 GLU cc_start: 0.8346 (mt-10) cc_final: 0.8104 (mp0) REVERT: B 215 GLU cc_start: 0.8246 (mm-30) cc_final: 0.7983 (mm-30) REVERT: B 262 MET cc_start: 0.8395 (tpt) cc_final: 0.8013 (tpp) REVERT: B 264 TYR cc_start: 0.8618 (m-80) cc_final: 0.8334 (m-80) REVERT: B 271 CYS cc_start: 0.6710 (p) cc_final: 0.6016 (p) REVERT: B 290 ASP cc_start: 0.7449 (m-30) cc_final: 0.6922 (m-30) REVERT: G 12 LYS cc_start: 0.7624 (mttt) cc_final: 0.7265 (mmmt) REVERT: R 44 MET cc_start: 0.8880 (tpp) cc_final: 0.8642 (tpp) REVERT: R 68 LEU cc_start: 0.8894 (tt) cc_final: 0.8655 (mp) REVERT: R 69 ARG cc_start: 0.8163 (ttp-170) cc_final: 0.7640 (ttm-80) REVERT: R 145 ASN cc_start: 0.8446 (t0) cc_final: 0.8208 (t0) REVERT: R 176 SER cc_start: 0.9222 (p) cc_final: 0.8832 (m) outliers start: 20 outliers final: 5 residues processed: 173 average time/residue: 0.1017 time to fit residues: 23.1195 Evaluate side-chains 131 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 126 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain R residue 290 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 55.4892 > 50: distance: 42 - 45: 4.190 distance: 45 - 46: 16.866 distance: 46 - 47: 24.789 distance: 46 - 49: 15.343 distance: 47 - 48: 30.200 distance: 47 - 53: 25.899 distance: 49 - 50: 4.559 distance: 49 - 51: 10.430 distance: 50 - 52: 6.371 distance: 53 - 54: 10.208 distance: 54 - 55: 9.857 distance: 54 - 57: 5.693 distance: 55 - 56: 7.661 distance: 55 - 61: 3.568 distance: 57 - 58: 4.452 distance: 57 - 59: 5.550 distance: 58 - 60: 4.841 distance: 63 - 64: 7.659 distance: 63 - 72: 6.224 distance: 72 - 73: 5.659 distance: 73 - 74: 6.769 distance: 73 - 76: 4.136 distance: 74 - 75: 12.239 distance: 74 - 78: 13.822 distance: 76 - 77: 5.958 distance: 78 - 79: 6.320 distance: 79 - 80: 6.261 distance: 79 - 82: 3.300 distance: 80 - 81: 7.329 distance: 80 - 85: 11.797 distance: 82 - 83: 4.179 distance: 85 - 86: 15.868 distance: 86 - 87: 32.239 distance: 86 - 89: 12.439 distance: 87 - 88: 25.666 distance: 87 - 90: 28.958 distance: 90 - 91: 12.896 distance: 91 - 92: 27.139 distance: 91 - 94: 11.300 distance: 92 - 93: 28.404 distance: 92 - 98: 24.102 distance: 94 - 95: 11.096 distance: 95 - 96: 20.574 distance: 95 - 97: 5.947 distance: 98 - 99: 27.331 distance: 99 - 100: 35.152 distance: 99 - 102: 4.557 distance: 100 - 101: 25.915 distance: 100 - 104: 12.326 distance: 102 - 103: 27.208 distance: 105 - 106: 14.437 distance: 105 - 108: 14.349 distance: 106 - 107: 15.853 distance: 106 - 112: 11.748 distance: 108 - 109: 5.953 distance: 109 - 110: 9.336 distance: 109 - 111: 10.545 distance: 112 - 113: 6.876 distance: 113 - 114: 11.288 distance: 113 - 116: 4.250 distance: 114 - 115: 6.666 distance: 114 - 124: 9.489 distance: 118 - 120: 4.703 distance: 120 - 122: 3.816 distance: 121 - 122: 5.419 distance: 122 - 123: 5.458