Starting phenix.real_space_refine on Sat Aug 23 00:18:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w8r_37357/08_2025/8w8r_37357_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w8r_37357/08_2025/8w8r_37357.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8w8r_37357/08_2025/8w8r_37357_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w8r_37357/08_2025/8w8r_37357_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8w8r_37357/08_2025/8w8r_37357.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w8r_37357/08_2025/8w8r_37357.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.010 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: 5 Type Number sf(0) Gaussians S 57 5.16 5 C 5759 2.51 5 N 1552 2.21 5 O 1644 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s 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: 9018 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1955 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 6, 'TRANS': 229} Chain breaks: 1 Chain: "B" Number of atoms: 2572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2572 Classifications: {'peptide': 335} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 329} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "R" Number of atoms: 2223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2223 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 13, 'TRANS': 266} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "S" Number of atoms: 1782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1782 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "Y" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 444 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "R" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 42 Unusual residues: {'U7D': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.83, per 1000 atoms: 0.20 Number of scatterers: 9018 At special positions: 0 Unit cell: (125.8, 123.25, 96.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 57 16.00 F 6 9.00 O 1644 8.00 N 1552 7.00 C 5759 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 104 " - pdb=" SG CYS R 182 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.04 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: 0.73 Conformation dependent library (CDL) restraints added in 359.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2148 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 14 sheets defined 35.2% alpha, 23.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 25 through 49 removed outlier: 3.906A pdb=" N ALA A 49 " --> pdb=" O GLN A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 72 Processing helix chain 'A' and resid 243 through 249 removed outlier: 3.842A pdb=" N GLN A 246 " --> pdb=" O LYS A 243 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N CYS A 247 " --> pdb=" O TRP A 244 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE A 248 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ASN A 249 " --> pdb=" O GLN A 246 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 243 through 249' Processing helix chain 'A' and resid 265 through 278 removed outlier: 3.906A pdb=" N ALA A 269 " --> pdb=" O ARG A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 304 removed outlier: 3.585A pdb=" N GLU A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 351 removed outlier: 3.803A pdb=" N ALA A 337 " --> pdb=" O ARG A 333 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 390 removed outlier: 3.621A pdb=" N ILE A 375 " --> pdb=" O ASN A 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'R' and resid 29 through 59 removed outlier: 3.817A pdb=" N VAL R 39 " --> pdb=" O SER R 35 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ILE R 40 " --> pdb=" O THR R 36 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N PHE R 41 " --> pdb=" O VAL R 37 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N LEU R 42 " --> pdb=" O LEU R 38 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL R 47 " --> pdb=" O ALA R 43 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LYS R 59 " --> pdb=" O VAL R 55 " (cutoff:3.500A) Processing helix chain 'R' and resid 65 through 93 removed outlier: 3.994A pdb=" N PHE R 69 " --> pdb=" O VAL R 65 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASP R 77 " --> pdb=" O LEU R 73 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU R 78 " --> pdb=" O LEU R 74 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLN R 80 " --> pdb=" O THR R 76 " (cutoff:3.500A) Proline residue: R 86 - end of helix removed outlier: 3.869A pdb=" N SER R 92 " --> pdb=" O VAL R 88 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N VAL R 93 " --> pdb=" O VAL R 89 " (cutoff:3.500A) Processing helix chain 'R' and resid 103 through 134 removed outlier: 3.807A pdb=" N VAL R 108 " --> pdb=" O CYS R 104 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N SER R 109 " --> pdb=" O THR R 105 " (cutoff:3.500A) Processing helix chain 'R' and resid 144 through 164 Processing helix chain 'R' and resid 165 through 168 Processing helix chain 'R' and resid 186 through 188 No H-bonds generated for 'chain 'R' and resid 186 through 188' Processing helix chain 'R' and resid 189 through 201 Processing helix chain 'R' and resid 201 through 228 removed outlier: 4.156A pdb=" N VAL R 214 " --> pdb=" O ALA R 210 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL R 215 " --> pdb=" O CYS R 211 " (cutoff:3.500A) Processing helix chain 'R' and resid 397 through 422 removed outlier: 4.031A pdb=" N ILE R 401 " --> pdb=" O ALA R 397 " (cutoff:3.500A) Proline residue: R 414 - end of helix Processing helix chain 'R' and resid 432 through 445 removed outlier: 3.731A pdb=" N PHE R 444 " --> pdb=" O ILE R 440 " (cutoff:3.500A) Processing helix chain 'R' and resid 445 through 455 Proline residue: R 451 - end of helix Processing helix chain 'R' and resid 458 through 473 Processing helix chain 'S' and resid 28 through 32 removed outlier: 3.542A pdb=" N PHE S 32 " --> pdb=" O PHE S 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 62 through 65 removed outlier: 3.861A pdb=" N LYS S 65 " --> pdb=" O ASP S 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 62 through 65' Processing helix chain 'S' and resid 220 through 224 removed outlier: 3.811A pdb=" N ASP S 223 " --> pdb=" O GLU S 220 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N VAL S 224 " --> pdb=" O ALA S 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 220 through 224' Processing helix chain 'Y' and resid 10 through 22 removed outlier: 3.796A pdb=" N LEU Y 15 " --> pdb=" O GLN Y 11 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N VAL Y 16 " --> pdb=" O ALA Y 12 " (cutoff:3.500A) Processing helix chain 'Y' and resid 29 through 44 removed outlier: 3.542A pdb=" N ALA Y 33 " --> pdb=" O LYS Y 29 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 217 through 223 removed outlier: 6.439A pdb=" N HIS A 51 " --> pdb=" O HIS A 230 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N PHE A 232 " --> pdb=" O HIS A 51 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N LEU A 53 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 8.722A pdb=" N VAL A 234 " --> pdb=" O LEU A 53 " (cutoff:3.500A) removed outlier: 8.895A pdb=" N LEU A 55 " --> pdb=" O VAL A 234 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N ARG A 52 " --> pdb=" O ALA A 253 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N ILE A 255 " --> pdb=" O ARG A 52 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LEU A 54 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N VAL A 257 " --> pdb=" O LEU A 54 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LEU A 56 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 8.499A pdb=" N ASP A 259 " --> pdb=" O LEU A 56 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.875A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.732A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 3.524A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 152 removed outlier: 3.552A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.050A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.328A 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: 6.693A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.646A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'R' and resid 172 through 174 removed outlier: 4.407A pdb=" N GLN R 172 " --> pdb=" O ILE R 185 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12 removed outlier: 3.648A pdb=" N ALA S 49 " --> pdb=" O TRP S 36 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 10 through 12 removed outlier: 4.557A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 140 through 142 Processing sheet with id=AB5, first strand: chain 'S' and resid 146 through 148 removed outlier: 6.866A pdb=" N VAL S 147 " --> pdb=" O GLU S 246 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY S 225 " --> pdb=" O LEU S 245 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) 407 hydrogen bonds defined for protein. 1167 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: 0.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1461 1.32 - 1.45: 2593 1.45 - 1.57: 5084 1.57 - 1.70: 2 1.70 - 1.83: 79 Bond restraints: 9219 Sorted by residual: bond pdb=" C07 U7D R 602 " pdb=" N02 U7D R 602 " ideal model delta sigma weight residual 1.353 1.453 -0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" C07 U7D R 601 " pdb=" N02 U7D R 601 " ideal model delta sigma weight residual 1.353 1.453 -0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" C07 U7D R 602 " pdb=" N03 U7D R 602 " ideal model delta sigma weight residual 1.359 1.454 -0.095 2.00e-02 2.50e+03 2.24e+01 bond pdb=" N LEU B 308 " pdb=" CA LEU B 308 " ideal model delta sigma weight residual 1.455 1.516 -0.061 1.32e-02 5.74e+03 2.14e+01 bond pdb=" C07 U7D R 601 " pdb=" N03 U7D R 601 " ideal model delta sigma weight residual 1.359 1.451 -0.092 2.00e-02 2.50e+03 2.13e+01 ... (remaining 9214 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 12018 2.10 - 4.20: 436 4.20 - 6.30: 46 6.30 - 8.40: 9 8.40 - 10.50: 4 Bond angle restraints: 12513 Sorted by residual: angle pdb=" N PRO R 165 " pdb=" CA PRO R 165 " pdb=" C PRO R 165 " ideal model delta sigma weight residual 110.70 119.95 -9.25 1.22e+00 6.72e-01 5.75e+01 angle pdb=" CA ILE B 232 " pdb=" C ILE B 232 " pdb=" O ILE B 232 " ideal model delta sigma weight residual 120.96 116.19 4.77 8.40e-01 1.42e+00 3.22e+01 angle pdb=" N ALA B 309 " pdb=" CA ALA B 309 " pdb=" C ALA B 309 " ideal model delta sigma weight residual 107.73 114.61 -6.88 1.34e+00 5.57e-01 2.63e+01 angle pdb=" CA GLY B 310 " pdb=" C GLY B 310 " pdb=" O GLY B 310 " ideal model delta sigma weight residual 119.01 124.56 -5.55 1.11e+00 8.12e-01 2.50e+01 angle pdb=" N THR R 105 " pdb=" CA THR R 105 " pdb=" C THR R 105 " ideal model delta sigma weight residual 113.50 107.50 6.00 1.23e+00 6.61e-01 2.38e+01 ... (remaining 12508 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.55: 4677 17.55 - 35.11: 588 35.11 - 52.66: 147 52.66 - 70.22: 31 70.22 - 87.77: 9 Dihedral angle restraints: 5452 sinusoidal: 2125 harmonic: 3327 Sorted by residual: dihedral pdb=" N LEU B 190 " pdb=" C LEU B 190 " pdb=" CA LEU B 190 " pdb=" CB LEU B 190 " ideal model delta harmonic sigma weight residual 122.80 113.13 9.67 0 2.50e+00 1.60e-01 1.50e+01 dihedral pdb=" CB CYS S 22 " pdb=" SG CYS S 22 " pdb=" SG CYS S 96 " pdb=" CB CYS S 96 " ideal model delta sinusoidal sigma weight residual -86.00 -117.74 31.74 1 1.00e+01 1.00e-02 1.44e+01 dihedral pdb=" CA ARG S 191 " pdb=" C ARG S 191 " pdb=" N MET S 192 " pdb=" CA MET S 192 " ideal model delta harmonic sigma weight residual 180.00 161.17 18.83 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 5449 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1180 0.067 - 0.134: 189 0.134 - 0.200: 32 0.200 - 0.267: 12 0.267 - 0.334: 2 Chirality restraints: 1415 Sorted by residual: chirality pdb=" CA LEU B 190 " pdb=" N LEU B 190 " pdb=" C LEU B 190 " pdb=" CB LEU B 190 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.79e+00 chirality pdb=" CA ILE B 232 " pdb=" N ILE B 232 " pdb=" C ILE B 232 " pdb=" CB ILE B 232 " both_signs ideal model delta sigma weight residual False 2.43 2.76 -0.33 2.00e-01 2.50e+01 2.68e+00 chirality pdb=" CA ILE B 58 " pdb=" N ILE B 58 " pdb=" C ILE B 58 " pdb=" CB ILE B 58 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.25 2.00e-01 2.50e+01 1.59e+00 ... (remaining 1412 not shown) Planarity restraints: 1577 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 307 " -0.025 2.00e-02 2.50e+03 4.91e-02 2.41e+01 pdb=" C VAL B 307 " 0.085 2.00e-02 2.50e+03 pdb=" O VAL B 307 " -0.032 2.00e-02 2.50e+03 pdb=" N LEU B 308 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO S 236 " -0.019 2.00e-02 2.50e+03 3.90e-02 1.52e+01 pdb=" C PRO S 236 " 0.067 2.00e-02 2.50e+03 pdb=" O PRO S 236 " -0.026 2.00e-02 2.50e+03 pdb=" N LEU S 237 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 234 " 0.015 2.00e-02 2.50e+03 3.16e-02 9.97e+00 pdb=" C PHE B 234 " -0.055 2.00e-02 2.50e+03 pdb=" O PHE B 234 " 0.021 2.00e-02 2.50e+03 pdb=" N PHE B 235 " 0.019 2.00e-02 2.50e+03 ... (remaining 1574 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1382 2.76 - 3.30: 7813 3.30 - 3.83: 13690 3.83 - 4.37: 15924 4.37 - 4.90: 29526 Nonbonded interactions: 68335 Sorted by model distance: nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP Y 48 " model vdw 2.227 3.040 nonbonded pdb=" O THR S 144 " pdb=" OG1 THR S 243 " model vdw 2.250 3.040 nonbonded pdb=" O ASP B 163 " pdb=" OG1 THR B 164 " model vdw 2.289 3.040 nonbonded pdb=" O LEU A 346 " pdb=" OG1 THR A 350 " model vdw 2.294 3.040 nonbonded pdb=" NE2 GLN B 176 " pdb=" OG1 THR B 179 " model vdw 2.306 3.120 ... (remaining 68330 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 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: 0.320 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.540 Find NCS groups from input model: 0.030 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:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.100 9222 Z= 0.417 Angle : 0.848 10.497 12519 Z= 0.558 Chirality : 0.056 0.334 1415 Planarity : 0.005 0.049 1577 Dihedral : 16.671 87.770 3295 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 1.64 % Allowed : 22.87 % Favored : 75.49 % 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: -0.20 (0.25), residues: 1126 helix: 1.42 (0.28), residues: 368 sheet: 0.60 (0.33), residues: 251 loop : -1.78 (0.25), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 221 TYR 0.012 0.002 TYR A 47 PHE 0.021 0.001 PHE B 241 TRP 0.026 0.002 TRP B 82 HIS 0.005 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00635 ( 9219) covalent geometry : angle 0.84695 (12513) SS BOND : bond 0.00626 ( 3) SS BOND : angle 1.96366 ( 6) hydrogen bonds : bond 0.13993 ( 402) hydrogen bonds : angle 5.45217 ( 1167) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 87 time to evaluate : 0.219 Fit side-chains REVERT: B 251 ARG cc_start: 0.8946 (OUTLIER) cc_final: 0.7456 (mtt90) outliers start: 16 outliers final: 9 residues processed: 101 average time/residue: 0.0955 time to fit residues: 12.8179 Evaluate side-chains 96 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain R residue 97 TRP Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain R residue 164 THR Chi-restraints excluded: chain R residue 170 TRP Chi-restraints excluded: chain R residue 425 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 40.0000 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 10.0000 chunk 106 optimal weight: 8.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 179 ASN S 82 GLN S 194 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.156608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.121948 restraints weight = 10280.383| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 1.79 r_work: 0.2997 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.0674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9222 Z= 0.129 Angle : 0.560 9.244 12519 Z= 0.300 Chirality : 0.043 0.143 1415 Planarity : 0.004 0.043 1577 Dihedral : 5.278 58.313 1274 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.87 % Allowed : 21.74 % Favored : 75.38 % 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: 0.05 (0.25), residues: 1126 helix: 1.76 (0.27), residues: 375 sheet: 0.49 (0.31), residues: 276 loop : -1.72 (0.26), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 221 TYR 0.018 0.001 TYR S 235 PHE 0.013 0.001 PHE B 241 TRP 0.023 0.001 TRP B 82 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 9219) covalent geometry : angle 0.55911 (12513) SS BOND : bond 0.00699 ( 3) SS BOND : angle 1.48727 ( 6) hydrogen bonds : bond 0.05307 ( 402) hydrogen bonds : angle 4.42630 ( 1167) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 89 time to evaluate : 0.197 Fit side-chains REVERT: A 297 LEU cc_start: 0.6796 (OUTLIER) cc_final: 0.6556 (tp) REVERT: B 151 PHE cc_start: 0.8560 (OUTLIER) cc_final: 0.7392 (t80) REVERT: R 470 LYS cc_start: 0.5327 (mptt) cc_final: 0.4760 (tttp) outliers start: 28 outliers final: 18 residues processed: 111 average time/residue: 0.0831 time to fit residues: 12.4960 Evaluate side-chains 106 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 86 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 151 PHE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain R residue 164 THR Chi-restraints excluded: chain R residue 170 TRP Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 185 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 105 optimal weight: 5.9990 chunk 69 optimal weight: 0.8980 chunk 39 optimal weight: 10.0000 chunk 63 optimal weight: 0.5980 chunk 60 optimal weight: 0.8980 chunk 57 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 72 optimal weight: 0.7980 chunk 10 optimal weight: 10.0000 chunk 14 optimal weight: 7.9990 chunk 13 optimal weight: 2.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.159335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.125256 restraints weight = 10303.481| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.71 r_work: 0.3034 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.0967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9222 Z= 0.103 Angle : 0.501 7.916 12519 Z= 0.268 Chirality : 0.041 0.140 1415 Planarity : 0.004 0.045 1577 Dihedral : 4.300 41.424 1264 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.97 % Allowed : 21.95 % Favored : 75.08 % 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: 0.29 (0.25), residues: 1126 helix: 2.06 (0.27), residues: 377 sheet: 0.64 (0.32), residues: 271 loop : -1.70 (0.26), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG Y 62 TYR 0.014 0.001 TYR S 190 PHE 0.011 0.001 PHE B 199 TRP 0.022 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00215 ( 9219) covalent geometry : angle 0.50021 (12513) SS BOND : bond 0.00582 ( 3) SS BOND : angle 1.17885 ( 6) hydrogen bonds : bond 0.04362 ( 402) hydrogen bonds : angle 4.13598 ( 1167) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 91 time to evaluate : 0.221 Fit side-chains REVERT: A 297 LEU cc_start: 0.6823 (OUTLIER) cc_final: 0.6616 (tp) REVERT: B 151 PHE cc_start: 0.8582 (OUTLIER) cc_final: 0.7451 (t80) REVERT: R 470 LYS cc_start: 0.5332 (mptt) cc_final: 0.4699 (tttp) REVERT: Y 48 ASP cc_start: 0.7861 (p0) cc_final: 0.7637 (p0) outliers start: 29 outliers final: 18 residues processed: 116 average time/residue: 0.0867 time to fit residues: 13.3585 Evaluate side-chains 109 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 89 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 151 PHE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 79 LEU Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain R residue 132 SER Chi-restraints excluded: chain R residue 164 THR Chi-restraints excluded: chain R residue 170 TRP Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 185 ILE Chi-restraints excluded: chain Y residue 6 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 85 optimal weight: 10.0000 chunk 111 optimal weight: 0.8980 chunk 63 optimal weight: 0.0970 chunk 73 optimal weight: 0.0770 chunk 22 optimal weight: 0.9990 chunk 78 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 23 optimal weight: 20.0000 chunk 25 optimal weight: 0.3980 chunk 2 optimal weight: 1.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 49 ASN S 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.166066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.129922 restraints weight = 10336.455| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 1.82 r_work: 0.3164 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9222 Z= 0.085 Angle : 0.457 5.866 12519 Z= 0.243 Chirality : 0.040 0.144 1415 Planarity : 0.003 0.039 1577 Dihedral : 3.922 31.974 1264 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.26 % Allowed : 22.67 % Favored : 75.08 % 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: 0.54 (0.25), residues: 1126 helix: 2.42 (0.28), residues: 372 sheet: 0.79 (0.32), residues: 272 loop : -1.67 (0.26), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 221 TYR 0.014 0.001 TYR S 190 PHE 0.011 0.001 PHE A 222 TRP 0.019 0.001 TRP B 82 HIS 0.002 0.000 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00170 ( 9219) covalent geometry : angle 0.45705 (12513) SS BOND : bond 0.00417 ( 3) SS BOND : angle 0.87784 ( 6) hydrogen bonds : bond 0.03391 ( 402) hydrogen bonds : angle 3.83230 ( 1167) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 103 time to evaluate : 0.301 Fit side-chains REVERT: B 151 PHE cc_start: 0.8428 (OUTLIER) cc_final: 0.7457 (t80) REVERT: R 102 HIS cc_start: 0.5701 (OUTLIER) cc_final: 0.4941 (m170) REVERT: R 221 ARG cc_start: 0.7176 (ttt90) cc_final: 0.6949 (ttm110) REVERT: R 470 LYS cc_start: 0.5349 (mptt) cc_final: 0.4722 (tttp) REVERT: S 82 GLN cc_start: 0.6698 (tp40) cc_final: 0.6440 (mm-40) REVERT: Y 48 ASP cc_start: 0.7926 (p0) cc_final: 0.7631 (p0) outliers start: 22 outliers final: 12 residues processed: 122 average time/residue: 0.0750 time to fit residues: 12.5659 Evaluate side-chains 106 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 151 PHE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 97 TRP Chi-restraints excluded: chain R residue 102 HIS Chi-restraints excluded: chain R residue 164 THR Chi-restraints excluded: chain R residue 170 TRP Chi-restraints excluded: chain R residue 185 ILE Chi-restraints excluded: chain S residue 91 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 8 optimal weight: 0.2980 chunk 95 optimal weight: 10.0000 chunk 70 optimal weight: 6.9990 chunk 97 optimal weight: 30.0000 chunk 27 optimal weight: 8.9990 chunk 4 optimal weight: 10.0000 chunk 2 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 50 optimal weight: 8.9990 chunk 56 optimal weight: 40.0000 chunk 80 optimal weight: 3.9990 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.158996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.122257 restraints weight = 10245.883| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 1.82 r_work: 0.3029 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9222 Z= 0.149 Angle : 0.570 10.238 12519 Z= 0.299 Chirality : 0.043 0.196 1415 Planarity : 0.004 0.043 1577 Dihedral : 4.072 23.635 1260 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.69 % Allowed : 22.05 % Favored : 74.26 % 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: 0.36 (0.25), residues: 1126 helix: 2.12 (0.27), residues: 377 sheet: 0.65 (0.32), residues: 277 loop : -1.66 (0.25), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Y 62 TYR 0.019 0.002 TYR A 47 PHE 0.015 0.002 PHE B 241 TRP 0.019 0.001 TRP B 82 HIS 0.006 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 9219) covalent geometry : angle 0.56887 (12513) SS BOND : bond 0.00748 ( 3) SS BOND : angle 1.48352 ( 6) hydrogen bonds : bond 0.05224 ( 402) hydrogen bonds : angle 4.15087 ( 1167) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 99 time to evaluate : 0.225 Fit side-chains REVERT: B 151 PHE cc_start: 0.8650 (OUTLIER) cc_final: 0.7415 (t80) REVERT: B 186 ASP cc_start: 0.8006 (p0) cc_final: 0.7497 (p0) REVERT: R 102 HIS cc_start: 0.5946 (OUTLIER) cc_final: 0.5045 (m170) REVERT: R 470 LYS cc_start: 0.5366 (mptt) cc_final: 0.4756 (tttp) REVERT: Y 48 ASP cc_start: 0.8059 (p0) cc_final: 0.7778 (p0) outliers start: 36 outliers final: 26 residues processed: 126 average time/residue: 0.0867 time to fit residues: 14.7382 Evaluate side-chains 125 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 97 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 151 PHE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 50 ILE Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 102 HIS Chi-restraints excluded: chain R residue 132 SER Chi-restraints excluded: chain R residue 170 TRP Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 185 ILE Chi-restraints excluded: chain R residue 438 ILE Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain Y residue 6 THR Chi-restraints excluded: chain Y residue 21 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 60 optimal weight: 3.9990 chunk 111 optimal weight: 0.5980 chunk 33 optimal weight: 6.9990 chunk 84 optimal weight: 4.9990 chunk 15 optimal weight: 0.5980 chunk 75 optimal weight: 7.9990 chunk 22 optimal weight: 0.8980 chunk 4 optimal weight: 10.0000 chunk 57 optimal weight: 6.9990 chunk 47 optimal weight: 0.9980 chunk 6 optimal weight: 8.9990 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.161569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.125328 restraints weight = 10242.996| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 1.80 r_work: 0.3072 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9222 Z= 0.105 Angle : 0.512 12.232 12519 Z= 0.268 Chirality : 0.042 0.191 1415 Planarity : 0.003 0.041 1577 Dihedral : 3.902 23.542 1259 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 3.90 % Allowed : 21.44 % Favored : 74.67 % 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: 0.48 (0.25), residues: 1126 helix: 2.37 (0.28), residues: 372 sheet: 0.78 (0.32), residues: 270 loop : -1.72 (0.25), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG Y 62 TYR 0.013 0.001 TYR S 60 PHE 0.013 0.001 PHE B 199 TRP 0.022 0.001 TRP B 82 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00225 ( 9219) covalent geometry : angle 0.51103 (12513) SS BOND : bond 0.00596 ( 3) SS BOND : angle 1.19430 ( 6) hydrogen bonds : bond 0.04296 ( 402) hydrogen bonds : angle 4.01015 ( 1167) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 95 time to evaluate : 0.198 Fit side-chains REVERT: B 129 ARG cc_start: 0.6941 (tpp-160) cc_final: 0.6285 (tpt-90) REVERT: B 151 PHE cc_start: 0.8592 (OUTLIER) cc_final: 0.7429 (t80) REVERT: B 186 ASP cc_start: 0.7861 (p0) cc_final: 0.7361 (p0) REVERT: R 102 HIS cc_start: 0.5862 (OUTLIER) cc_final: 0.5023 (m170) REVERT: R 470 LYS cc_start: 0.5286 (mptt) cc_final: 0.4712 (tttp) REVERT: Y 48 ASP cc_start: 0.8036 (p0) cc_final: 0.7755 (p0) outliers start: 38 outliers final: 26 residues processed: 128 average time/residue: 0.0892 time to fit residues: 15.3396 Evaluate side-chains 120 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 92 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 151 PHE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 38 LEU Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 97 TRP Chi-restraints excluded: chain R residue 102 HIS Chi-restraints excluded: chain R residue 132 SER Chi-restraints excluded: chain R residue 170 TRP Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 185 ILE Chi-restraints excluded: chain R residue 425 VAL Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain Y residue 6 THR Chi-restraints excluded: chain Y residue 54 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 35 optimal weight: 3.9990 chunk 26 optimal weight: 9.9990 chunk 103 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 58 optimal weight: 0.8980 chunk 19 optimal weight: 10.0000 chunk 12 optimal weight: 0.8980 chunk 25 optimal weight: 6.9990 chunk 101 optimal weight: 4.9990 chunk 50 optimal weight: 0.9980 chunk 59 optimal weight: 5.9990 overall best weight: 2.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 35 ASN S 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.158810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.121527 restraints weight = 10295.054| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 1.86 r_work: 0.2998 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9222 Z= 0.133 Angle : 0.556 11.925 12519 Z= 0.289 Chirality : 0.043 0.176 1415 Planarity : 0.004 0.041 1577 Dihedral : 4.043 23.544 1259 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.69 % Allowed : 21.54 % Favored : 74.77 % 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: 0.38 (0.25), residues: 1126 helix: 2.19 (0.27), residues: 377 sheet: 0.63 (0.32), residues: 277 loop : -1.69 (0.25), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 221 TYR 0.017 0.002 TYR A 47 PHE 0.014 0.001 PHE B 241 TRP 0.020 0.001 TRP B 82 HIS 0.005 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 9219) covalent geometry : angle 0.55485 (12513) SS BOND : bond 0.00728 ( 3) SS BOND : angle 1.41158 ( 6) hydrogen bonds : bond 0.04989 ( 402) hydrogen bonds : angle 4.12882 ( 1167) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 93 time to evaluate : 0.222 Fit side-chains REVERT: B 129 ARG cc_start: 0.6980 (tpp-160) cc_final: 0.6333 (tpt-90) REVERT: B 151 PHE cc_start: 0.8672 (OUTLIER) cc_final: 0.7377 (t80) REVERT: B 186 ASP cc_start: 0.8012 (p0) cc_final: 0.7499 (p0) REVERT: R 102 HIS cc_start: 0.5974 (OUTLIER) cc_final: 0.5074 (m170) REVERT: R 470 LYS cc_start: 0.5474 (mptt) cc_final: 0.4821 (tttp) REVERT: S 116 THR cc_start: 0.7735 (OUTLIER) cc_final: 0.7463 (m) REVERT: Y 48 ASP cc_start: 0.8086 (p0) cc_final: 0.7758 (p0) outliers start: 36 outliers final: 29 residues processed: 123 average time/residue: 0.0890 time to fit residues: 14.9103 Evaluate side-chains 125 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 93 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 151 PHE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 38 LEU Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 97 TRP Chi-restraints excluded: chain R residue 102 HIS Chi-restraints excluded: chain R residue 132 SER Chi-restraints excluded: chain R residue 170 TRP Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 185 ILE Chi-restraints excluded: chain R residue 425 VAL Chi-restraints excluded: chain R residue 438 ILE Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain Y residue 6 THR Chi-restraints excluded: chain Y residue 21 MET Chi-restraints excluded: chain Y residue 54 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 54 optimal weight: 1.9990 chunk 111 optimal weight: 6.9990 chunk 12 optimal weight: 6.9990 chunk 58 optimal weight: 0.9980 chunk 90 optimal weight: 4.9990 chunk 100 optimal weight: 7.9990 chunk 75 optimal weight: 4.9990 chunk 38 optimal weight: 7.9990 chunk 43 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 76 optimal weight: 0.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.157896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.120344 restraints weight = 10206.256| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 1.87 r_work: 0.2970 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9222 Z= 0.148 Angle : 0.570 11.683 12519 Z= 0.299 Chirality : 0.044 0.183 1415 Planarity : 0.004 0.044 1577 Dihedral : 4.170 23.524 1259 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 4.21 % Allowed : 21.23 % Favored : 74.56 % 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: 0.30 (0.25), residues: 1126 helix: 2.12 (0.27), residues: 377 sheet: 0.58 (0.32), residues: 277 loop : -1.73 (0.25), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 221 TYR 0.017 0.002 TYR A 47 PHE 0.014 0.001 PHE B 241 TRP 0.021 0.001 TRP B 82 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 9219) covalent geometry : angle 0.56932 (12513) SS BOND : bond 0.00767 ( 3) SS BOND : angle 1.50594 ( 6) hydrogen bonds : bond 0.05289 ( 402) hydrogen bonds : angle 4.20322 ( 1167) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 91 time to evaluate : 0.270 Fit side-chains REVERT: B 129 ARG cc_start: 0.6968 (tpp-160) cc_final: 0.6347 (tpt-90) REVERT: B 151 PHE cc_start: 0.8729 (OUTLIER) cc_final: 0.7436 (t80) REVERT: B 186 ASP cc_start: 0.7970 (p0) cc_final: 0.7441 (p0) REVERT: R 470 LYS cc_start: 0.5539 (mptt) cc_final: 0.4847 (tttp) REVERT: S 116 THR cc_start: 0.7605 (OUTLIER) cc_final: 0.7336 (m) REVERT: Y 48 ASP cc_start: 0.8119 (p0) cc_final: 0.7785 (p0) outliers start: 41 outliers final: 31 residues processed: 124 average time/residue: 0.0931 time to fit residues: 15.5095 Evaluate side-chains 125 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 92 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 151 PHE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 50 ILE Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain R residue 97 TRP Chi-restraints excluded: chain R residue 102 HIS Chi-restraints excluded: chain R residue 132 SER Chi-restraints excluded: chain R residue 170 TRP Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 185 ILE Chi-restraints excluded: chain R residue 425 VAL Chi-restraints excluded: chain R residue 438 ILE Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain Y residue 6 THR Chi-restraints excluded: chain Y residue 21 MET Chi-restraints excluded: chain Y residue 54 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 7 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 6 optimal weight: 4.9990 chunk 61 optimal weight: 8.9990 chunk 96 optimal weight: 20.0000 chunk 21 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 70 optimal weight: 20.0000 chunk 111 optimal weight: 0.2980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.161259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.124387 restraints weight = 10175.443| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 1.82 r_work: 0.3046 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9222 Z= 0.101 Angle : 0.509 11.072 12519 Z= 0.267 Chirality : 0.041 0.159 1415 Planarity : 0.004 0.041 1577 Dihedral : 3.934 23.483 1259 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 3.08 % Allowed : 22.46 % Favored : 74.46 % 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: 0.46 (0.25), residues: 1126 helix: 2.44 (0.28), residues: 371 sheet: 0.67 (0.32), residues: 277 loop : -1.75 (0.25), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 221 TYR 0.014 0.001 TYR S 60 PHE 0.013 0.001 PHE B 199 TRP 0.023 0.001 TRP B 82 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00215 ( 9219) covalent geometry : angle 0.50876 (12513) SS BOND : bond 0.00571 ( 3) SS BOND : angle 1.13941 ( 6) hydrogen bonds : bond 0.04235 ( 402) hydrogen bonds : angle 4.02232 ( 1167) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 93 time to evaluate : 0.356 Fit side-chains REVERT: B 129 ARG cc_start: 0.6941 (tpp-160) cc_final: 0.6350 (tpt-90) REVERT: B 151 PHE cc_start: 0.8633 (OUTLIER) cc_final: 0.7324 (t80) REVERT: B 186 ASP cc_start: 0.7916 (p0) cc_final: 0.7394 (p0) REVERT: R 102 HIS cc_start: 0.5964 (OUTLIER) cc_final: 0.5109 (m170) REVERT: R 470 LYS cc_start: 0.5541 (mptt) cc_final: 0.4828 (tttp) REVERT: S 116 THR cc_start: 0.7619 (OUTLIER) cc_final: 0.7385 (m) REVERT: Y 48 ASP cc_start: 0.8055 (p0) cc_final: 0.7756 (p0) outliers start: 30 outliers final: 23 residues processed: 120 average time/residue: 0.0959 time to fit residues: 15.3943 Evaluate side-chains 119 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 93 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 151 PHE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 97 TRP Chi-restraints excluded: chain R residue 102 HIS Chi-restraints excluded: chain R residue 132 SER Chi-restraints excluded: chain R residue 170 TRP Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 185 ILE Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 149 VAL Chi-restraints excluded: chain Y residue 6 THR Chi-restraints excluded: chain Y residue 54 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 90 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 39 optimal weight: 5.9990 chunk 25 optimal weight: 0.0970 chunk 59 optimal weight: 7.9990 chunk 24 optimal weight: 7.9990 chunk 81 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 78 optimal weight: 6.9990 chunk 27 optimal weight: 6.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.162033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.125350 restraints weight = 10245.880| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 1.86 r_work: 0.3053 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9222 Z= 0.100 Angle : 0.504 10.586 12519 Z= 0.264 Chirality : 0.041 0.156 1415 Planarity : 0.004 0.042 1577 Dihedral : 3.846 23.538 1259 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.67 % Allowed : 22.87 % Favored : 74.46 % 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: 0.51 (0.25), residues: 1126 helix: 2.51 (0.28), residues: 371 sheet: 0.70 (0.32), residues: 277 loop : -1.75 (0.25), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 221 TYR 0.013 0.001 TYR S 190 PHE 0.012 0.001 PHE A 222 TRP 0.021 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00213 ( 9219) covalent geometry : angle 0.50356 (12513) SS BOND : bond 0.00565 ( 3) SS BOND : angle 1.09987 ( 6) hydrogen bonds : bond 0.04112 ( 402) hydrogen bonds : angle 3.94696 ( 1167) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 95 time to evaluate : 0.238 Fit side-chains REVERT: B 129 ARG cc_start: 0.6931 (tpp-160) cc_final: 0.6306 (tpt-90) REVERT: B 151 PHE cc_start: 0.8597 (OUTLIER) cc_final: 0.7336 (t80) REVERT: B 186 ASP cc_start: 0.7854 (p0) cc_final: 0.7329 (p0) REVERT: R 102 HIS cc_start: 0.5899 (OUTLIER) cc_final: 0.5096 (m170) REVERT: R 470 LYS cc_start: 0.5529 (mptt) cc_final: 0.4814 (tttp) REVERT: S 116 THR cc_start: 0.7640 (OUTLIER) cc_final: 0.7412 (m) REVERT: Y 48 ASP cc_start: 0.8062 (p0) cc_final: 0.7756 (p0) outliers start: 26 outliers final: 22 residues processed: 120 average time/residue: 0.0829 time to fit residues: 13.7689 Evaluate side-chains 119 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 94 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 151 PHE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 97 TRP Chi-restraints excluded: chain R residue 102 HIS Chi-restraints excluded: chain R residue 132 SER Chi-restraints excluded: chain R residue 170 TRP Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 185 ILE Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 149 VAL Chi-restraints excluded: chain Y residue 6 THR Chi-restraints excluded: chain Y residue 54 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- 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: 71.7809 > 50: distance: 9 - 15: 10.635 distance: 15 - 16: 21.300 distance: 16 - 17: 22.415 distance: 16 - 19: 39.852 distance: 17 - 18: 23.552 distance: 17 - 26: 11.155 distance: 19 - 20: 26.147 distance: 20 - 21: 21.306 distance: 21 - 22: 28.321 distance: 22 - 23: 10.782 distance: 23 - 24: 14.955 distance: 23 - 25: 21.892 distance: 26 - 27: 34.110 distance: 27 - 28: 28.276 distance: 27 - 30: 46.698 distance: 28 - 29: 39.353 distance: 28 - 34: 39.370 distance: 30 - 31: 25.255 distance: 31 - 32: 13.576 distance: 31 - 33: 25.064 distance: 34 - 35: 31.358 distance: 35 - 36: 38.306 distance: 35 - 38: 42.373 distance: 36 - 37: 34.005 distance: 36 - 43: 26.969 distance: 38 - 39: 36.619 distance: 39 - 40: 31.838 distance: 40 - 41: 44.428 distance: 40 - 42: 34.348 distance: 43 - 44: 4.026 distance: 44 - 45: 23.312 distance: 44 - 47: 18.712 distance: 45 - 46: 40.194 distance: 45 - 54: 42.578 distance: 47 - 48: 34.622 distance: 48 - 49: 22.080 distance: 49 - 50: 20.982 distance: 50 - 51: 13.272 distance: 51 - 52: 10.948 distance: 51 - 53: 14.181 distance: 54 - 55: 41.453 distance: 55 - 56: 25.432 distance: 55 - 58: 45.091 distance: 56 - 57: 38.702 distance: 56 - 65: 35.181 distance: 58 - 59: 53.685 distance: 59 - 60: 27.795 distance: 60 - 61: 33.929 distance: 61 - 62: 18.771 distance: 62 - 63: 40.539 distance: 62 - 64: 45.465 distance: 65 - 66: 23.045 distance: 66 - 67: 15.398 distance: 66 - 69: 15.618 distance: 67 - 68: 31.002 distance: 67 - 74: 36.045 distance: 69 - 70: 27.495 distance: 70 - 71: 43.757 distance: 71 - 72: 44.041 distance: 72 - 73: 13.313 distance: 74 - 75: 52.704 distance: 75 - 76: 39.259 distance: 75 - 78: 25.236 distance: 76 - 77: 18.075 distance: 76 - 88: 52.458 distance: 78 - 79: 32.738 distance: 79 - 80: 32.196 distance: 79 - 81: 4.862 distance: 80 - 82: 11.136 distance: 81 - 83: 21.254 distance: 81 - 84: 16.550 distance: 82 - 83: 26.112 distance: 83 - 85: 11.509 distance: 84 - 86: 15.871 distance: 85 - 87: 20.837 distance: 86 - 87: 15.914 distance: 88 - 89: 50.190 distance: 89 - 90: 12.257 distance: 89 - 92: 32.473 distance: 90 - 91: 57.186 distance: 90 - 96: 59.662 distance: 92 - 93: 50.542 distance: 92 - 94: 28.542 distance: 93 - 95: 50.326 distance: 96 - 97: 29.873 distance: 97 - 98: 40.929 distance: 97 - 100: 58.409 distance: 98 - 99: 44.252 distance: 98 - 105: 11.883 distance: 100 - 101: 40.922 distance: 101 - 102: 58.577 distance: 102 - 103: 39.323 distance: 102 - 104: 30.864 distance: 105 - 106: 22.281 distance: 106 - 107: 42.540 distance: 106 - 109: 38.299 distance: 107 - 108: 52.415 distance: 107 - 111: 26.142 distance: 109 - 110: 14.049