Starting phenix.real_space_refine on Fri Aug 22 21:18:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pok_17793/08_2025/8pok_17793.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pok_17793/08_2025/8pok_17793.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 { model { file = "/net/cci-nas-00/data/ceres_data/8pok_17793/08_2025/8pok_17793.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pok_17793/08_2025/8pok_17793.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8pok_17793/08_2025/8pok_17793.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pok_17793/08_2025/8pok_17793.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.064 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 51 5.16 5 C 5082 2.51 5 N 1416 2.21 5 O 1493 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 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: 8042 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2169 Classifications: {'peptide': 278} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 7, 'TRANS': 270} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 1825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1825 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 212} Chain breaks: 2 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 2606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2606 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "D" Number of atoms: 461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 461 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 4, 'TRANS': 55} Chain: "E" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "A" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'HSM': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.09, per 1000 atoms: 0.26 Number of scatterers: 8042 At special positions: 0 Unit cell: (80.388, 106.26, 133.98, 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 51 16.00 O 1493 8.00 N 1416 7.00 C 5082 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 180 " 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: 0.65 Conformation dependent library (CDL) restraints added in 384.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1926 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 12 sheets defined 38.5% alpha, 18.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 20 through 51 removed outlier: 3.545A pdb=" N ILE A 27 " --> pdb=" O CYS A 23 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL A 45 " --> pdb=" O GLY A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 59 No H-bonds generated for 'chain 'A' and resid 57 through 59' Processing helix chain 'A' and resid 60 through 68 Processing helix chain 'A' and resid 70 through 77 removed outlier: 3.655A pdb=" N VAL A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 87 Processing helix chain 'A' and resid 93 through 128 removed outlier: 3.654A pdb=" N ILE A 99 " --> pdb=" O VAL A 95 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N THR A 101 " --> pdb=" O CYS A 97 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N SER A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N VAL A 105 " --> pdb=" O THR A 101 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N CYS A 108 " --> pdb=" O ASP A 104 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU A 115 " --> pdb=" O SER A 111 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N PHE A 116 " --> pdb=" O ILE A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 136 removed outlier: 3.580A pdb=" N LEU A 135 " --> pdb=" O ARG A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 161 removed outlier: 3.738A pdb=" N ILE A 143 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU A 147 " --> pdb=" O ILE A 143 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU A 158 " --> pdb=" O THR A 154 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N SER A 159 " --> pdb=" O LEU A 155 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ILE A 160 " --> pdb=" O SER A 156 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N HIS A 161 " --> pdb=" O PHE A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 193 removed outlier: 3.622A pdb=" N VAL A 191 " --> pdb=" O VAL A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 216 removed outlier: 3.663A pdb=" N ARG A 210 " --> pdb=" O ILE A 206 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE A 211 " --> pdb=" O THR A 207 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE A 212 " --> pdb=" O TYR A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 224 removed outlier: 4.042A pdb=" N LYS A 220 " --> pdb=" O ARG A 216 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG A 221 " --> pdb=" O ASP A 217 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N ILE A 222 " --> pdb=" O GLN A 218 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASN A 223 " --> pdb=" O ALA A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 266 removed outlier: 3.831A pdb=" N PHE A 249 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Proline residue: A 255 - end of helix Processing helix chain 'A' and resid 275 through 296 removed outlier: 3.589A pdb=" N GLY A 283 " --> pdb=" O VAL A 279 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TYR A 284 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASN A 286 " --> pdb=" O LEU A 282 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N SER A 287 " --> pdb=" O GLY A 283 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ALA A 288 " --> pdb=" O TYR A 284 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU A 289 " --> pdb=" O ALA A 285 " (cutoff:3.500A) Proline residue: A 291 - end of helix Processing helix chain 'B' and resid 9 through 39 removed outlier: 3.562A pdb=" N ASN B 14 " --> pdb=" O GLU B 10 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU B 16 " --> pdb=" O GLN B 12 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN B 29 " --> pdb=" O LYS B 25 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLN B 35 " --> pdb=" O GLN B 31 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL B 36 " --> pdb=" O LYS B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 224 removed outlier: 3.902A pdb=" N GLN B 222 " --> pdb=" O LYS B 219 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N CYS B 223 " --> pdb=" O TRP B 220 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N PHE B 224 " --> pdb=" O ILE B 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 219 through 224' Processing helix chain 'B' and resid 251 through 264 removed outlier: 3.691A pdb=" N LYS B 260 " --> pdb=" O LEU B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 287 removed outlier: 4.117A pdb=" N LYS B 286 " --> pdb=" O LEU B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 302 removed outlier: 4.011A pdb=" N ALA B 302 " --> pdb=" O PRO B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 337 removed outlier: 3.529A pdb=" N THR B 321 " --> pdb=" O ASP B 317 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR B 325 " --> pdb=" O THR B 321 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE B 326 " --> pdb=" O ARG B 322 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE B 327 " --> pdb=" O ALA B 323 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASP B 329 " --> pdb=" O TYR B 325 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE B 331 " --> pdb=" O ILE B 327 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE B 334 " --> pdb=" O GLU B 330 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA B 337 " --> pdb=" O ARG B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 377 removed outlier: 3.548A pdb=" N ARG B 366 " --> pdb=" O PHE B 362 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ASP B 367 " --> pdb=" O ASN B 363 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG B 375 " --> pdb=" O ARG B 371 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLN B 376 " --> pdb=" O MET B 372 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TYR B 377 " --> pdb=" O HIS B 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 31 removed outlier: 3.594A pdb=" N LEU C 12 " --> pdb=" O GLU C 8 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG C 13 " --> pdb=" O LEU C 9 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN C 18 " --> pdb=" O GLN C 14 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA C 31 " --> pdb=" O ARG C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 40 removed outlier: 3.664A pdb=" N ILE C 38 " --> pdb=" O THR C 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 22 Processing helix chain 'D' and resid 23 through 25 No H-bonds generated for 'chain 'D' and resid 23 through 25' Processing helix chain 'D' and resid 29 through 44 removed outlier: 3.622A pdb=" N ALA D 35 " --> pdb=" O SER D 31 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ASP D 36 " --> pdb=" O LYS D 32 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU D 37 " --> pdb=" O ALA D 33 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N MET D 38 " --> pdb=" O ALA D 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.649A pdb=" N ASN E 31 " --> pdb=" O THR E 28 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N TYR E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 28 through 32' Processing sheet with id=AA1, first strand: chain 'B' and resid 195 through 196 removed outlier: 3.516A pdb=" N MET B 207 " --> pdb=" O THR B 196 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 195 through 196 removed outlier: 3.516A pdb=" N MET B 207 " --> pdb=" O THR B 196 " (cutoff:3.500A) removed outlier: 9.820A pdb=" N ALA B 229 " --> pdb=" O THR B 40 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N ARG B 42 " --> pdb=" O ALA B 229 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N ILE B 231 " --> pdb=" O ARG B 42 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N LEU B 44 " --> pdb=" O ILE B 231 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N VAL B 233 " --> pdb=" O LEU B 44 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N LEU B 46 " --> pdb=" O VAL B 233 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ILE B 230 " --> pdb=" O ILE B 274 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N PHE B 276 " --> pdb=" O ILE B 230 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N PHE B 232 " --> pdb=" O PHE B 276 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N VAL B 273 " --> pdb=" O TYR B 346 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 54 through 56 removed outlier: 3.536A pdb=" N ARG C 54 " --> pdb=" O ILE C 343 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU C 341 " --> pdb=" O LEU C 56 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N CYS C 322 " --> pdb=" O GLY C 335 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 63 through 68 removed outlier: 6.943A pdb=" N ALA C 78 " --> pdb=" O TYR C 64 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N MET C 66 " --> pdb=" O VAL C 76 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N VAL C 76 " --> pdb=" O MET C 66 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N TRP C 68 " --> pdb=" O LEU C 74 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N LEU C 74 " --> pdb=" O TRP C 68 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE C 85 " --> pdb=" O SER C 77 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER C 79 " --> pdb=" O LYS C 83 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N LYS C 83 " --> pdb=" O SER C 79 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LEU C 84 " --> pdb=" O ALA C 97 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ALA C 97 " --> pdb=" O LEU C 84 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ILE C 86 " --> pdb=" O VAL C 95 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP C 88 " --> pdb=" O ASN C 93 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ASN C 93 " --> pdb=" O ASP C 88 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 105 through 108 removed outlier: 6.722A pdb=" N GLY C 120 " --> pdb=" O MET C 106 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N CYS C 108 " --> pdb=" O ALA C 118 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ALA C 118 " --> pdb=" O CYS C 108 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N CYS C 126 " --> pdb=" O GLU C 143 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N GLU C 143 " --> pdb=" O CYS C 126 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ILE C 128 " --> pdb=" O SER C 141 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASN C 130 " --> pdb=" O ARG C 139 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ARG C 139 " --> pdb=" O ASN C 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 151 through 158 removed outlier: 6.783A pdb=" N SER C 165 " --> pdb=" O SER C 152 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N CYS C 154 " --> pdb=" O VAL C 163 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N VAL C 163 " --> pdb=" O CYS C 154 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N PHE C 156 " --> pdb=" O GLN C 161 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N GLN C 161 " --> pdb=" O PHE C 156 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE C 162 " --> pdb=" O TRP C 174 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N THR C 170 " --> pdb=" O SER C 166 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N CYS C 171 " --> pdb=" O THR C 184 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N THR C 184 " --> pdb=" O CYS C 171 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N LEU C 173 " --> pdb=" O THR C 182 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 192 through 197 removed outlier: 7.118A pdb=" N GLY C 207 " --> pdb=" O MET C 193 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N LEU C 195 " --> pdb=" O VAL C 205 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL C 205 " --> pdb=" O LEU C 195 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N LEU C 197 " --> pdb=" O LEU C 203 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N LEU C 203 " --> pdb=" O LEU C 197 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N PHE C 204 " --> pdb=" O TRP C 216 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N SER C 212 " --> pdb=" O ALA C 208 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 234 through 239 removed outlier: 3.530A pdb=" N ALA C 247 " --> pdb=" O CYS C 238 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N THR C 254 " --> pdb=" O SER C 250 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N CYS C 255 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N MET C 267 " --> pdb=" O LEU C 257 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N ASP C 259 " --> pdb=" O GLU C 265 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N GLU C 265 " --> pdb=" O ASP C 259 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 281 through 283 removed outlier: 3.611A pdb=" N GLY C 311 " --> pdb=" O VAL C 301 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 3 through 7 removed outlier: 4.130A pdb=" N GLN E 3 " --> pdb=" O SER E 25 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SER E 25 " --> pdb=" O GLN E 3 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N THR E 78 " --> pdb=" O ASP E 73 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ASP E 73 " --> pdb=" O THR E 78 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER E 71 " --> pdb=" O TYR E 80 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 11 through 12 Processing sheet with id=AB3, first strand: chain 'E' and resid 58 through 60 removed outlier: 3.531A pdb=" N SER E 59 " --> pdb=" O ASP E 50 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ASP E 50 " --> pdb=" O SER E 59 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE E 51 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N MET E 34 " --> pdb=" O ILE E 51 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASN E 35 " --> pdb=" O ALA E 97 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N VAL E 93 " --> pdb=" O GLN E 39 " (cutoff:3.500A) 302 hydrogen bonds defined for protein. 885 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: 0.93 Time building geometry restraints manager: 0.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 1320 1.28 - 1.41: 2069 1.41 - 1.54: 4728 1.54 - 1.68: 7 1.68 - 1.81: 69 Bond restraints: 8193 Sorted by residual: bond pdb=" CA ILE B 193 " pdb=" C ILE B 193 " ideal model delta sigma weight residual 1.524 1.441 0.083 8.60e-03 1.35e+04 9.33e+01 bond pdb=" CA VAL A 182 " pdb=" CB VAL A 182 " ideal model delta sigma weight residual 1.537 1.457 0.080 9.90e-03 1.02e+04 6.49e+01 bond pdb=" C CYS C 238 " pdb=" O CYS C 238 " ideal model delta sigma weight residual 1.235 1.142 0.093 1.26e-02 6.30e+03 5.43e+01 bond pdb=" CA ASP B 317 " pdb=" C ASP B 317 " ideal model delta sigma weight residual 1.528 1.456 0.072 1.13e-02 7.83e+03 4.02e+01 bond pdb=" C TYR A 284 " pdb=" O TYR A 284 " ideal model delta sigma weight residual 1.237 1.175 0.061 1.19e-02 7.06e+03 2.67e+01 ... (remaining 8188 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.84: 10828 2.84 - 5.67: 231 5.67 - 8.51: 31 8.51 - 11.35: 7 11.35 - 14.19: 3 Bond angle restraints: 11100 Sorted by residual: angle pdb=" N TRP A 164 " pdb=" CA TRP A 164 " pdb=" C TRP A 164 " ideal model delta sigma weight residual 112.45 98.26 14.19 1.39e+00 5.18e-01 1.04e+02 angle pdb=" C ILE B 193 " pdb=" CA ILE B 193 " pdb=" CB ILE B 193 " ideal model delta sigma weight residual 113.22 103.03 10.19 1.12e+00 7.97e-01 8.27e+01 angle pdb=" N GLN A 183 " pdb=" CA GLN A 183 " pdb=" C GLN A 183 " ideal model delta sigma weight residual 110.14 122.62 -12.48 1.55e+00 4.16e-01 6.49e+01 angle pdb=" N LEU A 162 " pdb=" CA LEU A 162 " pdb=" C LEU A 162 " ideal model delta sigma weight residual 111.28 100.71 10.57 1.35e+00 5.49e-01 6.13e+01 angle pdb=" N HIS A 161 " pdb=" CA HIS A 161 " pdb=" C HIS A 161 " ideal model delta sigma weight residual 110.50 99.69 10.81 1.41e+00 5.03e-01 5.88e+01 ... (remaining 11095 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.85: 4434 12.85 - 25.71: 341 25.71 - 38.56: 86 38.56 - 51.41: 26 51.41 - 64.26: 6 Dihedral angle restraints: 4893 sinusoidal: 1916 harmonic: 2977 Sorted by residual: dihedral pdb=" C ASP A 104 " pdb=" N ASP A 104 " pdb=" CA ASP A 104 " pdb=" CB ASP A 104 " ideal model delta harmonic sigma weight residual -122.60 -136.63 14.03 0 2.50e+00 1.60e-01 3.15e+01 dihedral pdb=" N VAL A 105 " pdb=" C VAL A 105 " pdb=" CA VAL A 105 " pdb=" CB VAL A 105 " ideal model delta harmonic sigma weight residual 123.40 110.43 12.97 0 2.50e+00 1.60e-01 2.69e+01 dihedral pdb=" C TYR A 284 " pdb=" N TYR A 284 " pdb=" CA TYR A 284 " pdb=" CB TYR A 284 " ideal model delta harmonic sigma weight residual -122.60 -109.89 -12.71 0 2.50e+00 1.60e-01 2.59e+01 ... (remaining 4890 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 1150 0.100 - 0.200: 95 0.200 - 0.300: 19 0.300 - 0.401: 1 0.401 - 0.501: 2 Chirality restraints: 1267 Sorted by residual: chirality pdb=" CA ASP A 104 " pdb=" N ASP A 104 " pdb=" C ASP A 104 " pdb=" CB ASP A 104 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.27e+00 chirality pdb=" CA VAL A 105 " pdb=" N VAL A 105 " pdb=" C VAL A 105 " pdb=" CB VAL A 105 " both_signs ideal model delta sigma weight residual False 2.44 2.90 -0.46 2.00e-01 2.50e+01 5.23e+00 chirality pdb=" CA LEU C 157 " pdb=" N LEU C 157 " pdb=" C LEU C 157 " pdb=" CB LEU C 157 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.58e+00 ... (remaining 1264 not shown) Planarity restraints: 1418 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS A 180 " 0.022 2.00e-02 2.50e+03 4.30e-02 1.85e+01 pdb=" C CYS A 180 " -0.074 2.00e-02 2.50e+03 pdb=" O CYS A 180 " 0.028 2.00e-02 2.50e+03 pdb=" N LYS A 181 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 161 " 0.020 2.00e-02 2.50e+03 4.13e-02 1.71e+01 pdb=" C HIS A 161 " -0.071 2.00e-02 2.50e+03 pdb=" O HIS A 161 " 0.026 2.00e-02 2.50e+03 pdb=" N LEU A 162 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 350 " -0.018 2.00e-02 2.50e+03 3.61e-02 1.30e+01 pdb=" C THR B 350 " 0.062 2.00e-02 2.50e+03 pdb=" O THR B 350 " -0.024 2.00e-02 2.50e+03 pdb=" N CYS B 351 " -0.021 2.00e-02 2.50e+03 ... (remaining 1415 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 166 2.67 - 3.23: 7268 3.23 - 3.79: 10789 3.79 - 4.34: 14974 4.34 - 4.90: 25200 Nonbonded interactions: 58397 Sorted by model distance: nonbonded pdb=" O GLY C 167 " pdb=" OD1 ASP C 191 " model vdw 2.115 3.040 nonbonded pdb=" OG SER C 166 " pdb=" OD1 ASP C 168 " model vdw 2.181 3.040 nonbonded pdb=" O SER A 65 " pdb=" OG1 THR A 69 " model vdw 2.278 3.040 nonbonded pdb=" O ASP B 317 " pdb=" C PRO B 318 " model vdw 2.373 3.270 nonbonded pdb=" OD1 ASN D 59 " pdb=" N ARG D 62 " model vdw 2.388 3.120 ... (remaining 58392 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: 1.380 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: 0.090 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 8.240 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 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 : 0.007 0.093 8194 Z= 0.508 Angle : 0.994 14.187 11102 Z= 0.681 Chirality : 0.062 0.501 1267 Planarity : 0.005 0.054 1418 Dihedral : 10.579 64.263 2964 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.52 % Favored : 89.48 % Rotamer: Outliers : 0.46 % Allowed : 7.48 % Favored : 92.06 % Cbeta Deviations : 0.42 % 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: -2.24 (0.25), residues: 1008 helix: -0.60 (0.27), residues: 351 sheet: -0.87 (0.37), residues: 201 loop : -2.50 (0.25), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 216 TYR 0.017 0.001 TYR A 284 PHE 0.053 0.002 PHE C 240 TRP 0.012 0.001 TRP E 47 HIS 0.014 0.001 HIS C 147 Details of bonding type rmsd covalent geometry : bond 0.00736 ( 8193) covalent geometry : angle 0.99402 (11100) SS BOND : bond 0.00127 ( 1) SS BOND : angle 0.68777 ( 2) hydrogen bonds : bond 0.32276 ( 301) hydrogen bonds : angle 7.98169 ( 885) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 262 time to evaluate : 0.304 Fit side-chains REVERT: A 81 SER cc_start: 0.9224 (t) cc_final: 0.8913 (p) REVERT: A 100 TYR cc_start: 0.8883 (t80) cc_final: 0.8659 (t80) REVERT: A 119 SER cc_start: 0.8673 (t) cc_final: 0.8207 (p) REVERT: A 131 ARG cc_start: 0.7870 (mtm180) cc_final: 0.7552 (mtt180) REVERT: A 139 VAL cc_start: 0.8666 (t) cc_final: 0.8458 (m) REVERT: B 20 ARG cc_start: 0.8378 (mtm180) cc_final: 0.8163 (mtm180) REVERT: B 38 ARG cc_start: 0.8256 (mtt90) cc_final: 0.7906 (mtp-110) REVERT: B 325 TYR cc_start: 0.8425 (m-80) cc_final: 0.8192 (m-80) REVERT: B 342 ARG cc_start: 0.7586 (mtt180) cc_final: 0.7308 (mmm-85) REVERT: C 22 GLN cc_start: 0.8766 (tt0) cc_final: 0.8428 (tt0) REVERT: C 49 GLN cc_start: 0.8070 (mt0) cc_final: 0.7862 (mt0) REVERT: C 303 ASP cc_start: 0.8604 (t0) cc_final: 0.8197 (t0) REVERT: C 312 VAL cc_start: 0.9034 (m) cc_final: 0.8815 (t) REVERT: E 65 LYS cc_start: 0.8788 (tttm) cc_final: 0.8500 (tttp) outliers start: 4 outliers final: 4 residues processed: 266 average time/residue: 0.0850 time to fit residues: 30.3807 Evaluate side-chains 213 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 209 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 191 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 0.6980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 ASN B 225 ASN C 41 ASN C 235 ASN C 242 ASN E 3 GLN E 31 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.182609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.142062 restraints weight = 9811.319| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.40 r_work: 0.3087 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8194 Z= 0.139 Angle : 0.564 6.106 11102 Z= 0.311 Chirality : 0.043 0.157 1267 Planarity : 0.004 0.043 1418 Dihedral : 5.281 53.313 1128 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 3.45 % Allowed : 12.66 % Favored : 83.89 % 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: -1.34 (0.26), residues: 1008 helix: 0.52 (0.27), residues: 374 sheet: -0.64 (0.36), residues: 209 loop : -2.35 (0.26), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 105 TYR 0.010 0.001 TYR A 256 PHE 0.015 0.001 PHE E 108 TRP 0.012 0.001 TRP B 220 HIS 0.003 0.001 HIS C 188 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 8193) covalent geometry : angle 0.56364 (11100) SS BOND : bond 0.00028 ( 1) SS BOND : angle 0.32537 ( 2) hydrogen bonds : bond 0.06704 ( 301) hydrogen bonds : angle 4.98618 ( 885) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 215 time to evaluate : 0.317 Fit side-chains REVERT: A 78 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8183 (tp) REVERT: A 81 SER cc_start: 0.9115 (t) cc_final: 0.8726 (p) REVERT: A 98 ASN cc_start: 0.8459 (m-40) cc_final: 0.8237 (m-40) REVERT: A 185 ASN cc_start: 0.8974 (p0) cc_final: 0.8691 (p0) REVERT: A 204 MET cc_start: 0.8408 (mtp) cc_final: 0.8197 (mtp) REVERT: A 213 LYS cc_start: 0.8179 (OUTLIER) cc_final: 0.7350 (tptp) REVERT: B 20 ARG cc_start: 0.8291 (mtm180) cc_final: 0.8056 (mtm110) REVERT: B 38 ARG cc_start: 0.8208 (mtt90) cc_final: 0.7867 (mtp180) REVERT: B 40 THR cc_start: 0.9256 (m) cc_final: 0.8814 (p) REVERT: B 342 ARG cc_start: 0.8029 (mtt180) cc_final: 0.7804 (mmm-85) REVERT: B 356 GLU cc_start: 0.8362 (mp0) cc_final: 0.7984 (mp0) REVERT: B 366 ARG cc_start: 0.8199 (ttp80) cc_final: 0.7815 (ptm-80) REVERT: C 22 GLN cc_start: 0.8740 (tt0) cc_final: 0.8445 (tt0) REVERT: C 295 ASP cc_start: 0.8389 (t0) cc_final: 0.8053 (t0) REVERT: C 303 ASP cc_start: 0.8908 (t0) cc_final: 0.8652 (t70) REVERT: C 312 VAL cc_start: 0.8929 (m) cc_final: 0.8612 (t) REVERT: E 69 THR cc_start: 0.7114 (OUTLIER) cc_final: 0.6900 (p) REVERT: E 80 TYR cc_start: 0.8034 (m-80) cc_final: 0.7817 (m-80) REVERT: E 83 MET cc_start: 0.7217 (mtt) cc_final: 0.6952 (mtp) REVERT: E 112 SER cc_start: 0.7637 (OUTLIER) cc_final: 0.7366 (m) outliers start: 30 outliers final: 17 residues processed: 228 average time/residue: 0.0784 time to fit residues: 24.3244 Evaluate side-chains 220 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 199 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 213 LYS Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain C residue 64 TYR Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 239 PHE Chi-restraints excluded: chain C residue 322 CYS Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain E residue 114 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 62 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 83 optimal weight: 5.9990 chunk 22 optimal weight: 0.6980 chunk 87 optimal weight: 0.9990 chunk 86 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 206 HIS C 242 ASN E 3 GLN E 82 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.167892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.126878 restraints weight = 9719.311| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.53 r_work: 0.3062 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8194 Z= 0.123 Angle : 0.531 5.742 11102 Z= 0.289 Chirality : 0.041 0.140 1267 Planarity : 0.004 0.042 1418 Dihedral : 4.761 56.833 1122 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 5.06 % Allowed : 14.73 % Favored : 80.21 % 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: -1.00 (0.26), residues: 1008 helix: 0.85 (0.27), residues: 375 sheet: -0.46 (0.36), residues: 219 loop : -2.23 (0.27), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 54 TYR 0.012 0.001 TYR A 100 PHE 0.012 0.001 PHE E 108 TRP 0.010 0.001 TRP B 220 HIS 0.004 0.001 HIS C 147 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 8193) covalent geometry : angle 0.53152 (11100) SS BOND : bond 0.00015 ( 1) SS BOND : angle 0.33948 ( 2) hydrogen bonds : bond 0.05696 ( 301) hydrogen bonds : angle 4.57180 ( 885) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 195 time to evaluate : 0.308 Fit side-chains revert: symmetry clash REVERT: A 81 SER cc_start: 0.9122 (t) cc_final: 0.8676 (p) REVERT: A 121 ASP cc_start: 0.8631 (t0) cc_final: 0.8390 (t0) REVERT: A 204 MET cc_start: 0.8242 (mtp) cc_final: 0.7981 (mtp) REVERT: A 213 LYS cc_start: 0.8209 (mtpt) cc_final: 0.7486 (tptt) REVERT: B 20 ARG cc_start: 0.8198 (mtm180) cc_final: 0.7889 (mtm110) REVERT: B 40 THR cc_start: 0.9180 (m) cc_final: 0.8758 (p) REVERT: B 329 ASP cc_start: 0.7772 (m-30) cc_final: 0.7474 (m-30) REVERT: B 356 GLU cc_start: 0.8297 (mp0) cc_final: 0.7929 (mp0) REVERT: B 366 ARG cc_start: 0.8074 (ttp80) cc_final: 0.7710 (ptm-80) REVERT: C 22 GLN cc_start: 0.8669 (tt0) cc_final: 0.8406 (tt0) REVERT: C 157 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7747 (mp) REVERT: C 295 ASP cc_start: 0.8272 (t0) cc_final: 0.7962 (t0) REVERT: C 303 ASP cc_start: 0.8706 (t0) cc_final: 0.8505 (t70) REVERT: C 312 VAL cc_start: 0.8926 (m) cc_final: 0.8599 (t) REVERT: E 65 LYS cc_start: 0.8774 (OUTLIER) cc_final: 0.8504 (mtpt) REVERT: E 80 TYR cc_start: 0.8058 (m-80) cc_final: 0.7849 (m-80) outliers start: 44 outliers final: 29 residues processed: 222 average time/residue: 0.0697 time to fit residues: 21.6584 Evaluate side-chains 221 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 190 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain C residue 41 ASN Chi-restraints excluded: chain C residue 64 TYR Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 181 GLN Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 239 PHE Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain C residue 322 CYS Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 336 SER Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 65 LYS Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 112 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 2 optimal weight: 4.9990 chunk 37 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 6 optimal weight: 0.3980 chunk 79 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 65 optimal weight: 0.5980 chunk 92 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 242 ASN C 244 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.167835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.127829 restraints weight = 10004.791| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.56 r_work: 0.3055 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8194 Z= 0.117 Angle : 0.515 5.486 11102 Z= 0.279 Chirality : 0.041 0.139 1267 Planarity : 0.003 0.041 1418 Dihedral : 4.589 50.348 1122 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 4.72 % Allowed : 16.92 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.86 (0.26), residues: 1008 helix: 0.99 (0.28), residues: 375 sheet: -0.25 (0.36), residues: 222 loop : -2.29 (0.27), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 261 TYR 0.012 0.001 TYR A 100 PHE 0.012 0.001 PHE A 249 TRP 0.009 0.001 TRP C 87 HIS 0.004 0.001 HIS C 147 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 8193) covalent geometry : angle 0.51480 (11100) SS BOND : bond 0.00052 ( 1) SS BOND : angle 0.15499 ( 2) hydrogen bonds : bond 0.05129 ( 301) hydrogen bonds : angle 4.43220 ( 885) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 188 time to evaluate : 0.318 Fit side-chains REVERT: A 81 SER cc_start: 0.9112 (t) cc_final: 0.8647 (p) REVERT: A 121 ASP cc_start: 0.8569 (t0) cc_final: 0.8335 (t0) REVERT: A 204 MET cc_start: 0.8197 (mtp) cc_final: 0.7938 (mtp) REVERT: A 213 LYS cc_start: 0.8181 (mtpt) cc_final: 0.7462 (tptt) REVERT: B 20 ARG cc_start: 0.8150 (mtm180) cc_final: 0.7842 (mtm110) REVERT: B 40 THR cc_start: 0.9154 (m) cc_final: 0.8717 (p) REVERT: B 329 ASP cc_start: 0.7858 (m-30) cc_final: 0.7456 (m-30) REVERT: B 344 TYR cc_start: 0.9062 (m-80) cc_final: 0.8814 (m-80) REVERT: B 356 GLU cc_start: 0.8240 (mp0) cc_final: 0.7885 (mp0) REVERT: B 366 ARG cc_start: 0.8045 (ttp80) cc_final: 0.7661 (ptm-80) REVERT: C 22 GLN cc_start: 0.8680 (tt0) cc_final: 0.8406 (tt0) REVERT: C 157 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7672 (mp) REVERT: C 295 ASP cc_start: 0.8270 (t0) cc_final: 0.7932 (t0) REVERT: C 303 ASP cc_start: 0.8686 (t0) cc_final: 0.8466 (t70) REVERT: C 312 VAL cc_start: 0.8917 (m) cc_final: 0.8609 (t) REVERT: E 65 LYS cc_start: 0.8760 (OUTLIER) cc_final: 0.8526 (mtpt) outliers start: 41 outliers final: 33 residues processed: 212 average time/residue: 0.0821 time to fit residues: 24.3132 Evaluate side-chains 220 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 185 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain C residue 41 ASN Chi-restraints excluded: chain C residue 64 TYR Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 181 GLN Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 239 PHE Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain C residue 322 CYS Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 336 SER Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 65 LYS Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 112 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 66 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 90 optimal weight: 0.8980 chunk 41 optimal weight: 5.9990 chunk 94 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 40 optimal weight: 0.0970 chunk 95 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.167358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.127362 restraints weight = 9894.291| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.54 r_work: 0.3052 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8194 Z= 0.116 Angle : 0.509 5.301 11102 Z= 0.275 Chirality : 0.041 0.158 1267 Planarity : 0.003 0.042 1418 Dihedral : 4.439 37.273 1122 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 4.95 % Allowed : 17.15 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.77 (0.26), residues: 1008 helix: 1.08 (0.28), residues: 375 sheet: -0.28 (0.36), residues: 221 loop : -2.20 (0.27), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 261 TYR 0.013 0.001 TYR A 100 PHE 0.012 0.001 PHE A 249 TRP 0.009 0.001 TRP C 87 HIS 0.003 0.001 HIS C 147 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 8193) covalent geometry : angle 0.50932 (11100) SS BOND : bond 0.00080 ( 1) SS BOND : angle 0.10252 ( 2) hydrogen bonds : bond 0.04939 ( 301) hydrogen bonds : angle 4.33390 ( 885) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 191 time to evaluate : 0.334 Fit side-chains revert: symmetry clash REVERT: A 81 SER cc_start: 0.9110 (t) cc_final: 0.8614 (p) REVERT: A 121 ASP cc_start: 0.8548 (t0) cc_final: 0.8319 (t0) REVERT: A 204 MET cc_start: 0.8182 (mtp) cc_final: 0.7927 (mtp) REVERT: A 213 LYS cc_start: 0.8162 (mtpt) cc_final: 0.7338 (tptt) REVERT: B 20 ARG cc_start: 0.8097 (mtm180) cc_final: 0.7873 (mtm110) REVERT: B 40 THR cc_start: 0.9065 (m) cc_final: 0.8656 (p) REVERT: B 329 ASP cc_start: 0.7850 (m-30) cc_final: 0.7411 (m-30) REVERT: B 344 TYR cc_start: 0.9056 (m-80) cc_final: 0.8821 (m-80) REVERT: B 356 GLU cc_start: 0.8238 (mp0) cc_final: 0.7854 (mp0) REVERT: B 366 ARG cc_start: 0.8094 (ttp80) cc_final: 0.7665 (ptm-80) REVERT: C 22 GLN cc_start: 0.8659 (tt0) cc_final: 0.8397 (tt0) REVERT: C 157 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.7666 (mp) REVERT: C 295 ASP cc_start: 0.8227 (t0) cc_final: 0.7869 (t0) REVERT: C 303 ASP cc_start: 0.8681 (t0) cc_final: 0.8437 (t70) REVERT: C 312 VAL cc_start: 0.8917 (m) cc_final: 0.8616 (t) REVERT: E 65 LYS cc_start: 0.8726 (OUTLIER) cc_final: 0.8486 (mtpt) outliers start: 43 outliers final: 34 residues processed: 214 average time/residue: 0.0822 time to fit residues: 24.6258 Evaluate side-chains 223 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 187 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain C residue 64 TYR Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 181 GLN Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 239 PHE Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain C residue 322 CYS Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 336 SER Chi-restraints excluded: chain D residue 21 MET Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 65 LYS Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain E residue 114 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 36 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 chunk 48 optimal weight: 20.0000 chunk 11 optimal weight: 0.7980 chunk 88 optimal weight: 0.7980 chunk 55 optimal weight: 0.7980 chunk 91 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 225 ASN C 41 ASN C 235 ASN C 242 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.167420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.126987 restraints weight = 9766.989| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.55 r_work: 0.3048 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8194 Z= 0.123 Angle : 0.519 5.629 11102 Z= 0.281 Chirality : 0.041 0.140 1267 Planarity : 0.003 0.042 1418 Dihedral : 4.346 24.953 1122 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 4.95 % Allowed : 17.61 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.76 (0.26), residues: 1008 helix: 1.09 (0.28), residues: 374 sheet: -0.15 (0.36), residues: 225 loop : -2.29 (0.26), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 261 TYR 0.019 0.001 TYR A 256 PHE 0.012 0.001 PHE A 249 TRP 0.009 0.001 TRP C 87 HIS 0.003 0.001 HIS C 147 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 8193) covalent geometry : angle 0.51907 (11100) SS BOND : bond 0.00012 ( 1) SS BOND : angle 0.02919 ( 2) hydrogen bonds : bond 0.04979 ( 301) hydrogen bonds : angle 4.32891 ( 885) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 185 time to evaluate : 0.310 Fit side-chains revert: symmetry clash REVERT: A 81 SER cc_start: 0.9130 (t) cc_final: 0.8632 (p) REVERT: A 121 ASP cc_start: 0.8537 (t0) cc_final: 0.8306 (t0) REVERT: A 213 LYS cc_start: 0.8176 (mtpt) cc_final: 0.7350 (tptt) REVERT: B 20 ARG cc_start: 0.8097 (mtm180) cc_final: 0.7873 (mtm110) REVERT: B 40 THR cc_start: 0.9056 (m) cc_final: 0.8626 (p) REVERT: B 344 TYR cc_start: 0.9059 (m-80) cc_final: 0.8818 (m-80) REVERT: B 356 GLU cc_start: 0.8257 (mp0) cc_final: 0.7873 (mp0) REVERT: B 366 ARG cc_start: 0.8113 (ttp80) cc_final: 0.7661 (ptm-80) REVERT: C 22 GLN cc_start: 0.8660 (tt0) cc_final: 0.8390 (tt0) REVERT: C 157 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7607 (mp) REVERT: C 295 ASP cc_start: 0.8241 (t0) cc_final: 0.7872 (t0) REVERT: C 303 ASP cc_start: 0.8646 (t0) cc_final: 0.8434 (t70) REVERT: C 312 VAL cc_start: 0.8934 (m) cc_final: 0.8632 (t) outliers start: 43 outliers final: 35 residues processed: 206 average time/residue: 0.0871 time to fit residues: 24.8591 Evaluate side-chains 219 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 183 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain C residue 41 ASN Chi-restraints excluded: chain C residue 64 TYR Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 181 GLN Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 239 PHE Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain C residue 322 CYS Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 336 SER Chi-restraints excluded: chain D residue 21 MET Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 114 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 14 optimal weight: 4.9990 chunk 83 optimal weight: 0.0270 chunk 50 optimal weight: 6.9990 chunk 26 optimal weight: 0.6980 chunk 65 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 3 optimal weight: 0.3980 chunk 91 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 overall best weight: 0.6040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 343 HIS C 41 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.168422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.128140 restraints weight = 9899.020| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.64 r_work: 0.3053 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.3401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8194 Z= 0.110 Angle : 0.507 5.377 11102 Z= 0.274 Chirality : 0.041 0.141 1267 Planarity : 0.003 0.042 1418 Dihedral : 4.180 24.615 1122 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.74 % Favored : 92.26 % Rotamer: Outliers : 4.37 % Allowed : 18.99 % Favored : 76.64 % 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: -0.70 (0.26), residues: 1008 helix: 1.17 (0.28), residues: 375 sheet: -0.21 (0.36), residues: 222 loop : -2.22 (0.26), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 54 TYR 0.013 0.001 TYR A 100 PHE 0.011 0.001 PHE A 249 TRP 0.009 0.001 TRP C 87 HIS 0.003 0.001 HIS C 147 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 8193) covalent geometry : angle 0.50684 (11100) SS BOND : bond 0.00055 ( 1) SS BOND : angle 0.00998 ( 2) hydrogen bonds : bond 0.04634 ( 301) hydrogen bonds : angle 4.22435 ( 885) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 182 time to evaluate : 0.291 Fit side-chains revert: symmetry clash REVERT: A 81 SER cc_start: 0.9122 (t) cc_final: 0.8616 (p) REVERT: A 121 ASP cc_start: 0.8554 (t0) cc_final: 0.8340 (t0) REVERT: A 213 LYS cc_start: 0.8167 (mtpt) cc_final: 0.7341 (tptt) REVERT: B 20 ARG cc_start: 0.8083 (mtm180) cc_final: 0.7860 (mtm110) REVERT: B 40 THR cc_start: 0.9044 (m) cc_final: 0.8635 (p) REVERT: B 344 TYR cc_start: 0.9042 (m-80) cc_final: 0.8821 (m-80) REVERT: B 356 GLU cc_start: 0.8189 (mp0) cc_final: 0.7799 (mp0) REVERT: B 366 ARG cc_start: 0.8120 (ttp80) cc_final: 0.7685 (ptm-80) REVERT: C 22 GLN cc_start: 0.8661 (tt0) cc_final: 0.8395 (tt0) REVERT: C 157 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7582 (mp) REVERT: C 267 MET cc_start: 0.7873 (tpp) cc_final: 0.7128 (mmp) REVERT: C 295 ASP cc_start: 0.8313 (t0) cc_final: 0.7948 (t0) REVERT: C 303 ASP cc_start: 0.8631 (t0) cc_final: 0.8325 (t0) REVERT: C 312 VAL cc_start: 0.8917 (m) cc_final: 0.8609 (t) outliers start: 38 outliers final: 33 residues processed: 203 average time/residue: 0.0821 time to fit residues: 23.0745 Evaluate side-chains 217 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 183 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain C residue 64 TYR Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 181 GLN Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 239 PHE Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain C residue 322 CYS Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 336 SER Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 114 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 90 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 chunk 94 optimal weight: 0.0040 chunk 12 optimal weight: 0.7980 chunk 22 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 41 ASN C 242 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.168164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.127763 restraints weight = 9815.452| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.60 r_work: 0.3053 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.3510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8194 Z= 0.109 Angle : 0.508 6.823 11102 Z= 0.273 Chirality : 0.040 0.138 1267 Planarity : 0.003 0.042 1418 Dihedral : 4.136 24.581 1122 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 4.37 % Allowed : 18.76 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.64 (0.26), residues: 1008 helix: 1.21 (0.28), residues: 375 sheet: -0.14 (0.36), residues: 222 loop : -2.19 (0.26), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 54 TYR 0.013 0.001 TYR A 100 PHE 0.011 0.001 PHE A 249 TRP 0.009 0.001 TRP B 263 HIS 0.005 0.001 HIS B 343 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 8193) covalent geometry : angle 0.50824 (11100) SS BOND : bond 0.00026 ( 1) SS BOND : angle 0.05964 ( 2) hydrogen bonds : bond 0.04481 ( 301) hydrogen bonds : angle 4.17817 ( 885) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 180 time to evaluate : 0.334 Fit side-chains revert: symmetry clash REVERT: A 81 SER cc_start: 0.9114 (t) cc_final: 0.8594 (p) REVERT: A 121 ASP cc_start: 0.8588 (t0) cc_final: 0.8374 (t0) REVERT: A 213 LYS cc_start: 0.8183 (mtpt) cc_final: 0.7372 (tptt) REVERT: B 20 ARG cc_start: 0.8066 (mtm180) cc_final: 0.7838 (mtm110) REVERT: B 40 THR cc_start: 0.9031 (m) cc_final: 0.8632 (p) REVERT: B 344 TYR cc_start: 0.9045 (m-80) cc_final: 0.8839 (m-80) REVERT: B 356 GLU cc_start: 0.8142 (mp0) cc_final: 0.7755 (mp0) REVERT: B 366 ARG cc_start: 0.8137 (ttp80) cc_final: 0.7706 (ptm-80) REVERT: C 22 GLN cc_start: 0.8654 (tt0) cc_final: 0.8440 (tt0) REVERT: C 47 ARG cc_start: 0.7682 (ttp80) cc_final: 0.7455 (ttp80) REVERT: C 157 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7536 (mp) REVERT: C 295 ASP cc_start: 0.8301 (t0) cc_final: 0.7936 (t0) REVERT: C 303 ASP cc_start: 0.8634 (t0) cc_final: 0.8327 (t0) REVERT: C 312 VAL cc_start: 0.8921 (m) cc_final: 0.8619 (t) outliers start: 38 outliers final: 34 residues processed: 201 average time/residue: 0.0835 time to fit residues: 23.3636 Evaluate side-chains 219 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 184 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain C residue 41 ASN Chi-restraints excluded: chain C residue 64 TYR Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 181 GLN Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 239 PHE Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 280 SER Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain C residue 322 CYS Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 336 SER Chi-restraints excluded: chain D residue 21 MET Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 114 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 20 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 48 optimal weight: 7.9990 chunk 12 optimal weight: 0.7980 chunk 95 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 69 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 ASN C 41 ASN C 244 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.164532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.124935 restraints weight = 9797.187| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.68 r_work: 0.3003 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.3379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8194 Z= 0.180 Angle : 0.593 6.966 11102 Z= 0.318 Chirality : 0.043 0.168 1267 Planarity : 0.004 0.042 1418 Dihedral : 4.515 23.420 1122 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % Rotamer: Outliers : 4.83 % Allowed : 18.76 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.78 (0.26), residues: 1008 helix: 1.07 (0.28), residues: 375 sheet: -0.21 (0.37), residues: 210 loop : -2.21 (0.26), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 54 TYR 0.017 0.001 TYR E 95 PHE 0.016 0.002 PHE A 260 TRP 0.010 0.001 TRP C 87 HIS 0.008 0.001 HIS B 343 Details of bonding type rmsd covalent geometry : bond 0.00423 ( 8193) covalent geometry : angle 0.59301 (11100) SS BOND : bond 0.00028 ( 1) SS BOND : angle 0.24917 ( 2) hydrogen bonds : bond 0.05838 ( 301) hydrogen bonds : angle 4.50357 ( 885) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 189 time to evaluate : 0.302 Fit side-chains REVERT: A 81 SER cc_start: 0.9140 (t) cc_final: 0.8632 (p) REVERT: A 121 ASP cc_start: 0.8639 (t0) cc_final: 0.8321 (t0) REVERT: B 20 ARG cc_start: 0.8160 (mtm180) cc_final: 0.7930 (mtm110) REVERT: B 40 THR cc_start: 0.9088 (m) cc_final: 0.8657 (p) REVERT: B 321 THR cc_start: 0.8695 (OUTLIER) cc_final: 0.8484 (p) REVERT: B 330 GLU cc_start: 0.8083 (mm-30) cc_final: 0.7756 (mm-30) REVERT: B 344 TYR cc_start: 0.9051 (m-80) cc_final: 0.8834 (m-80) REVERT: B 356 GLU cc_start: 0.8193 (mp0) cc_final: 0.7794 (mp0) REVERT: B 366 ARG cc_start: 0.8188 (ttp80) cc_final: 0.7715 (ptm-80) REVERT: C 22 GLN cc_start: 0.8682 (tt0) cc_final: 0.8410 (tt0) REVERT: C 157 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.7873 (mp) REVERT: C 303 ASP cc_start: 0.8701 (t0) cc_final: 0.8446 (t70) REVERT: C 312 VAL cc_start: 0.8947 (m) cc_final: 0.8648 (t) outliers start: 42 outliers final: 30 residues processed: 211 average time/residue: 0.0896 time to fit residues: 25.8564 Evaluate side-chains 218 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 186 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 64 TYR Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 181 GLN Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 239 PHE Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 280 SER Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain C residue 322 CYS Chi-restraints excluded: chain C residue 336 SER Chi-restraints excluded: chain D residue 21 MET Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 124 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 96 optimal weight: 0.7980 chunk 43 optimal weight: 0.0470 chunk 8 optimal weight: 0.8980 chunk 97 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 58 optimal weight: 0.4980 chunk 88 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 ASN C 41 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.167924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.128177 restraints weight = 9914.837| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.70 r_work: 0.3052 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.3616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8194 Z= 0.112 Angle : 0.525 6.126 11102 Z= 0.284 Chirality : 0.041 0.166 1267 Planarity : 0.004 0.048 1418 Dihedral : 4.308 24.973 1122 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 3.80 % Allowed : 20.25 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.65 (0.26), residues: 1008 helix: 1.21 (0.28), residues: 375 sheet: -0.16 (0.36), residues: 221 loop : -2.21 (0.26), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 266 TYR 0.013 0.001 TYR A 256 PHE 0.011 0.001 PHE A 249 TRP 0.009 0.001 TRP B 220 HIS 0.005 0.001 HIS B 343 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 8193) covalent geometry : angle 0.52549 (11100) SS BOND : bond 0.00069 ( 1) SS BOND : angle 0.09886 ( 2) hydrogen bonds : bond 0.04589 ( 301) hydrogen bonds : angle 4.23025 ( 885) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 185 time to evaluate : 0.330 Fit side-chains REVERT: A 81 SER cc_start: 0.9139 (t) cc_final: 0.8638 (p) REVERT: A 121 ASP cc_start: 0.8536 (t0) cc_final: 0.8318 (t0) REVERT: A 213 LYS cc_start: 0.8182 (mtpt) cc_final: 0.7372 (tptt) REVERT: B 20 ARG cc_start: 0.8133 (mtm180) cc_final: 0.7820 (mtm180) REVERT: B 40 THR cc_start: 0.9048 (m) cc_final: 0.8645 (p) REVERT: B 344 TYR cc_start: 0.9031 (m-80) cc_final: 0.8827 (m-80) REVERT: B 366 ARG cc_start: 0.8173 (ttp80) cc_final: 0.7717 (ptm-80) REVERT: C 22 GLN cc_start: 0.8667 (tt0) cc_final: 0.8448 (tt0) REVERT: C 47 ARG cc_start: 0.7776 (ttp80) cc_final: 0.7562 (ttp80) REVERT: C 157 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.7661 (mp) REVERT: C 312 VAL cc_start: 0.8937 (m) cc_final: 0.8625 (t) outliers start: 33 outliers final: 30 residues processed: 203 average time/residue: 0.0835 time to fit residues: 23.9175 Evaluate side-chains 217 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 186 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain C residue 41 ASN Chi-restraints excluded: chain C residue 64 TYR Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 181 GLN Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 239 PHE Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 280 SER Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain C residue 322 CYS Chi-restraints excluded: chain C residue 336 SER Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 124 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 45 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 78 optimal weight: 0.0970 chunk 15 optimal weight: 3.9990 chunk 83 optimal weight: 0.5980 chunk 69 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 94 optimal weight: 0.2980 chunk 36 optimal weight: 0.8980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 ASN ** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.167722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.127854 restraints weight = 9870.921| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.70 r_work: 0.3049 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.3645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8194 Z= 0.113 Angle : 0.539 6.087 11102 Z= 0.290 Chirality : 0.041 0.169 1267 Planarity : 0.004 0.048 1418 Dihedral : 4.248 24.399 1122 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 3.57 % Allowed : 20.48 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.61 (0.26), residues: 1008 helix: 1.24 (0.28), residues: 375 sheet: -0.11 (0.36), residues: 221 loop : -2.20 (0.26), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 266 TYR 0.013 0.001 TYR A 256 PHE 0.011 0.001 PHE A 249 TRP 0.009 0.001 TRP C 87 HIS 0.004 0.001 HIS B 343 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 8193) covalent geometry : angle 0.53928 (11100) SS BOND : bond 0.00046 ( 1) SS BOND : angle 0.07490 ( 2) hydrogen bonds : bond 0.04538 ( 301) hydrogen bonds : angle 4.21067 ( 885) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2006.55 seconds wall clock time: 35 minutes 3.44 seconds (2103.44 seconds total)