Starting phenix.real_space_refine on Wed Jan 15 12:00:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ikg_35511/01_2025/8ikg_35511_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ikg_35511/01_2025/8ikg_35511.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ikg_35511/01_2025/8ikg_35511.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ikg_35511/01_2025/8ikg_35511.map" model { file = "/net/cci-nas-00/data/ceres_data/8ikg_35511/01_2025/8ikg_35511_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ikg_35511/01_2025/8ikg_35511_neut.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.083 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 60 5.16 5 C 5414 2.51 5 N 1445 2.21 5 O 1537 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 8456 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1675 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 2, 'TRANS': 214} Chain breaks: 2 Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 47 Chain: "B" Number of atoms: 2474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2474 Classifications: {'peptide': 324} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 318} Chain breaks: 5 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 406 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 48} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "R" Number of atoms: 2167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2167 Classifications: {'peptide': 275} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 8, 'TRANS': 266} Chain breaks: 2 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "S" Number of atoms: 1709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1709 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 10, 'TRANS': 218} Chain breaks: 3 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 6, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 44 Chain: "R" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'Q2B': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.08, per 1000 atoms: 0.60 Number of scatterers: 8456 At special positions: 0 Unit cell: (94.34, 124.6, 126.38, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 60 16.00 O 1537 8.00 N 1445 7.00 C 5414 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 257 " - pdb=" SG CYS R 264 " 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: 2.32 Conformation dependent library (CDL) restraints added in 975.9 milliseconds 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2054 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 13 sheets defined 37.5% alpha, 19.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 6 through 28 removed outlier: 3.562A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLU A 14 " --> pdb=" O LYS A 10 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ARG A 15 " --> pdb=" O ALA A 11 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N SER A 16 " --> pdb=" O ALA A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 removed outlier: 4.351A pdb=" N LYS A 51 " --> pdb=" O SER A 47 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLN A 52 " --> pdb=" O THR A 48 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS A 54 " --> pdb=" O VAL A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 216 removed outlier: 3.545A pdb=" N CYS A 214 " --> pdb=" O TRP A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 270 through 277 removed outlier: 3.772A pdb=" N PHE A 274 " --> pdb=" O LYS A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 281 removed outlier: 3.885A pdb=" N SER A 281 " --> pdb=" O ILE A 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 278 through 281' Processing helix chain 'A' and resid 282 through 287 removed outlier: 4.207A pdb=" N CYS A 286 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.965A pdb=" N ALA A 299 " --> pdb=" O THR A 295 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 352 Processing helix chain 'B' and resid 4 through 22 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 128 through 132 removed outlier: 3.775A pdb=" N GLY B 131 " --> pdb=" O THR B 128 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASN B 132 " --> pdb=" O ARG B 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 128 through 132' Processing helix chain 'C' and resid 8 through 23 removed outlier: 4.251A pdb=" N GLN C 18 " --> pdb=" O LYS C 14 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU C 19 " --> pdb=" O LEU C 15 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS C 20 " --> pdb=" O VAL C 16 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N MET C 21 " --> pdb=" O GLU C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 removed outlier: 3.698A pdb=" N ALA C 33 " --> pdb=" O LYS C 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 119 through 142 Processing helix chain 'R' and resid 146 through 149 removed outlier: 3.612A pdb=" N CYS R 149 " --> pdb=" O SER R 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 146 through 149' Processing helix chain 'R' and resid 150 through 171 removed outlier: 3.656A pdb=" N HIS R 154 " --> pdb=" O ARG R 150 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLY R 157 " --> pdb=" O TYR R 153 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER R 158 " --> pdb=" O HIS R 154 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU R 159 " --> pdb=" O PHE R 155 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL R 171 " --> pdb=" O SER R 167 " (cutoff:3.500A) Processing helix chain 'R' and resid 172 through 178 removed outlier: 3.797A pdb=" N ILE R 175 " --> pdb=" O TYR R 172 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ASP R 176 " --> pdb=" O SER R 173 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE R 177 " --> pdb=" O PHE R 174 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N HIS R 178 " --> pdb=" O ILE R 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 172 through 178' Processing helix chain 'R' and resid 185 through 197 removed outlier: 3.995A pdb=" N PHE R 189 " --> pdb=" O SER R 185 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLY R 195 " --> pdb=" O PHE R 191 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL R 196 " --> pdb=" O LYS R 192 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR R 197 " --> pdb=" O LEU R 193 " (cutoff:3.500A) Processing helix chain 'R' and resid 200 through 220 removed outlier: 3.647A pdb=" N ILE R 218 " --> pdb=" O ARG R 214 " (cutoff:3.500A) Processing helix chain 'R' and resid 223 through 228 Processing helix chain 'R' and resid 229 through 254 removed outlier: 3.899A pdb=" N VAL R 235 " --> pdb=" O PRO R 231 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N ALA R 236 " --> pdb=" O LYS R 232 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE R 237 " --> pdb=" O ALA R 233 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N TRP R 241 " --> pdb=" O PHE R 237 " (cutoff:3.500A) Proline residue: R 251 - end of helix Processing helix chain 'R' and resid 272 through 312 removed outlier: 3.763A pdb=" N VAL R 285 " --> pdb=" O GLY R 281 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU R 286 " --> pdb=" O VAL R 282 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL R 291 " --> pdb=" O LEU R 287 " (cutoff:3.500A) Processing helix chain 'R' and resid 336 through 356 removed outlier: 3.918A pdb=" N LEU R 347 " --> pdb=" O LYS R 343 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE R 348 " --> pdb=" O THR R 344 " (cutoff:3.500A) Processing helix chain 'R' and resid 356 through 366 removed outlier: 3.908A pdb=" N LEU R 360 " --> pdb=" O TRP R 356 " (cutoff:3.500A) Processing helix chain 'R' and resid 372 through 388 removed outlier: 4.517A pdb=" N MET R 384 " --> pdb=" O ALA R 380 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LEU R 385 " --> pdb=" O PHE R 381 " (cutoff:3.500A) Processing helix chain 'R' and resid 388 through 401 Proline residue: R 394 - end of helix removed outlier: 4.214A pdb=" N SER R 401 " --> pdb=" O TYR R 397 " (cutoff:3.500A) Processing helix chain 'R' and resid 401 through 408 removed outlier: 3.935A pdb=" N ARG R 405 " --> pdb=" O SER R 401 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 191 removed outlier: 6.179A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N VAL A 201 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N LEU A 38 " --> pdb=" O VAL A 201 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.543A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 62 through 63 removed outlier: 3.894A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 104 through 105 removed outlier: 5.966A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.703A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.647A 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: 6.989A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.549A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU B 252 " --> pdb=" O MET B 262 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.123A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.793A 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 removed outlier: 3.931A pdb=" N GLN S 3 " --> pdb=" O SER S 25 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 12 removed outlier: 3.817A pdb=" N VAL S 12 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA S 49 " --> pdb=" O TRP S 36 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12 removed outlier: 3.817A pdb=" N VAL S 12 " --> pdb=" O THR S 118 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 144 through 148 Processing sheet with id=AB4, first strand: chain 'S' and resid 166 through 167 376 hydrogen bonds defined for protein. 1056 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.53 Time building geometry restraints manager: 2.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.27: 1337 1.27 - 1.41: 2216 1.41 - 1.54: 4952 1.54 - 1.68: 32 1.68 - 1.81: 87 Bond restraints: 8624 Sorted by residual: bond pdb=" N2 Q2B R 501 " pdb=" O25 Q2B R 501 " ideal model delta sigma weight residual 1.207 1.385 -0.178 2.00e-02 2.50e+03 7.92e+01 bond pdb=" C LYS B 78 " pdb=" O LYS B 78 " ideal model delta sigma weight residual 1.234 1.139 0.095 1.22e-02 6.72e+03 6.06e+01 bond pdb=" C GLY B 53 " pdb=" O GLY B 53 " ideal model delta sigma weight residual 1.235 1.171 0.064 1.35e-02 5.49e+03 2.23e+01 bond pdb=" C LEU B 55 " pdb=" O LEU B 55 " ideal model delta sigma weight residual 1.233 1.159 0.074 1.58e-02 4.01e+03 2.22e+01 bond pdb=" CA LYS B 78 " pdb=" C LYS B 78 " ideal model delta sigma weight residual 1.521 1.463 0.058 1.26e-02 6.30e+03 2.12e+01 ... (remaining 8619 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 11393 1.95 - 3.91: 235 3.91 - 5.86: 39 5.86 - 7.82: 9 7.82 - 9.77: 6 Bond angle restraints: 11682 Sorted by residual: angle pdb=" O ARG R 145 " pdb=" C ARG R 145 " pdb=" N SER R 146 " ideal model delta sigma weight residual 122.19 130.27 -8.08 1.31e+00 5.83e-01 3.80e+01 angle pdb=" CA ARG R 145 " pdb=" C ARG R 145 " pdb=" N SER R 146 " ideal model delta sigma weight residual 117.60 109.24 8.36 1.39e+00 5.18e-01 3.62e+01 angle pdb=" C ARG R 145 " pdb=" N SER R 146 " pdb=" CA SER R 146 " ideal model delta sigma weight residual 121.52 111.75 9.77 1.74e+00 3.30e-01 3.15e+01 angle pdb=" CA HIS B 54 " pdb=" C HIS B 54 " pdb=" N LEU B 55 " ideal model delta sigma weight residual 116.20 122.24 -6.04 1.25e+00 6.40e-01 2.34e+01 angle pdb=" C LYS B 78 " pdb=" CA LYS B 78 " pdb=" CB LYS B 78 " ideal model delta sigma weight residual 109.68 101.72 7.96 1.98e+00 2.55e-01 1.62e+01 ... (remaining 11677 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.08: 4502 16.08 - 32.16: 441 32.16 - 48.24: 118 48.24 - 64.33: 21 64.33 - 80.41: 2 Dihedral angle restraints: 5084 sinusoidal: 1912 harmonic: 3172 Sorted by residual: dihedral pdb=" CB CYS R 257 " pdb=" SG CYS R 257 " pdb=" SG CYS R 264 " pdb=" CB CYS R 264 " ideal model delta sinusoidal sigma weight residual 93.00 152.60 -59.60 1 1.00e+01 1.00e-02 4.74e+01 dihedral pdb=" C LYS B 78 " pdb=" N LYS B 78 " pdb=" CA LYS B 78 " pdb=" CB LYS B 78 " ideal model delta harmonic sigma weight residual -122.60 -109.77 -12.83 0 2.50e+00 1.60e-01 2.63e+01 dihedral pdb=" CA PHE S 27 " pdb=" C PHE S 27 " pdb=" N ALA S 28 " pdb=" CA ALA S 28 " ideal model delta harmonic sigma weight residual 180.00 157.01 22.99 0 5.00e+00 4.00e-02 2.11e+01 ... (remaining 5081 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 1240 0.076 - 0.152: 113 0.152 - 0.228: 3 0.228 - 0.304: 0 0.304 - 0.380: 1 Chirality restraints: 1357 Sorted by residual: chirality pdb=" C4 Q2B R 501 " pdb=" C10 Q2B R 501 " pdb=" C3 Q2B R 501 " pdb=" C5 Q2B R 501 " both_signs ideal model delta sigma weight residual False -2.50 -2.88 0.38 2.00e-01 2.50e+01 3.60e+00 chirality pdb=" CA PHE R 191 " pdb=" N PHE R 191 " pdb=" C PHE R 191 " pdb=" CB PHE R 191 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CB ILE S 58 " pdb=" CA ILE S 58 " pdb=" CG1 ILE S 58 " pdb=" CG2 ILE S 58 " both_signs ideal model delta sigma weight residual False 2.64 2.85 -0.20 2.00e-01 2.50e+01 1.00e+00 ... (remaining 1354 not shown) Planarity restraints: 1456 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG B 52 " -0.021 2.00e-02 2.50e+03 4.46e-02 1.99e+01 pdb=" C ARG B 52 " 0.077 2.00e-02 2.50e+03 pdb=" O ARG B 52 " -0.030 2.00e-02 2.50e+03 pdb=" N GLY B 53 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B 193 " 0.046 5.00e-02 4.00e+02 7.02e-02 7.88e+00 pdb=" N PRO B 194 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO B 194 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 194 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 54 " -0.024 2.00e-02 2.50e+03 1.97e-02 5.84e+00 pdb=" CG HIS B 54 " 0.022 2.00e-02 2.50e+03 pdb=" ND1 HIS B 54 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 HIS B 54 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 HIS B 54 " -0.025 2.00e-02 2.50e+03 pdb=" NE2 HIS B 54 " -0.004 2.00e-02 2.50e+03 ... (remaining 1453 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1273 2.76 - 3.29: 7837 3.29 - 3.83: 13215 3.83 - 4.36: 14620 4.36 - 4.90: 26285 Nonbonded interactions: 63230 Sorted by model distance: nonbonded pdb=" OG1 THR B 143 " pdb=" OD2 ASP B 163 " model vdw 2.225 3.040 nonbonded pdb=" OH TYR B 264 " pdb=" O ALA B 299 " model vdw 2.229 3.040 nonbonded pdb=" NH2 ARG R 186 " pdb=" O PRO R 269 " model vdw 2.254 3.120 nonbonded pdb=" O GLY S 8 " pdb=" OG1 THR S 115 " model vdw 2.275 3.040 nonbonded pdb=" O SER S 149 " pdb=" OG1 THR S 198 " model vdw 2.280 3.040 ... (remaining 63225 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: 1.250 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: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 21.960 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 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 : 0.005 0.178 8624 Z= 0.320 Angle : 0.705 9.771 11682 Z= 0.385 Chirality : 0.044 0.380 1357 Planarity : 0.005 0.070 1456 Dihedral : 13.858 80.408 3027 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 0.34 % Allowed : 0.34 % Favored : 99.33 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.26), residues: 1062 helix: 1.45 (0.29), residues: 350 sheet: -0.38 (0.33), residues: 270 loop : -1.21 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 339 HIS 0.013 0.001 HIS B 54 PHE 0.022 0.001 PHE B 241 TYR 0.013 0.001 TYR S 161 ARG 0.008 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 151 time to evaluate : 0.856 Fit side-chains REVERT: C 15 LEU cc_start: 0.8010 (mm) cc_final: 0.7681 (tp) REVERT: R 191 PHE cc_start: 0.6091 (OUTLIER) cc_final: 0.5224 (t80) outliers start: 3 outliers final: 2 residues processed: 154 average time/residue: 0.2265 time to fit residues: 47.2379 Evaluate side-chains 121 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 118 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain R residue 191 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 5.9990 chunk 81 optimal weight: 0.9980 chunk 45 optimal weight: 7.9990 chunk 27 optimal weight: 0.0470 chunk 54 optimal weight: 8.9990 chunk 43 optimal weight: 1.9990 chunk 83 optimal weight: 7.9990 chunk 32 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 overall best weight: 2.0084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 HIS ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 HIS ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 GLN R 112 ASN R 270 HIS S 157 ASN S 159 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.186559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.152401 restraints weight = 11697.711| |-----------------------------------------------------------------------------| r_work (start): 0.3882 rms_B_bonded: 2.18 r_work: 0.3738 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3603 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 8624 Z= 0.287 Angle : 0.622 6.946 11682 Z= 0.326 Chirality : 0.044 0.157 1357 Planarity : 0.004 0.062 1456 Dihedral : 6.423 57.768 1198 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.46 % Allowed : 10.41 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.27), residues: 1062 helix: 1.25 (0.29), residues: 373 sheet: -0.42 (0.33), residues: 256 loop : -1.35 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP S 36 HIS 0.009 0.001 HIS S 220 PHE 0.025 0.002 PHE B 199 TYR 0.016 0.002 TYR S 161 ARG 0.007 0.001 ARG R 311 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 126 time to evaluate : 0.879 Fit side-chains revert: symmetry clash REVERT: A 275 GLU cc_start: 0.6734 (OUTLIER) cc_final: 0.6399 (tt0) REVERT: C 15 LEU cc_start: 0.8176 (mm) cc_final: 0.7949 (mm) REVERT: R 191 PHE cc_start: 0.5816 (OUTLIER) cc_final: 0.5201 (t80) REVERT: R 277 MET cc_start: 0.7663 (tmm) cc_final: 0.6899 (tpp) outliers start: 22 outliers final: 13 residues processed: 134 average time/residue: 0.2221 time to fit residues: 40.4164 Evaluate side-chains 131 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 116 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain R residue 112 ASN Chi-restraints excluded: chain R residue 164 LEU Chi-restraints excluded: chain R residue 191 PHE Chi-restraints excluded: chain R residue 306 VAL Chi-restraints excluded: chain R residue 339 ILE Chi-restraints excluded: chain R residue 383 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 84 optimal weight: 0.9980 chunk 94 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 55 optimal weight: 7.9990 chunk 13 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 75 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 HIS ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.188111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.154296 restraints weight = 11842.584| |-----------------------------------------------------------------------------| r_work (start): 0.3914 rms_B_bonded: 2.26 r_work: 0.3754 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 8624 Z= 0.191 Angle : 0.549 6.698 11682 Z= 0.288 Chirality : 0.041 0.142 1357 Planarity : 0.004 0.057 1456 Dihedral : 5.946 49.720 1198 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 3.02 % Allowed : 13.77 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.27), residues: 1062 helix: 1.36 (0.29), residues: 367 sheet: -0.48 (0.33), residues: 257 loop : -1.31 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP S 36 HIS 0.007 0.001 HIS S 220 PHE 0.017 0.001 PHE B 199 TYR 0.011 0.001 TYR S 161 ARG 0.005 0.000 ARG S 87 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 123 time to evaluate : 0.905 Fit side-chains REVERT: A 28 GLU cc_start: 0.7380 (pp20) cc_final: 0.6936 (tm-30) REVERT: B 45 MET cc_start: 0.8116 (mtm) cc_final: 0.7623 (ptp) REVERT: R 191 PHE cc_start: 0.5727 (OUTLIER) cc_final: 0.5214 (t80) REVERT: S 70 ILE cc_start: 0.6287 (OUTLIER) cc_final: 0.5953 (mm) outliers start: 27 outliers final: 18 residues processed: 138 average time/residue: 0.2156 time to fit residues: 41.0167 Evaluate side-chains 134 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 114 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 213 HIS Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain R residue 164 LEU Chi-restraints excluded: chain R residue 191 PHE Chi-restraints excluded: chain R residue 295 MET Chi-restraints excluded: chain R residue 306 VAL Chi-restraints excluded: chain R residue 308 MET Chi-restraints excluded: chain R residue 383 SER Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 70 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 84 optimal weight: 6.9990 chunk 53 optimal weight: 7.9990 chunk 28 optimal weight: 0.0170 chunk 5 optimal weight: 4.9990 chunk 70 optimal weight: 8.9990 chunk 54 optimal weight: 0.7980 chunk 58 optimal weight: 0.0270 chunk 63 optimal weight: 1.9990 chunk 99 optimal weight: 0.0470 chunk 45 optimal weight: 8.9990 chunk 24 optimal weight: 2.9990 overall best weight: 0.5776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.192447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.157576 restraints weight = 11793.397| |-----------------------------------------------------------------------------| r_work (start): 0.3925 rms_B_bonded: 2.29 r_work: 0.3779 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.070 8624 Z= 0.139 Angle : 0.503 6.160 11682 Z= 0.262 Chirality : 0.040 0.136 1357 Planarity : 0.004 0.053 1456 Dihedral : 5.028 47.673 1194 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.79 % Allowed : 16.46 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.27), residues: 1062 helix: 1.44 (0.29), residues: 373 sheet: -0.48 (0.33), residues: 257 loop : -1.32 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 339 HIS 0.006 0.001 HIS R 154 PHE 0.014 0.001 PHE S 80 TYR 0.010 0.001 TYR S 161 ARG 0.007 0.000 ARG S 87 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 132 time to evaluate : 0.933 Fit side-chains REVERT: A 28 GLU cc_start: 0.7209 (pp20) cc_final: 0.6828 (mm-30) REVERT: B 32 GLN cc_start: 0.8000 (tm-30) cc_final: 0.7710 (tt0) REVERT: B 45 MET cc_start: 0.8131 (mtm) cc_final: 0.7666 (ptp) REVERT: C 18 GLN cc_start: 0.8117 (tp-100) cc_final: 0.7666 (tp40) REVERT: R 191 PHE cc_start: 0.5704 (OUTLIER) cc_final: 0.5407 (t80) REVERT: R 277 MET cc_start: 0.7419 (tmm) cc_final: 0.6697 (tpp) REVERT: S 157 ASN cc_start: 0.5905 (m-40) cc_final: 0.5460 (m-40) outliers start: 16 outliers final: 8 residues processed: 137 average time/residue: 0.2248 time to fit residues: 42.5380 Evaluate side-chains 126 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 117 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 HIS Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain R residue 133 GLU Chi-restraints excluded: chain R residue 191 PHE Chi-restraints excluded: chain R residue 306 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 72.4112 > 50: distance: 0 - 1: 16.461 distance: 1 - 2: 28.080 distance: 1 - 4: 45.679 distance: 2 - 3: 38.898 distance: 2 - 8: 24.445 distance: 4 - 5: 40.548 distance: 5 - 6: 40.309 distance: 6 - 7: 17.336 distance: 8 - 9: 45.647 distance: 9 - 10: 39.365 distance: 9 - 12: 16.905 distance: 10 - 11: 43.984 distance: 10 - 15: 53.965 distance: 12 - 13: 69.139 distance: 12 - 14: 41.005 distance: 15 - 16: 39.755 distance: 16 - 17: 54.092 distance: 16 - 19: 39.647 distance: 17 - 23: 40.368 distance: 19 - 20: 55.323 distance: 20 - 21: 40.112 distance: 20 - 22: 39.287 distance: 23 - 24: 45.306 distance: 24 - 25: 42.955 distance: 24 - 27: 48.260 distance: 25 - 26: 33.165 distance: 25 - 31: 70.390 distance: 27 - 28: 41.734 distance: 28 - 29: 19.143 distance: 28 - 30: 39.308 distance: 31 - 32: 57.055 distance: 31 - 37: 64.046 distance: 32 - 33: 55.145 distance: 32 - 35: 41.265 distance: 33 - 34: 41.178 distance: 33 - 38: 56.833 distance: 35 - 36: 41.349 distance: 36 - 37: 66.114 distance: 38 - 39: 21.494 distance: 39 - 40: 48.042 distance: 39 - 42: 32.230 distance: 40 - 41: 39.854 distance: 40 - 44: 42.464 distance: 42 - 43: 8.820 distance: 44 - 45: 42.859 distance: 45 - 48: 39.245 distance: 46 - 47: 39.462 distance: 48 - 49: 39.650 distance: 50 - 52: 56.864 distance: 53 - 54: 62.466 distance: 54 - 55: 56.337 distance: 54 - 57: 63.810 distance: 55 - 56: 42.526 distance: 55 - 58: 44.922 distance: 58 - 59: 20.646 distance: 60 - 61: 50.013 distance: 60 - 66: 35.345 distance: 63 - 65: 39.084