Starting phenix.real_space_refine on Wed Feb 12 14:31:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pok_17793/02_2025/8pok_17793.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pok_17793/02_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8pok_17793/02_2025/8pok_17793.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pok_17793/02_2025/8pok_17793.map" model { file = "/net/cci-nas-00/data/ceres_data/8pok_17793/02_2025/8pok_17793.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pok_17793/02_2025/8pok_17793.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 5.23, per 1000 atoms: 0.65 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: 1.80 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.87 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: 2.08 Time building geometry restraints manager: 2.08 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: 1.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 21.160 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.050 ------------------------------------------------------------------------------- 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 8193 Z= 0.494 Angle : 0.994 14.187 11100 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.012 0.001 TRP E 47 HIS 0.014 0.001 HIS C 147 PHE 0.053 0.002 PHE C 240 TYR 0.017 0.001 TYR A 284 ARG 0.002 0.000 ARG A 216 *********************** 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 : 0.924 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: 0.8162 (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: 0.2121 time to fit residues: 74.4954 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 : 0.856 ------------------------------------------------------------------------------- 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 83 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 41 optimal weight: 0.0270 chunk 25 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 chunk 47 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 89 optimal weight: 0.4980 overall best weight: 0.5638 ------------------------------------------------------------------------------- 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 = 0.3781 r_free = 0.3781 target = 0.169744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.127542 restraints weight = 9823.677| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.56 r_work: 0.3075 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8193 Z= 0.175 Angle : 0.552 5.755 11100 Z= 0.305 Chirality : 0.042 0.160 1267 Planarity : 0.004 0.043 1418 Dihedral : 5.224 55.423 1128 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.26), residues: 1008 helix: 0.55 (0.27), residues: 374 sheet: -0.66 (0.36), residues: 214 loop : -2.33 (0.27), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 220 HIS 0.003 0.001 HIS C 188 PHE 0.012 0.001 PHE E 108 TYR 0.010 0.001 TYR A 256 ARG 0.002 0.000 ARG E 105 *********************** 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 : 0.968 Fit side-chains REVERT: A 78 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8209 (tp) REVERT: A 81 SER cc_start: 0.9095 (t) cc_final: 0.8719 (p) REVERT: A 98 ASN cc_start: 0.8428 (m-40) cc_final: 0.8214 (m-40) REVERT: A 185 ASN cc_start: 0.8988 (p0) cc_final: 0.8654 (p0) REVERT: A 204 MET cc_start: 0.8330 (mtp) cc_final: 0.8113 (mtp) REVERT: A 213 LYS cc_start: 0.8202 (OUTLIER) cc_final: 0.7377 (tptp) REVERT: B 20 ARG cc_start: 0.8268 (mtm180) cc_final: 0.8030 (mtm110) REVERT: B 38 ARG cc_start: 0.8101 (mtt90) cc_final: 0.7839 (mtp180) REVERT: B 40 THR cc_start: 0.9213 (m) cc_final: 0.8790 (p) REVERT: B 342 ARG cc_start: 0.7909 (mtt180) cc_final: 0.7695 (mmm-85) REVERT: B 356 GLU cc_start: 0.8338 (mp0) cc_final: 0.8021 (mp0) REVERT: B 366 ARG cc_start: 0.8107 (ttp80) cc_final: 0.7889 (ptm-80) REVERT: C 22 GLN cc_start: 0.8723 (tt0) cc_final: 0.8436 (tt0) REVERT: C 295 ASP cc_start: 0.8196 (t0) cc_final: 0.7932 (t0) REVERT: C 303 ASP cc_start: 0.8776 (t0) cc_final: 0.8566 (t70) REVERT: C 312 VAL cc_start: 0.8866 (m) cc_final: 0.8565 (t) REVERT: E 69 THR cc_start: 0.7084 (OUTLIER) cc_final: 0.6878 (p) REVERT: E 80 TYR cc_start: 0.8080 (m-80) cc_final: 0.7812 (m-80) REVERT: E 83 MET cc_start: 0.7181 (mtt) cc_final: 0.6936 (mtp) REVERT: E 112 SER cc_start: 0.7545 (OUTLIER) cc_final: 0.7274 (m) outliers start: 30 outliers final: 17 residues processed: 229 average time/residue: 0.2009 time to fit residues: 62.2354 Evaluate side-chains 217 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 196 time to evaluate : 0.877 ------------------------------------------------------------------------------- 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 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 D residue 57 SER 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 82 optimal weight: 10.0000 chunk 77 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 72 optimal weight: 0.5980 chunk 40 optimal weight: 0.0980 chunk 62 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 242 ASN E 3 GLN E 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.167372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.127853 restraints weight = 9842.073| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.62 r_work: 0.3046 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8193 Z= 0.206 Angle : 0.553 6.217 11100 Z= 0.301 Chirality : 0.042 0.156 1267 Planarity : 0.004 0.040 1418 Dihedral : 4.867 57.875 1122 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 4.72 % Allowed : 15.30 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.26), residues: 1008 helix: 0.76 (0.27), residues: 375 sheet: -0.51 (0.36), residues: 219 loop : -2.25 (0.27), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 87 HIS 0.004 0.001 HIS C 147 PHE 0.014 0.002 PHE E 108 TYR 0.012 0.001 TYR A 100 ARG 0.002 0.000 ARG C 51 *********************** 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 235 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 194 time to evaluate : 0.894 Fit side-chains revert: symmetry clash REVERT: A 81 SER cc_start: 0.9113 (t) cc_final: 0.8677 (p) REVERT: A 121 ASP cc_start: 0.8676 (t0) cc_final: 0.8372 (t0) REVERT: A 204 MET cc_start: 0.8222 (mtp) cc_final: 0.7971 (mtp) REVERT: B 20 ARG cc_start: 0.8214 (mtm180) cc_final: 0.7951 (mtm110) REVERT: B 40 THR cc_start: 0.9202 (m) cc_final: 0.8751 (p) REVERT: B 329 ASP cc_start: 0.7765 (m-30) cc_final: 0.7487 (m-30) REVERT: B 356 GLU cc_start: 0.8272 (mp0) cc_final: 0.7927 (mp0) REVERT: B 366 ARG cc_start: 0.8130 (ttp80) cc_final: 0.7761 (ptm-80) REVERT: C 22 GLN cc_start: 0.8714 (tt0) cc_final: 0.8442 (tt0) REVERT: C 303 ASP cc_start: 0.8715 (t0) cc_final: 0.8502 (t70) REVERT: C 312 VAL cc_start: 0.8941 (m) cc_final: 0.8629 (t) outliers start: 41 outliers final: 27 residues processed: 217 average time/residue: 0.1864 time to fit residues: 55.3989 Evaluate side-chains 215 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 188 time to evaluate : 0.869 ------------------------------------------------------------------------------- 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 153 ILE Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 251 ILE 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 64 TYR Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 133 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 279 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 43 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 96 optimal weight: 5.9990 chunk 89 optimal weight: 0.6980 chunk 81 optimal weight: 10.0000 chunk 16 optimal weight: 0.0070 chunk 31 optimal weight: 0.9980 chunk 56 optimal weight: 0.0870 chunk 30 optimal weight: 1.9990 chunk 42 optimal weight: 9.9990 chunk 23 optimal weight: 0.9980 overall best weight: 0.5576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 206 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 = 0.3773 r_free = 0.3773 target = 0.168876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.128352 restraints weight = 9806.860| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.53 r_work: 0.3072 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8193 Z= 0.154 Angle : 0.501 5.250 11100 Z= 0.271 Chirality : 0.041 0.141 1267 Planarity : 0.003 0.043 1418 Dihedral : 4.497 47.690 1122 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 3.68 % Allowed : 18.07 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.26), residues: 1008 helix: 0.97 (0.28), residues: 375 sheet: -0.24 (0.36), residues: 222 loop : -2.25 (0.27), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 87 HIS 0.003 0.001 HIS C 147 PHE 0.010 0.001 PHE A 249 TYR 0.013 0.001 TYR A 100 ARG 0.006 0.000 ARG C 261 *********************** 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 223 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 191 time to evaluate : 0.991 Fit side-chains REVERT: A 81 SER cc_start: 0.9106 (t) cc_final: 0.8644 (p) REVERT: A 121 ASP cc_start: 0.8571 (t0) cc_final: 0.8344 (t0) REVERT: A 213 LYS cc_start: 0.8178 (mtpt) cc_final: 0.7461 (tptt) REVERT: B 20 ARG cc_start: 0.8155 (mtm180) cc_final: 0.7852 (mtm110) REVERT: B 40 THR cc_start: 0.9128 (m) cc_final: 0.8687 (p) REVERT: B 329 ASP cc_start: 0.7849 (m-30) cc_final: 0.7464 (m-30) REVERT: B 344 TYR cc_start: 0.9062 (m-80) cc_final: 0.8821 (m-80) REVERT: B 356 GLU cc_start: 0.8234 (mp0) cc_final: 0.7884 (mp0) REVERT: B 366 ARG cc_start: 0.8045 (ttp80) cc_final: 0.7672 (ptm-80) REVERT: C 22 GLN cc_start: 0.8696 (tt0) cc_final: 0.8419 (tt0) REVERT: C 54 ARG cc_start: 0.8293 (tpp-160) cc_final: 0.8009 (mmt90) REVERT: C 295 ASP cc_start: 0.8249 (m-30) cc_final: 0.7871 (m-30) REVERT: C 312 VAL cc_start: 0.8909 (m) cc_final: 0.8603 (t) REVERT: E 65 LYS cc_start: 0.8743 (OUTLIER) cc_final: 0.8500 (mtpt) outliers start: 32 outliers final: 28 residues processed: 210 average time/residue: 0.1777 time to fit residues: 51.6160 Evaluate side-chains 215 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 186 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 PHE 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 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 98 ILE 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 42 optimal weight: 7.9990 chunk 64 optimal weight: 1.9990 chunk 34 optimal weight: 0.0470 chunk 38 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 chunk 61 optimal weight: 0.0980 chunk 37 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 97 optimal weight: 0.9990 chunk 25 optimal weight: 0.2980 overall best weight: 0.4678 ------------------------------------------------------------------------------- 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 = 0.3938 r_free = 0.3938 target = 0.183414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.142785 restraints weight = 9673.342| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.62 r_work: 0.3089 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.3219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8193 Z= 0.143 Angle : 0.492 5.907 11100 Z= 0.266 Chirality : 0.041 0.156 1267 Planarity : 0.003 0.041 1418 Dihedral : 4.273 35.312 1122 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 3.68 % Allowed : 19.22 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.27), residues: 1008 helix: 1.15 (0.28), residues: 375 sheet: -0.10 (0.36), residues: 221 loop : -2.21 (0.27), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 87 HIS 0.003 0.000 HIS C 147 PHE 0.010 0.001 PHE A 249 TYR 0.013 0.001 TYR A 100 ARG 0.004 0.000 ARG C 261 *********************** 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 220 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 188 time to evaluate : 0.868 Fit side-chains revert: symmetry clash REVERT: A 81 SER cc_start: 0.9115 (t) cc_final: 0.8612 (p) REVERT: A 121 ASP cc_start: 0.8799 (t0) cc_final: 0.8568 (t0) REVERT: A 213 LYS cc_start: 0.8106 (mtpt) cc_final: 0.7377 (tptt) REVERT: B 20 ARG cc_start: 0.8125 (mtm180) cc_final: 0.7817 (mtm110) REVERT: B 40 THR cc_start: 0.9115 (m) cc_final: 0.8695 (p) REVERT: B 329 ASP cc_start: 0.8079 (m-30) cc_final: 0.7647 (m-30) REVERT: B 344 TYR cc_start: 0.9086 (m-80) cc_final: 0.8857 (m-80) REVERT: B 356 GLU cc_start: 0.8212 (mp0) cc_final: 0.7802 (mp0) REVERT: B 366 ARG cc_start: 0.8047 (ttp80) cc_final: 0.7843 (ptm-80) REVERT: C 22 GLN cc_start: 0.8656 (tt0) cc_final: 0.8389 (tt0) REVERT: C 54 ARG cc_start: 0.8464 (tpp-160) cc_final: 0.8140 (mmt90) REVERT: C 264 GLN cc_start: 0.8242 (pt0) cc_final: 0.8015 (mt0) REVERT: C 295 ASP cc_start: 0.8352 (m-30) cc_final: 0.7983 (m-30) REVERT: C 312 VAL cc_start: 0.8923 (m) cc_final: 0.8627 (t) REVERT: E 65 LYS cc_start: 0.8761 (OUTLIER) cc_final: 0.8501 (mtpt) outliers start: 32 outliers final: 27 residues processed: 204 average time/residue: 0.1872 time to fit residues: 52.6598 Evaluate side-chains 214 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 186 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 96 PHE 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 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 321 THR Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain C residue 64 TYR Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 239 PHE Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 279 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 75 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 86 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 60 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.180325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.139687 restraints weight = 9737.389| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.81 r_work: 0.3046 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8193 Z= 0.200 Angle : 0.526 5.560 11100 Z= 0.284 Chirality : 0.041 0.138 1267 Planarity : 0.003 0.041 1418 Dihedral : 4.387 26.110 1122 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 4.37 % Allowed : 18.64 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.26), residues: 1008 helix: 1.14 (0.28), residues: 374 sheet: -0.16 (0.36), residues: 220 loop : -2.23 (0.26), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 87 HIS 0.004 0.001 HIS C 147 PHE 0.013 0.001 PHE A 249 TYR 0.019 0.001 TYR A 256 ARG 0.003 0.000 ARG C 261 *********************** 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 229 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 191 time to evaluate : 0.900 Fit side-chains revert: symmetry clash REVERT: A 81 SER cc_start: 0.9135 (t) cc_final: 0.8634 (p) REVERT: A 121 ASP cc_start: 0.8777 (t0) cc_final: 0.8518 (t0) REVERT: B 20 ARG cc_start: 0.8167 (mtm180) cc_final: 0.7947 (mtm110) REVERT: B 40 THR cc_start: 0.9111 (m) cc_final: 0.8665 (p) REVERT: B 344 TYR cc_start: 0.9104 (m-80) cc_final: 0.8858 (m-80) REVERT: B 356 GLU cc_start: 0.8242 (mp0) cc_final: 0.7797 (mp0) REVERT: B 366 ARG cc_start: 0.8217 (ttp80) cc_final: 0.7806 (ptm-80) REVERT: C 22 GLN cc_start: 0.8671 (tt0) cc_final: 0.8404 (tt0) REVERT: C 54 ARG cc_start: 0.8579 (tpp-160) cc_final: 0.8242 (mmt90) REVERT: C 264 GLN cc_start: 0.8430 (pt0) cc_final: 0.8100 (mt0) REVERT: C 295 ASP cc_start: 0.8477 (m-30) cc_final: 0.8170 (m-30) REVERT: C 312 VAL cc_start: 0.8950 (m) cc_final: 0.8661 (t) REVERT: E 65 LYS cc_start: 0.8790 (OUTLIER) cc_final: 0.8568 (mtpt) outliers start: 38 outliers final: 31 residues processed: 210 average time/residue: 0.1901 time to fit residues: 54.9492 Evaluate side-chains 223 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 191 time to evaluate : 1.119 ------------------------------------------------------------------------------- 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 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 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 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 279 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 51 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 59 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3742 r_free = 0.3742 target = 0.166087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.124674 restraints weight = 9841.963| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.56 r_work: 0.3008 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.3277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8193 Z= 0.198 Angle : 0.536 5.368 11100 Z= 0.289 Chirality : 0.041 0.142 1267 Planarity : 0.003 0.041 1418 Dihedral : 4.322 24.250 1122 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 4.37 % Allowed : 19.33 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.26), residues: 1008 helix: 1.14 (0.28), residues: 374 sheet: -0.15 (0.36), residues: 220 loop : -2.27 (0.26), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 87 HIS 0.004 0.001 HIS C 147 PHE 0.012 0.001 PHE A 249 TYR 0.013 0.001 TYR A 256 ARG 0.003 0.000 ARG C 261 *********************** 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 226 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 188 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 SER cc_start: 0.9137 (t) cc_final: 0.8644 (p) REVERT: A 121 ASP cc_start: 0.8564 (t0) cc_final: 0.8321 (t0) REVERT: B 20 ARG cc_start: 0.8100 (mtm180) cc_final: 0.7883 (mtm110) REVERT: B 40 THR cc_start: 0.9091 (m) cc_final: 0.8636 (p) REVERT: B 344 TYR cc_start: 0.9061 (m-80) cc_final: 0.8830 (m-80) REVERT: B 356 GLU cc_start: 0.8151 (mp0) cc_final: 0.7744 (mp0) REVERT: B 366 ARG cc_start: 0.8151 (ttp80) cc_final: 0.7697 (ptm-80) REVERT: C 22 GLN cc_start: 0.8661 (tt0) cc_final: 0.8400 (tt0) REVERT: C 54 ARG cc_start: 0.8552 (tpp-160) cc_final: 0.8315 (mmt90) REVERT: C 264 GLN cc_start: 0.8448 (pt0) cc_final: 0.8070 (mt0) REVERT: C 295 ASP cc_start: 0.8381 (m-30) cc_final: 0.8097 (m-30) REVERT: C 312 VAL cc_start: 0.8931 (m) cc_final: 0.8633 (t) REVERT: E 65 LYS cc_start: 0.8742 (OUTLIER) cc_final: 0.8522 (mtpt) outliers start: 38 outliers final: 33 residues processed: 205 average time/residue: 0.1851 time to fit residues: 52.1389 Evaluate side-chains 222 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 188 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ARG 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 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 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 38 ILE 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 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 279 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 50 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 97 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 chunk 77 optimal weight: 0.0570 chunk 89 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 48 optimal weight: 5.9990 chunk 22 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 overall best weight: 0.8500 ------------------------------------------------------------------------------- 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 = 0.3751 r_free = 0.3751 target = 0.166508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.126869 restraints weight = 9938.722| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.68 r_work: 0.3033 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8193 Z= 0.197 Angle : 0.537 5.350 11100 Z= 0.289 Chirality : 0.042 0.167 1267 Planarity : 0.003 0.041 1418 Dihedral : 4.320 24.498 1122 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 3.91 % Allowed : 20.25 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.26), residues: 1008 helix: 1.16 (0.28), residues: 374 sheet: -0.14 (0.36), residues: 220 loop : -2.29 (0.26), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 87 HIS 0.004 0.001 HIS C 147 PHE 0.012 0.001 PHE A 249 TYR 0.014 0.001 TYR A 256 ARG 0.003 0.000 ARG C 261 *********************** 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 223 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 189 time to evaluate : 0.853 Fit side-chains revert: symmetry clash REVERT: A 81 SER cc_start: 0.9143 (t) cc_final: 0.8657 (p) REVERT: A 121 ASP cc_start: 0.8540 (t0) cc_final: 0.8301 (t0) REVERT: B 20 ARG cc_start: 0.8112 (mtm180) cc_final: 0.7892 (mtm110) REVERT: B 40 THR cc_start: 0.9083 (m) cc_final: 0.8639 (p) REVERT: B 344 TYR cc_start: 0.9051 (m-80) cc_final: 0.8822 (m-80) REVERT: B 356 GLU cc_start: 0.8181 (mp0) cc_final: 0.7795 (mp0) REVERT: B 366 ARG cc_start: 0.8166 (ttp80) cc_final: 0.7714 (ptm-80) REVERT: C 22 GLN cc_start: 0.8672 (tt0) cc_final: 0.8403 (tt0) REVERT: C 54 ARG cc_start: 0.8557 (tpp-160) cc_final: 0.8303 (mmt90) REVERT: C 295 ASP cc_start: 0.8368 (m-30) cc_final: 0.8079 (m-30) REVERT: C 312 VAL cc_start: 0.8946 (m) cc_final: 0.8652 (t) outliers start: 34 outliers final: 30 residues processed: 205 average time/residue: 0.1990 time to fit residues: 56.0527 Evaluate side-chains 221 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 191 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 77 VAL 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 303 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 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 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 279 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 33 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 22 optimal weight: 0.2980 chunk 53 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 61 optimal weight: 0.0030 chunk 58 optimal weight: 0.0870 chunk 94 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 overall best weight: 0.4370 ------------------------------------------------------------------------------- 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 C 242 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.181301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.141263 restraints weight = 9882.460| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 2.43 r_work: 0.3097 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.3573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8193 Z= 0.144 Angle : 0.503 5.479 11100 Z= 0.270 Chirality : 0.041 0.157 1267 Planarity : 0.003 0.043 1418 Dihedral : 4.076 24.716 1122 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 3.57 % Allowed : 20.60 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.26), residues: 1008 helix: 1.29 (0.28), residues: 374 sheet: -0.00 (0.36), residues: 219 loop : -2.24 (0.26), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 87 HIS 0.002 0.001 HIS C 147 PHE 0.009 0.001 PHE A 249 TYR 0.013 0.001 TYR A 100 ARG 0.004 0.000 ARG C 47 *********************** 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 220 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 189 time to evaluate : 0.927 Fit side-chains revert: symmetry clash REVERT: A 81 SER cc_start: 0.9144 (t) cc_final: 0.8637 (p) REVERT: A 121 ASP cc_start: 0.8760 (t0) cc_final: 0.8556 (t0) REVERT: A 213 LYS cc_start: 0.8171 (OUTLIER) cc_final: 0.7341 (tptt) REVERT: B 20 ARG cc_start: 0.8151 (mtm180) cc_final: 0.7847 (mtm180) REVERT: B 40 THR cc_start: 0.9056 (m) cc_final: 0.8657 (p) REVERT: B 329 ASP cc_start: 0.8041 (m-30) cc_final: 0.7631 (m-30) REVERT: B 344 TYR cc_start: 0.9073 (m-80) cc_final: 0.8848 (m-80) REVERT: B 356 GLU cc_start: 0.8127 (mp0) cc_final: 0.7692 (mp0) REVERT: B 366 ARG cc_start: 0.8146 (ttp80) cc_final: 0.7747 (ptm-80) REVERT: C 22 GLN cc_start: 0.8673 (tt0) cc_final: 0.8445 (tt0) REVERT: C 54 ARG cc_start: 0.8605 (tpp-160) cc_final: 0.8312 (mmt90) REVERT: C 295 ASP cc_start: 0.8340 (m-30) cc_final: 0.7864 (m-30) REVERT: C 312 VAL cc_start: 0.8937 (m) cc_final: 0.8652 (t) outliers start: 31 outliers final: 26 residues processed: 203 average time/residue: 0.1962 time to fit residues: 54.0746 Evaluate side-chains 213 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 186 time to evaluate : 0.967 ------------------------------------------------------------------------------- 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 213 LYS 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 183 THR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 239 PHE Chi-restraints excluded: chain C residue 279 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 62 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 87 optimal weight: 0.0170 chunk 19 optimal weight: 0.2980 chunk 2 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 3 optimal weight: 0.0170 chunk 40 optimal weight: 0.0670 overall best weight: 0.2594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 225 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.171187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.129846 restraints weight = 9737.890| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.58 r_work: 0.3099 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.3762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8193 Z= 0.137 Angle : 0.503 5.660 11100 Z= 0.270 Chirality : 0.040 0.165 1267 Planarity : 0.003 0.042 1418 Dihedral : 3.969 24.081 1122 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 2.76 % Allowed : 21.52 % Favored : 75.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.26), residues: 1008 helix: 1.40 (0.28), residues: 374 sheet: 0.08 (0.36), residues: 224 loop : -2.20 (0.26), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 220 HIS 0.003 0.001 HIS B 343 PHE 0.009 0.001 PHE A 249 TYR 0.013 0.001 TYR A 100 ARG 0.007 0.000 ARG B 266 ********************** 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 212 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 188 time to evaluate : 0.946 Fit side-chains revert: symmetry clash REVERT: A 81 SER cc_start: 0.9109 (t) cc_final: 0.8611 (p) REVERT: A 213 LYS cc_start: 0.8134 (ttpt) cc_final: 0.7335 (tptt) REVERT: B 20 ARG cc_start: 0.8079 (mtm180) cc_final: 0.7784 (mtm180) REVERT: B 40 THR cc_start: 0.8974 (m) cc_final: 0.8591 (p) REVERT: B 329 ASP cc_start: 0.7865 (m-30) cc_final: 0.7446 (m-30) REVERT: B 344 TYR cc_start: 0.9044 (m-80) cc_final: 0.8842 (m-80) REVERT: B 356 GLU cc_start: 0.8131 (mp0) cc_final: 0.7777 (mp0) REVERT: B 366 ARG cc_start: 0.8116 (ttp80) cc_final: 0.7791 (ptm-80) REVERT: C 22 GLN cc_start: 0.8630 (tt0) cc_final: 0.8404 (tt0) REVERT: C 54 ARG cc_start: 0.8466 (tpp-160) cc_final: 0.8180 (mmt90) REVERT: C 267 MET cc_start: 0.7852 (tpp) cc_final: 0.7162 (mmp) REVERT: C 295 ASP cc_start: 0.8276 (m-30) cc_final: 0.7765 (m-30) REVERT: C 312 VAL cc_start: 0.8888 (m) cc_final: 0.8638 (t) outliers start: 24 outliers final: 22 residues processed: 198 average time/residue: 0.1924 time to fit residues: 52.0028 Evaluate side-chains 205 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 183 time to evaluate : 0.955 ------------------------------------------------------------------------------- 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 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 64 TYR Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 239 PHE Chi-restraints excluded: chain C residue 279 THR 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 40 optimal weight: 5.9990 chunk 79 optimal weight: 0.9980 chunk 61 optimal weight: 0.4980 chunk 21 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 92 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 90 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 41 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.181203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.141381 restraints weight = 9814.288| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.40 r_work: 0.3064 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.3591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8193 Z= 0.201 Angle : 0.555 6.166 11100 Z= 0.296 Chirality : 0.042 0.164 1267 Planarity : 0.003 0.041 1418 Dihedral : 4.178 23.491 1122 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 2.76 % Allowed : 21.52 % Favored : 75.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.26), residues: 1008 helix: 1.32 (0.28), residues: 374 sheet: 0.01 (0.36), residues: 220 loop : -2.24 (0.26), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 87 HIS 0.006 0.001 HIS B 343 PHE 0.013 0.001 PHE A 249 TYR 0.014 0.001 TYR E 95 ARG 0.007 0.000 ARG B 266 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4399.66 seconds wall clock time: 78 minutes 32.27 seconds (4712.27 seconds total)