Starting phenix.real_space_refine on Fri Aug 22 21:07:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wc8_37434/08_2025/8wc8_37434_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wc8_37434/08_2025/8wc8_37434.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8wc8_37434/08_2025/8wc8_37434_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wc8_37434/08_2025/8wc8_37434_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wc8_37434/08_2025/8wc8_37434.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wc8_37434/08_2025/8wc8_37434.map" } resolution = 2.9 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= 0.003 sd= 0.098 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 Br 1 7.06 5 S 55 5.16 5 C 5174 2.51 5 N 1372 2.21 5 O 1460 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 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: 8062 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1695 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 3, 'TRANS': 218} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 155 Unresolved non-hydrogen angles: 185 Unresolved non-hydrogen dihedrals: 128 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 8, 'GLN:plan1': 1, 'PHE:plan': 1, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 101 Chain: "B" Number of atoms: 2333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2333 Classifications: {'peptide': 325} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 5, 'TRANS': 319} Chain breaks: 1 Unresolved non-hydrogen bonds: 161 Unresolved non-hydrogen angles: 197 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASN:plan1': 3, 'GLN:plan1': 5, 'ARG:plan': 9, 'ASP:plan': 11, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 119 Chain: "R" Number of atoms: 2030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2030 Classifications: {'peptide': 276} Incomplete info: {'truncation_to_alanine': 62} Link IDs: {'PTRANS': 11, 'TRANS': 264} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 217 Unresolved non-hydrogen angles: 273 Unresolved non-hydrogen dihedrals: 182 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'ASP:plan': 4, 'ARG:plan': 3, 'TYR:plan': 2, 'GLU:plan': 6, 'PHE:plan': 4, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 104 Chain: "S" Number of atoms: 1666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1666 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 10, 'TRANS': 218} Chain breaks: 2 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 7, 'ASP:plan': 3, 'ARG:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 70 Chain: "Y" Number of atoms: 328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 328 Classifications: {'peptide': 49} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 4, 'TRANS': 44} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "R" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Unusual residues: {'VMT': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.98, per 1000 atoms: 0.25 Number of scatterers: 8062 At special positions: 0 Unit cell: (86.92, 117.26, 121.36, 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) Br 1 34.99 S 55 16.00 O 1460 8.00 N 1372 7.00 C 5174 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 96 " - pdb=" SG CYS R 182 " distance=2.00 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.69 Conformation dependent library (CDL) restraints added in 473.7 milliseconds Enol-peptide restraints added in 1.2 microseconds 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2064 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 13 sheets defined 38.5% alpha, 22.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.563A pdb=" N ALA A 32 " --> pdb=" O GLN A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 210 through 216 removed outlier: 3.655A pdb=" N ASN A 216 " --> pdb=" O GLN A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 245 Processing helix chain 'A' and resid 260 through 271 Processing helix chain 'A' and resid 274 through 279 removed outlier: 3.932A pdb=" N TYR A 278 " --> pdb=" O LYS A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 283 removed outlier: 3.990A pdb=" N ALA A 283 " --> pdb=" O PRO A 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 280 through 283' Processing helix chain 'A' and resid 298 through 319 removed outlier: 4.280A pdb=" N ILE A 315 " --> pdb=" O GLU A 311 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER A 316 " --> pdb=" O PHE A 312 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N SER A 319 " --> pdb=" O ILE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 358 Processing helix chain 'B' and resid 16 through 26 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.585A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 22 through 51 Processing helix chain 'R' and resid 52 through 55 removed outlier: 3.772A pdb=" N HIS R 55 " --> pdb=" O LYS R 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 52 through 55' Processing helix chain 'R' and resid 56 through 86 removed outlier: 3.933A pdb=" N LEU R 61 " --> pdb=" O PRO R 57 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ILE R 62 " --> pdb=" O THR R 58 " (cutoff:3.500A) Proline residue: R 78 - end of helix Processing helix chain 'R' and resid 92 through 127 removed outlier: 3.543A pdb=" N ASP R 127 " --> pdb=" O TYR R 123 " (cutoff:3.500A) Processing helix chain 'R' and resid 130 through 135 Processing helix chain 'R' and resid 136 through 161 Proline residue: R 151 - end of helix removed outlier: 3.534A pdb=" N LEU R 161 " --> pdb=" O GLY R 157 " (cutoff:3.500A) Processing helix chain 'R' and resid 168 through 179 Processing helix chain 'R' and resid 187 through 200 removed outlier: 3.722A pdb=" N VAL R 192 " --> pdb=" O LYS R 188 " (cutoff:3.500A) Processing helix chain 'R' and resid 200 through 227 Processing helix chain 'R' and resid 248 through 277 removed outlier: 4.051A pdb=" N CYS R 263 " --> pdb=" O VAL R 259 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TRP R 264 " --> pdb=" O PHE R 260 " (cutoff:3.500A) Proline residue: R 266 - end of helix Proline residue: R 275 - end of helix Processing helix chain 'R' and resid 282 through 305 removed outlier: 3.679A pdb=" N GLY R 293 " --> pdb=" O LEU R 289 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N TYR R 294 " --> pdb=" O ILE R 290 " (cutoff:3.500A) Proline residue: R 301 - end of helix Processing helix chain 'R' and resid 308 through 315 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'Y' and resid 16 through 24 Processing helix chain 'Y' and resid 29 through 45 Processing helix chain 'Y' and resid 46 through 48 No H-bonds generated for 'chain 'Y' and resid 46 through 48' Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 191 removed outlier: 6.170A pdb=" N HIS A 34 " --> pdb=" O HIS A 197 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N PHE A 199 " --> pdb=" O HIS A 34 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N VAL A 201 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N LEU A 38 " --> pdb=" O VAL A 201 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA A 220 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE A 221 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N PHE A 257 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N PHE A 223 " --> pdb=" O PHE A 257 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N ASN A 259 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL A 225 " --> pdb=" O ASN A 259 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N VAL A 254 " --> pdb=" O TYR A 327 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N HIS A 329 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LEU A 256 " --> pdb=" O HIS A 329 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 52 removed outlier: 6.708A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.636A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.011A 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: 4.327A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.083A 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 151 removed outlier: 3.626A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.627A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N MET B 217 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.454A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.738A 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: 6.634A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 11 removed outlier: 5.414A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'S' and resid 58 through 60 removed outlier: 6.434A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 140 through 141 Processing sheet with id=AB4, first strand: chain 'S' and resid 194 through 195 removed outlier: 3.631A pdb=" N ASN S 194 " --> pdb=" O TYR S 190 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N TRP S 176 " --> pdb=" O LEU S 188 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N TYR S 190 " --> pdb=" O LEU S 174 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LEU S 174 " --> pdb=" O TYR S 190 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLY S 225 " --> pdb=" O LEU S 245 " (cutoff:3.500A) 426 hydrogen bonds defined for protein. 1236 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: 1.11 Time building geometry restraints manager: 0.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.41: 3495 1.41 - 1.65: 4668 1.65 - 1.89: 81 1.89 - 2.13: 1 2.13 - 2.37: 1 Bond restraints: 8246 Sorted by residual: bond pdb=" C GLY A 320 " pdb=" N GLY A 322 " ideal model delta sigma weight residual 1.331 2.375 -1.044 1.46e-02 4.69e+03 5.12e+03 bond pdb=" C LEU R 289 " pdb=" O LEU R 289 " ideal model delta sigma weight residual 1.237 1.169 0.067 1.17e-02 7.31e+03 3.33e+01 bond pdb=" C TYR R 294 " pdb=" O TYR R 294 " ideal model delta sigma weight residual 1.237 1.170 0.067 1.17e-02 7.31e+03 3.26e+01 bond pdb=" C PHE R 292 " pdb=" O PHE R 292 " ideal model delta sigma weight residual 1.237 1.174 0.063 1.16e-02 7.43e+03 2.94e+01 bond pdb=" C PHE R 185 " pdb=" O PHE R 185 " ideal model delta sigma weight residual 1.234 1.170 0.064 1.22e-02 6.72e+03 2.75e+01 ... (remaining 8241 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.79: 11237 7.79 - 15.59: 6 15.59 - 23.38: 0 23.38 - 31.18: 0 31.18 - 38.97: 2 Bond angle restraints: 11245 Sorted by residual: angle pdb=" O GLY A 320 " pdb=" C GLY A 320 " pdb=" N GLY A 322 " ideal model delta sigma weight residual 123.05 87.02 36.03 1.03e+00 9.43e-01 1.22e+03 angle pdb=" C GLY A 320 " pdb=" N GLY A 322 " pdb=" CA GLY A 322 " ideal model delta sigma weight residual 121.41 160.38 -38.97 1.96e+00 2.60e-01 3.95e+02 angle pdb=" N PRO S 236 " pdb=" CA PRO S 236 " pdb=" C PRO S 236 " ideal model delta sigma weight residual 112.47 97.97 14.50 2.06e+00 2.36e-01 4.96e+01 angle pdb=" C THR R 37 " pdb=" CA THR R 37 " pdb=" CB THR R 37 " ideal model delta sigma weight residual 110.96 100.82 10.14 1.54e+00 4.22e-01 4.33e+01 angle pdb=" CA GLY A 320 " pdb=" C GLY A 320 " pdb=" N GLY A 322 " ideal model delta sigma weight residual 114.28 123.01 -8.73 1.56e+00 4.11e-01 3.13e+01 ... (remaining 11240 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.31: 4384 17.31 - 34.62: 315 34.62 - 51.93: 53 51.93 - 69.23: 5 69.23 - 86.54: 5 Dihedral angle restraints: 4762 sinusoidal: 1563 harmonic: 3199 Sorted by residual: dihedral pdb=" CB CYS R 96 " pdb=" SG CYS R 96 " pdb=" SG CYS R 182 " pdb=" CB CYS R 182 " ideal model delta sinusoidal sigma weight residual -86.00 -162.39 76.39 1 1.00e+01 1.00e-02 7.34e+01 dihedral pdb=" CA GLY A 320 " pdb=" C GLY A 320 " pdb=" N GLY A 322 " pdb=" CA GLY A 322 " ideal model delta harmonic sigma weight residual -180.00 -148.86 -31.14 0 5.00e+00 4.00e-02 3.88e+01 dihedral pdb=" C PHE R 292 " pdb=" N PHE R 292 " pdb=" CA PHE R 292 " pdb=" CB PHE R 292 " ideal model delta harmonic sigma weight residual -122.60 -136.35 13.75 0 2.50e+00 1.60e-01 3.03e+01 ... (remaining 4759 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.136: 1293 0.136 - 0.273: 10 0.273 - 0.409: 1 0.409 - 0.546: 2 0.546 - 0.682: 4 Chirality restraints: 1310 Sorted by residual: chirality pdb=" CA LEU R 289 " pdb=" N LEU R 289 " pdb=" C LEU R 289 " pdb=" CB LEU R 289 " both_signs ideal model delta sigma weight residual False 2.51 1.83 0.68 2.00e-01 2.50e+01 1.16e+01 chirality pdb=" CA PHE R 292 " pdb=" N PHE R 292 " pdb=" C PHE R 292 " pdb=" CB PHE R 292 " both_signs ideal model delta sigma weight residual False 2.51 1.87 0.64 2.00e-01 2.50e+01 1.03e+01 chirality pdb=" CA TRP R 291 " pdb=" N TRP R 291 " pdb=" C TRP R 291 " pdb=" CB TRP R 291 " both_signs ideal model delta sigma weight residual False 2.51 1.92 0.59 2.00e-01 2.50e+01 8.74e+00 ... (remaining 1307 not shown) Planarity restraints: 1417 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 320 " -0.146 2.00e-02 2.50e+03 2.03e-01 4.13e+02 pdb=" C GLY A 320 " 0.347 2.00e-02 2.50e+03 pdb=" O GLY A 320 " -0.142 2.00e-02 2.50e+03 pdb=" N GLY A 322 " -0.059 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL S 199 " 0.055 5.00e-02 4.00e+02 8.42e-02 1.13e+01 pdb=" N PRO S 200 " -0.146 5.00e-02 4.00e+02 pdb=" CA PRO S 200 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO S 200 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR R 56 " -0.053 5.00e-02 4.00e+02 7.99e-02 1.02e+01 pdb=" N PRO R 57 " 0.138 5.00e-02 4.00e+02 pdb=" CA PRO R 57 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO R 57 " -0.044 5.00e-02 4.00e+02 ... (remaining 1414 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1841 2.78 - 3.31: 7558 3.31 - 3.84: 13764 3.84 - 4.37: 15780 4.37 - 4.90: 28412 Nonbonded interactions: 67355 Sorted by model distance: nonbonded pdb=" O ARG S 67 " pdb=" OG1 THR S 84 " model vdw 2.252 3.040 nonbonded pdb=" OG SER B 147 " pdb=" O VAL B 187 " model vdw 2.258 3.040 nonbonded pdb=" O ARG A 250 " pdb=" OG1 THR A 251 " model vdw 2.288 3.040 nonbonded pdb=" O SER S 52 " pdb=" NH1 ARG S 72 " model vdw 2.295 3.120 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.297 3.040 ... (remaining 67350 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: 1.100 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: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.820 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: 0.010 Load rotamer database and sin/cos tables:6.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 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 : 0.013 1.044 8248 Z= 0.845 Angle : 0.854 38.971 11249 Z= 0.555 Chirality : 0.060 0.682 1310 Planarity : 0.008 0.203 1417 Dihedral : 12.531 86.543 2692 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.26 % Allowed : 0.26 % Favored : 99.48 % Cbeta Deviations : 0.48 % 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: 1.02 (0.26), residues: 1077 helix: 2.57 (0.26), residues: 362 sheet: 0.07 (0.31), residues: 266 loop : -0.50 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 212 TYR 0.030 0.002 TYR S 235 PHE 0.036 0.002 PHE R 292 TRP 0.037 0.002 TRP R 291 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.01265 ( 8246) covalent geometry : angle 0.85384 (11245) SS BOND : bond 0.02097 ( 2) SS BOND : angle 1.90567 ( 4) hydrogen bonds : bond 0.12894 ( 426) hydrogen bonds : angle 5.79398 ( 1236) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 156 time to evaluate : 0.259 Fit side-chains REVERT: A 17 LYS cc_start: 0.7752 (mtmt) cc_final: 0.7537 (mtmt) REVERT: R 218 LYS cc_start: 0.7698 (ttpp) cc_final: 0.7218 (pttp) outliers start: 2 outliers final: 0 residues processed: 157 average time/residue: 0.4799 time to fit residues: 80.2045 Evaluate side-chains 118 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 6.9990 chunk 106 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN B 259 GLN ** R 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 194 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.166718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.129874 restraints weight = 9607.188| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 2.14 r_work: 0.3357 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.1002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8248 Z= 0.139 Angle : 0.538 7.316 11249 Z= 0.287 Chirality : 0.042 0.166 1310 Planarity : 0.005 0.067 1417 Dihedral : 4.222 24.536 1178 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.61 % Allowed : 10.57 % Favored : 86.81 % 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: 1.07 (0.26), residues: 1079 helix: 2.67 (0.26), residues: 368 sheet: 0.27 (0.32), residues: 257 loop : -0.68 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 134 TYR 0.012 0.001 TYR S 60 PHE 0.017 0.001 PHE A 189 TRP 0.020 0.001 TRP R 291 HIS 0.004 0.001 HIS R 113 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 8246) covalent geometry : angle 0.53764 (11245) SS BOND : bond 0.00519 ( 2) SS BOND : angle 1.19964 ( 4) hydrogen bonds : bond 0.03720 ( 426) hydrogen bonds : angle 4.85077 ( 1236) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 136 time to evaluate : 0.216 Fit side-chains REVERT: A 17 LYS cc_start: 0.7993 (mtmt) cc_final: 0.7758 (mtmt) REVERT: A 188 LYS cc_start: 0.8375 (OUTLIER) cc_final: 0.8132 (mmtt) REVERT: A 237 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7942 (mm) REVERT: A 356 ARG cc_start: 0.7852 (mtm110) cc_final: 0.7639 (mtm-85) REVERT: B 52 ARG cc_start: 0.8778 (OUTLIER) cc_final: 0.8320 (ptm160) REVERT: B 186 ASP cc_start: 0.8405 (p0) cc_final: 0.8200 (p0) REVERT: R 105 MET cc_start: 0.8510 (ttp) cc_final: 0.8261 (ttt) REVERT: R 196 MET cc_start: 0.7244 (OUTLIER) cc_final: 0.6610 (mpt) REVERT: R 218 LYS cc_start: 0.8091 (ttpp) cc_final: 0.7402 (pttp) REVERT: R 290 ILE cc_start: 0.8322 (OUTLIER) cc_final: 0.8058 (tp) REVERT: S 93 MET cc_start: 0.7452 (mmm) cc_final: 0.7236 (tpp) outliers start: 20 outliers final: 8 residues processed: 144 average time/residue: 0.4875 time to fit residues: 74.3567 Evaluate side-chains 136 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 123 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 LYS Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 196 MET Chi-restraints excluded: chain R residue 271 THR Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 138 ILE Chi-restraints excluded: chain S residue 139 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 89 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 99 optimal weight: 4.9990 chunk 52 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 chunk 69 optimal weight: 5.9990 chunk 56 optimal weight: 0.6980 chunk 43 optimal weight: 0.3980 chunk 12 optimal weight: 1.9990 chunk 94 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN B 259 GLN ** R 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.167381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.130413 restraints weight = 9469.167| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 2.12 r_work: 0.3339 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8248 Z= 0.121 Angle : 0.505 7.157 11249 Z= 0.272 Chirality : 0.042 0.163 1310 Planarity : 0.005 0.058 1417 Dihedral : 4.103 21.420 1178 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.22 % Allowed : 15.14 % Favored : 82.64 % 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: 1.07 (0.26), residues: 1079 helix: 2.72 (0.26), residues: 371 sheet: 0.32 (0.32), residues: 255 loop : -0.80 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 212 TYR 0.012 0.001 TYR A 30 PHE 0.015 0.001 PHE A 189 TRP 0.011 0.001 TRP B 82 HIS 0.004 0.001 HIS A 197 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 8246) covalent geometry : angle 0.50454 (11245) SS BOND : bond 0.00284 ( 2) SS BOND : angle 0.87545 ( 4) hydrogen bonds : bond 0.03399 ( 426) hydrogen bonds : angle 4.70300 ( 1236) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 131 time to evaluate : 0.192 Fit side-chains REVERT: A 17 LYS cc_start: 0.7979 (mtmt) cc_final: 0.7742 (mtmt) REVERT: A 188 LYS cc_start: 0.8344 (OUTLIER) cc_final: 0.8112 (mmtt) REVERT: B 52 ARG cc_start: 0.8793 (OUTLIER) cc_final: 0.8376 (ptm160) REVERT: B 186 ASP cc_start: 0.8429 (p0) cc_final: 0.8196 (p0) REVERT: R 105 MET cc_start: 0.8467 (ttp) cc_final: 0.8230 (ttt) REVERT: R 196 MET cc_start: 0.7306 (OUTLIER) cc_final: 0.6593 (mpt) REVERT: R 218 LYS cc_start: 0.8038 (ttpp) cc_final: 0.7335 (pttp) REVERT: S 113 GLN cc_start: 0.8404 (OUTLIER) cc_final: 0.8010 (mp10) outliers start: 17 outliers final: 6 residues processed: 137 average time/residue: 0.5336 time to fit residues: 77.4632 Evaluate side-chains 134 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 124 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 LYS Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 196 MET Chi-restraints excluded: chain R residue 271 THR Chi-restraints excluded: chain S residue 113 GLN Chi-restraints excluded: chain S residue 138 ILE Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 154 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 66 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 chunk 78 optimal weight: 0.0020 chunk 71 optimal weight: 0.9990 chunk 85 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN ** A 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN B 237 ASN R 41 ASN ** R 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 186 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.167459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.127754 restraints weight = 9722.519| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 2.19 r_work: 0.3330 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8248 Z= 0.115 Angle : 0.496 6.971 11249 Z= 0.266 Chirality : 0.042 0.172 1310 Planarity : 0.005 0.055 1417 Dihedral : 4.009 21.789 1178 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.39 % Allowed : 15.67 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.05 (0.26), residues: 1079 helix: 2.58 (0.26), residues: 379 sheet: 0.33 (0.33), residues: 253 loop : -0.75 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 134 TYR 0.012 0.001 TYR A 30 PHE 0.015 0.001 PHE A 189 TRP 0.010 0.001 TRP B 82 HIS 0.004 0.001 HIS A 197 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 8246) covalent geometry : angle 0.49564 (11245) SS BOND : bond 0.00289 ( 2) SS BOND : angle 0.64969 ( 4) hydrogen bonds : bond 0.03241 ( 426) hydrogen bonds : angle 4.58771 ( 1236) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 131 time to evaluate : 0.323 Fit side-chains REVERT: A 17 LYS cc_start: 0.7940 (mtmt) cc_final: 0.7694 (mtmt) REVERT: A 213 GLN cc_start: 0.8596 (mt0) cc_final: 0.8377 (mt0) REVERT: A 356 ARG cc_start: 0.7893 (mtm-85) cc_final: 0.7687 (mtm110) REVERT: B 52 ARG cc_start: 0.8746 (OUTLIER) cc_final: 0.8373 (ptm160) REVERT: B 155 ASN cc_start: 0.8475 (t0) cc_final: 0.8118 (t0) REVERT: B 186 ASP cc_start: 0.8376 (p0) cc_final: 0.8099 (p0) REVERT: R 105 MET cc_start: 0.8431 (ttp) cc_final: 0.8228 (ttt) REVERT: R 123 TYR cc_start: 0.8343 (m-80) cc_final: 0.8130 (m-80) REVERT: R 196 MET cc_start: 0.7248 (OUTLIER) cc_final: 0.6523 (mpt) REVERT: R 218 LYS cc_start: 0.8018 (ttpp) cc_final: 0.7303 (pttp) REVERT: R 290 ILE cc_start: 0.8260 (OUTLIER) cc_final: 0.8002 (tp) REVERT: S 113 GLN cc_start: 0.8417 (OUTLIER) cc_final: 0.8109 (mm-40) outliers start: 26 outliers final: 11 residues processed: 143 average time/residue: 0.5103 time to fit residues: 77.5005 Evaluate side-chains 139 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 124 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 184 VAL Chi-restraints excluded: chain R residue 196 MET Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 113 GLN Chi-restraints excluded: chain S residue 138 ILE Chi-restraints excluded: chain S residue 154 SER Chi-restraints excluded: chain S residue 245 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- 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: 69.9894 > 50: distance: 6 - 11: 29.499 distance: 11 - 12: 11.549 distance: 11 - 17: 29.658 distance: 12 - 13: 36.867 distance: 12 - 15: 50.889 distance: 13 - 14: 29.043 distance: 13 - 18: 14.431 distance: 15 - 16: 18.952 distance: 16 - 17: 31.951 distance: 18 - 19: 41.272 distance: 19 - 20: 56.148 distance: 19 - 22: 6.010 distance: 20 - 21: 48.292 distance: 20 - 25: 56.745 distance: 22 - 23: 54.099 distance: 22 - 24: 52.959 distance: 25 - 26: 56.531 distance: 26 - 27: 43.346 distance: 27 - 28: 45.751 distance: 27 - 32: 47.859 distance: 29 - 30: 39.807 distance: 29 - 31: 39.821 distance: 32 - 33: 40.661 distance: 32 - 38: 17.212 distance: 33 - 34: 46.350 distance: 34 - 35: 16.672 distance: 34 - 39: 15.702 distance: 36 - 37: 40.713 distance: 37 - 38: 39.723 distance: 39 - 40: 43.810 distance: 41 - 42: 38.950 distance: 41 - 43: 40.927 distance: 44 - 47: 20.913 distance: 45 - 46: 42.598 distance: 49 - 50: 40.287 distance: 50 - 54: 40.027 distance: 52 - 53: 39.332 distance: 54 - 55: 16.376 distance: 54 - 109: 33.685 distance: 55 - 56: 24.708 distance: 55 - 58: 31.162 distance: 56 - 57: 17.023 distance: 56 - 61: 40.194 distance: 57 - 106: 26.583 distance: 58 - 59: 8.819 distance: 58 - 60: 56.156 distance: 61 - 62: 39.449 distance: 62 - 63: 33.887 distance: 62 - 65: 3.235 distance: 63 - 64: 33.426 distance: 63 - 67: 24.153 distance: 65 - 66: 40.939 distance: 67 - 68: 17.018 distance: 67 - 97: 22.047 distance: 68 - 69: 8.939 distance: 69 - 70: 40.084 distance: 69 - 75: 30.911 distance: 70 - 94: 32.812 distance: 71 - 72: 3.934 distance: 72 - 74: 4.333