Starting phenix.real_space_refine on Sat Jul 4 04:38:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xiw_38391/07_2026/8xiw_38391.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xiw_38391/07_2026/8xiw_38391.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8xiw_38391/07_2026/8xiw_38391.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xiw_38391/07_2026/8xiw_38391.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xiw_38391/07_2026/8xiw_38391.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xiw_38391/07_2026/8xiw_38391.map" } resolution = 2.85 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.058 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 4 7.16 5 S 42 5.16 5 C 11699 2.51 5 N 3168 2.21 5 O 3484 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18397 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 4140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 4140 Classifications: {'peptide': 511} Link IDs: {'PTRANS': 22, 'TRANS': 488} Chain: "B" Number of atoms: 3181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3181 Classifications: {'peptide': 392} Link IDs: {'PTRANS': 13, 'TRANS': 378} Chain: "C" Number of atoms: 1342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1342 Classifications: {'peptide': 166} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 159} Chain: "D" Number of atoms: 1010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1010 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 2, 'TRANS': 130} Chain: "E" Number of atoms: 4140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 4140 Classifications: {'peptide': 511} Link IDs: {'PTRANS': 22, 'TRANS': 488} Chain: "F" Number of atoms: 3144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3144 Classifications: {'peptide': 387} Link IDs: {'PTRANS': 13, 'TRANS': 373} Chain: "G" Number of atoms: 1342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1342 Classifications: {'peptide': 166} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 159} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' FE': 2} Chain breaks: 2 Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' FE': 2} Chain breaks: 2 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "C" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "D" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "E" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "F" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "G" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 3.80, per 1000 atoms: 0.21 Number of scatterers: 18397 At special positions: 0 Unit cell: (147.726, 84.051, 114.615, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 4 26.01 S 42 16.00 O 3484 8.00 N 3168 7.00 C 11699 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.28 Conformation dependent library (CDL) restraints added in 805.9 milliseconds 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4228 Finding SS restraints... Secondary structure from input PDB file: 116 helices and 6 sheets defined 67.3% alpha, 2.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 24 through 31 removed outlier: 3.773A pdb=" N VAL A 28 " --> pdb=" O GLU A 24 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N TRP A 31 " --> pdb=" O GLU A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 36 removed outlier: 4.167A pdb=" N ASN A 36 " --> pdb=" O GLN A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 90 removed outlier: 4.282A pdb=" N LEU A 86 " --> pdb=" O LEU A 82 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N THR A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 94 removed outlier: 3.552A pdb=" N LYS A 94 " --> pdb=" O ALA A 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 91 through 94' Processing helix chain 'A' and resid 96 through 128 removed outlier: 3.733A pdb=" N VAL A 105 " --> pdb=" O GLU A 101 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ASN A 108 " --> pdb=" O LYS A 104 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA A 119 " --> pdb=" O TYR A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 162 Processing helix chain 'A' and resid 170 through 175 Processing helix chain 'A' and resid 179 through 189 removed outlier: 4.152A pdb=" N GLY A 183 " --> pdb=" O PRO A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 205 Processing helix chain 'A' and resid 212 through 227 Processing helix chain 'A' and resid 230 through 258 removed outlier: 3.606A pdb=" N THR A 234 " --> pdb=" O GLU A 230 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU A 237 " --> pdb=" O PRO A 233 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N SER A 238 " --> pdb=" O THR A 234 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR A 241 " --> pdb=" O LEU A 237 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ASP A 242 " --> pdb=" O SER A 238 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLU A 243 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU A 244 " --> pdb=" O GLU A 240 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ARG A 245 " --> pdb=" O THR A 241 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA A 248 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 292 removed outlier: 5.869A pdb=" N ASN A 268 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N THR A 269 " --> pdb=" O LYS A 265 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N TYR A 281 " --> pdb=" O THR A 277 " (cutoff:3.500A) Proline residue: A 284 - end of helix removed outlier: 3.541A pdb=" N GLY A 287 " --> pdb=" O THR A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 309 Processing helix chain 'A' and resid 312 through 317 Processing helix chain 'A' and resid 318 through 323 removed outlier: 4.143A pdb=" N LYS A 323 " --> pdb=" O ARG A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 353 removed outlier: 3.919A pdb=" N TYR A 340 " --> pdb=" O LYS A 336 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N TRP A 341 " --> pdb=" O THR A 337 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N HIS A 343 " --> pdb=" O ALA A 339 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N HIS A 344 " --> pdb=" O TYR A 340 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA A 349 " --> pdb=" O ASP A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 357 Processing helix chain 'A' and resid 365 through 376 Processing helix chain 'A' and resid 378 through 393 removed outlier: 3.779A pdb=" N HIS A 382 " --> pdb=" O GLY A 378 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N LYS A 385 " --> pdb=" O ASP A 381 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ILE A 386 " --> pdb=" O HIS A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 411 removed outlier: 3.657A pdb=" N TRP A 407 " --> pdb=" O ILE A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 460 Processing helix chain 'A' and resid 468 through 473 removed outlier: 3.730A pdb=" N GLN A 472 " --> pdb=" O ASN A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 485 Processing helix chain 'A' and resid 508 through 516 removed outlier: 3.581A pdb=" N ILE A 512 " --> pdb=" O THR A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 526 Processing helix chain 'B' and resid 16 through 27 Processing helix chain 'B' and resid 50 through 57 Processing helix chain 'B' and resid 87 through 91 removed outlier: 3.859A pdb=" N SER B 90 " --> pdb=" O GLY B 87 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N THR B 91 " --> pdb=" O ASN B 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 87 through 91' Processing helix chain 'B' and resid 108 through 134 Processing helix chain 'B' and resid 135 through 138 removed outlier: 3.619A pdb=" N THR B 138 " --> pdb=" O SER B 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 135 through 138' Processing helix chain 'B' and resid 140 through 147 Processing helix chain 'B' and resid 147 through 152 Processing helix chain 'B' and resid 154 through 165 removed outlier: 4.062A pdb=" N ASN B 158 " --> pdb=" O ALA B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 173 Processing helix chain 'B' and resid 175 through 207 removed outlier: 3.547A pdb=" N ARG B 179 " --> pdb=" O SER B 175 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU B 206 " --> pdb=" O PHE B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 224 Processing helix chain 'B' and resid 224 through 239 removed outlier: 4.321A pdb=" N GLY B 229 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N ALA B 230 " --> pdb=" O ILE B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 253 Processing helix chain 'B' and resid 254 through 265 removed outlier: 3.539A pdb=" N THR B 258 " --> pdb=" O VAL B 254 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N GLN B 261 " --> pdb=" O ALA B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 275 removed outlier: 3.567A pdb=" N THR B 273 " --> pdb=" O GLN B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 304 removed outlier: 3.923A pdb=" N PHE B 283 " --> pdb=" O LEU B 279 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLN B 286 " --> pdb=" O PHE B 282 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA B 297 " --> pdb=" O THR B 293 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR B 304 " --> pdb=" O ASP B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 339 removed outlier: 3.679A pdb=" N PHE B 319 " --> pdb=" O HIS B 315 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N HIS B 326 " --> pdb=" O ALA B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 345 removed outlier: 3.664A pdb=" N ALA B 343 " --> pdb=" O GLY B 340 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL B 345 " --> pdb=" O TYR B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 372 Processing helix chain 'B' and resid 372 through 377 removed outlier: 3.590A pdb=" N ILE B 376 " --> pdb=" O TYR B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 391 removed outlier: 3.525A pdb=" N LYS B 385 " --> pdb=" O ASP B 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 21 Processing helix chain 'C' and resid 25 through 41 Processing helix chain 'C' and resid 53 through 69 Processing helix chain 'C' and resid 74 through 81 Processing helix chain 'C' and resid 87 through 101 removed outlier: 3.776A pdb=" N VAL C 91 " --> pdb=" O ASP C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 119 removed outlier: 3.970A pdb=" N GLU C 109 " --> pdb=" O LYS C 105 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ARG C 110 " --> pdb=" O TYR C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 145 removed outlier: 3.611A pdb=" N ILE C 139 " --> pdb=" O ALA C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 161 Processing helix chain 'D' and resid 10 through 15 removed outlier: 3.575A pdb=" N MET D 13 " --> pdb=" O ALA D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 25 removed outlier: 3.669A pdb=" N PHE D 20 " --> pdb=" O THR D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 31 removed outlier: 4.200A pdb=" N VAL D 31 " --> pdb=" O GLU D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 55 Processing helix chain 'D' and resid 58 through 64 removed outlier: 3.778A pdb=" N ALA D 62 " --> pdb=" O LYS D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 96 Processing helix chain 'D' and resid 100 through 107 removed outlier: 3.844A pdb=" N ASN D 107 " --> pdb=" O ASP D 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 31 removed outlier: 3.668A pdb=" N VAL E 28 " --> pdb=" O GLU E 24 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N TRP E 31 " --> pdb=" O GLU E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 36 removed outlier: 4.110A pdb=" N ASN E 36 " --> pdb=" O GLN E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 90 removed outlier: 4.498A pdb=" N LEU E 86 " --> pdb=" O LEU E 82 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N THR E 87 " --> pdb=" O LEU E 83 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 128 removed outlier: 3.940A pdb=" N LYS E 104 " --> pdb=" O GLY E 100 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N VAL E 105 " --> pdb=" O GLU E 101 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE E 118 " --> pdb=" O GLU E 114 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA E 119 " --> pdb=" O TYR E 115 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA E 128 " --> pdb=" O LEU E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 161 removed outlier: 3.540A pdb=" N ILE E 145 " --> pdb=" O VAL E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 177 removed outlier: 4.206A pdb=" N ALA E 176 " --> pdb=" O ARG E 173 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE E 177 " --> pdb=" O THR E 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 173 through 177' Processing helix chain 'E' and resid 179 through 189 removed outlier: 4.203A pdb=" N GLY E 183 " --> pdb=" O PRO E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 196 through 205 Processing helix chain 'E' and resid 212 through 227 removed outlier: 3.747A pdb=" N VAL E 218 " --> pdb=" O ASN E 214 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 243 removed outlier: 3.557A pdb=" N THR E 234 " --> pdb=" O GLU E 230 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N SER E 238 " --> pdb=" O THR E 234 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR E 241 " --> pdb=" O LEU E 237 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ASP E 242 " --> pdb=" O SER E 238 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLU E 243 " --> pdb=" O VAL E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 257 removed outlier: 3.659A pdb=" N ALA E 248 " --> pdb=" O LEU E 244 " (cutoff:3.500A) Processing helix chain 'E' and resid 262 through 293 removed outlier: 3.658A pdb=" N TYR E 266 " --> pdb=" O ALA E 262 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N ASN E 268 " --> pdb=" O ALA E 264 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N THR E 269 " --> pdb=" O LYS E 265 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N TYR E 281 " --> pdb=" O THR E 277 " (cutoff:3.500A) Proline residue: E 284 - end of helix removed outlier: 3.814A pdb=" N GLY E 287 " --> pdb=" O THR E 283 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR E 288 " --> pdb=" O PRO E 284 " (cutoff:3.500A) Processing helix chain 'E' and resid 300 through 309 Processing helix chain 'E' and resid 311 through 316 Processing helix chain 'E' and resid 316 through 321 Processing helix chain 'E' and resid 322 through 325 removed outlier: 3.506A pdb=" N GLY E 325 " --> pdb=" O GLY E 322 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 322 through 325' Processing helix chain 'E' and resid 331 through 339 Processing helix chain 'E' and resid 341 through 353 Processing helix chain 'E' and resid 365 through 376 Processing helix chain 'E' and resid 378 through 393 removed outlier: 3.895A pdb=" N HIS E 382 " --> pdb=" O GLY E 378 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N LYS E 385 " --> pdb=" O ASP E 381 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ILE E 386 " --> pdb=" O HIS E 382 " (cutoff:3.500A) Processing helix chain 'E' and resid 403 through 411 removed outlier: 3.573A pdb=" N TRP E 407 " --> pdb=" O ILE E 403 " (cutoff:3.500A) Processing helix chain 'E' and resid 450 through 460 Processing helix chain 'E' and resid 461 through 464 removed outlier: 3.856A pdb=" N TYR E 464 " --> pdb=" O PRO E 461 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 461 through 464' Processing helix chain 'E' and resid 468 through 473 Processing helix chain 'E' and resid 477 through 485 Processing helix chain 'E' and resid 508 through 516 removed outlier: 3.639A pdb=" N GLY E 516 " --> pdb=" O ILE E 512 " (cutoff:3.500A) Processing helix chain 'E' and resid 521 through 525 removed outlier: 4.086A pdb=" N LYS E 525 " --> pdb=" O PRO E 522 " (cutoff:3.500A) Processing helix chain 'F' and resid 16 through 27 Processing helix chain 'F' and resid 50 through 57 Processing helix chain 'F' and resid 87 through 91 removed outlier: 3.945A pdb=" N SER F 90 " --> pdb=" O GLY F 87 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N THR F 91 " --> pdb=" O ASN F 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 87 through 91' Processing helix chain 'F' and resid 108 through 134 Processing helix chain 'F' and resid 135 through 139 removed outlier: 3.695A pdb=" N THR F 138 " --> pdb=" O SER F 135 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 146 Processing helix chain 'F' and resid 146 through 165 removed outlier: 3.870A pdb=" N TYR F 152 " --> pdb=" O LEU F 148 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N GLY F 153 " --> pdb=" O ASN F 149 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LEU F 156 " --> pdb=" O TYR F 152 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N TYR F 157 " --> pdb=" O GLY F 153 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ASN F 158 " --> pdb=" O ALA F 154 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 173 removed outlier: 3.835A pdb=" N ARG F 171 " --> pdb=" O SER F 167 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 207 Processing helix chain 'F' and resid 214 through 224 Processing helix chain 'F' and resid 224 through 239 removed outlier: 4.260A pdb=" N GLY F 229 " --> pdb=" O PRO F 225 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N ALA F 230 " --> pdb=" O ILE F 226 " (cutoff:3.500A) Processing helix chain 'F' and resid 243 through 253 Processing helix chain 'F' and resid 254 through 265 removed outlier: 4.430A pdb=" N GLN F 261 " --> pdb=" O ALA F 257 " (cutoff:3.500A) Processing helix chain 'F' and resid 267 through 275 Processing helix chain 'F' and resid 279 through 304 removed outlier: 3.586A pdb=" N PHE F 283 " --> pdb=" O LEU F 279 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLN F 286 " --> pdb=" O PHE F 282 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER F 287 " --> pdb=" O PHE F 283 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA F 297 " --> pdb=" O THR F 293 " (cutoff:3.500A) Processing helix chain 'F' and resid 312 through 339 removed outlier: 3.714A pdb=" N PHE F 319 " --> pdb=" O HIS F 315 " (cutoff:3.500A) Processing helix chain 'F' and resid 340 through 345 removed outlier: 3.901A pdb=" N ALA F 343 " --> pdb=" O GLY F 340 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL F 345 " --> pdb=" O TYR F 342 " (cutoff:3.500A) Processing helix chain 'F' and resid 353 through 372 Processing helix chain 'F' and resid 373 through 377 removed outlier: 3.956A pdb=" N GLY F 377 " --> pdb=" O ASP F 374 " (cutoff:3.500A) Processing helix chain 'F' and resid 381 through 391 removed outlier: 3.707A pdb=" N LYS F 385 " --> pdb=" O ASP F 381 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 21 Processing helix chain 'G' and resid 25 through 40 Processing helix chain 'G' and resid 53 through 72 Processing helix chain 'G' and resid 74 through 81 Processing helix chain 'G' and resid 87 through 101 removed outlier: 3.759A pdb=" N VAL G 91 " --> pdb=" O ASP G 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 104 through 120 Processing helix chain 'G' and resid 125 through 145 removed outlier: 3.531A pdb=" N PHE G 129 " --> pdb=" O PRO G 125 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE G 139 " --> pdb=" O ALA G 135 " (cutoff:3.500A) Processing helix chain 'G' and resid 152 through 161 Processing sheet with id=AA1, first strand: chain 'A' and resid 416 through 417 Processing sheet with id=AA2, first strand: chain 'A' and resid 444 through 448 removed outlier: 3.729A pdb=" N HIS C 166 " --> pdb=" O VAL A 438 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N GLU A 440 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N VAL C 164 " --> pdb=" O GLU A 440 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 68 through 71 removed outlier: 5.874A pdb=" N MET D 43 " --> pdb=" O VAL D 108 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N VAL D 108 " --> pdb=" O MET D 43 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 83 through 87 Processing sheet with id=AA5, first strand: chain 'E' and resid 416 through 417 Processing sheet with id=AA6, first strand: chain 'E' and resid 444 through 448 removed outlier: 6.690A pdb=" N VAL E 438 " --> pdb=" O LEU G 165 " (cutoff:3.500A) 992 hydrogen bonds defined for protein. 2895 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: 2.91 Time building geometry restraints manager: 1.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3284 1.32 - 1.44: 5293 1.44 - 1.57: 10161 1.57 - 1.69: 0 1.69 - 1.81: 68 Bond restraints: 18806 Sorted by residual: bond pdb=" N ILE F 376 " pdb=" CA ILE F 376 " ideal model delta sigma weight residual 1.456 1.496 -0.040 1.09e-02 8.42e+03 1.35e+01 bond pdb=" N ILE A 316 " pdb=" CA ILE A 316 " ideal model delta sigma weight residual 1.454 1.494 -0.040 1.19e-02 7.06e+03 1.10e+01 bond pdb=" N VAL A 254 " pdb=" CA VAL A 254 " ideal model delta sigma weight residual 1.462 1.498 -0.036 1.14e-02 7.69e+03 9.87e+00 bond pdb=" N SER E 194 " pdb=" CA SER E 194 " ideal model delta sigma weight residual 1.454 1.490 -0.036 1.15e-02 7.56e+03 9.77e+00 bond pdb=" N GLY E 432 " pdb=" CA GLY E 432 " ideal model delta sigma weight residual 1.444 1.474 -0.030 9.60e-03 1.09e+04 9.65e+00 ... (remaining 18801 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 24367 1.95 - 3.91: 1093 3.91 - 5.86: 67 5.86 - 7.81: 7 7.81 - 9.76: 3 Bond angle restraints: 25537 Sorted by residual: angle pdb=" N TRP G 16 " pdb=" CA TRP G 16 " pdb=" C TRP G 16 " ideal model delta sigma weight residual 111.28 119.53 -8.25 1.09e+00 8.42e-01 5.73e+01 angle pdb=" N GLY A 322 " pdb=" CA GLY A 322 " pdb=" C GLY A 322 " ideal model delta sigma weight residual 113.24 103.48 9.76 1.31e+00 5.83e-01 5.55e+01 angle pdb=" N TRP G 16 " pdb=" CA TRP G 16 " pdb=" CB TRP G 16 " ideal model delta sigma weight residual 110.12 103.79 6.33 1.47e+00 4.63e-01 1.85e+01 angle pdb=" N ILE E 145 " pdb=" CA ILE E 145 " pdb=" C ILE E 145 " ideal model delta sigma weight residual 111.00 106.67 4.33 1.09e+00 8.42e-01 1.58e+01 angle pdb=" N GLU A 396 " pdb=" CA GLU A 396 " pdb=" C GLU A 396 " ideal model delta sigma weight residual 113.12 118.07 -4.95 1.25e+00 6.40e-01 1.57e+01 ... (remaining 25532 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 9841 17.88 - 35.77: 918 35.77 - 53.65: 148 53.65 - 71.53: 37 71.53 - 89.42: 22 Dihedral angle restraints: 10966 sinusoidal: 4368 harmonic: 6598 Sorted by residual: dihedral pdb=" CA TRP B 108 " pdb=" C TRP B 108 " pdb=" N HIS B 109 " pdb=" CA HIS B 109 " ideal model delta harmonic sigma weight residual -180.00 -160.33 -19.67 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA TRP F 108 " pdb=" C TRP F 108 " pdb=" N HIS F 109 " pdb=" CA HIS F 109 " ideal model delta harmonic sigma weight residual -180.00 -160.66 -19.34 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA ARG B 107 " pdb=" C ARG B 107 " pdb=" N TRP B 108 " pdb=" CA TRP B 108 " ideal model delta harmonic sigma weight residual 180.00 161.28 18.72 0 5.00e+00 4.00e-02 1.40e+01 ... (remaining 10963 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1892 0.051 - 0.101: 538 0.101 - 0.152: 185 0.152 - 0.202: 35 0.202 - 0.253: 7 Chirality restraints: 2657 Sorted by residual: chirality pdb=" CA LEU G 124 " pdb=" N LEU G 124 " pdb=" C LEU G 124 " pdb=" CB LEU G 124 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" CA VAL A 16 " pdb=" N VAL A 16 " pdb=" C VAL A 16 " pdb=" CB VAL A 16 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CA ILE E 257 " pdb=" N ILE E 257 " pdb=" C ILE E 257 " pdb=" CB ILE E 257 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.23e+00 ... (remaining 2654 not shown) Planarity restraints: 3304 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 280 " 0.013 2.00e-02 2.50e+03 2.63e-02 6.92e+00 pdb=" C LYS A 280 " -0.045 2.00e-02 2.50e+03 pdb=" O LYS A 280 " 0.017 2.00e-02 2.50e+03 pdb=" N TYR A 281 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 79 " -0.013 2.00e-02 2.50e+03 2.60e-02 6.77e+00 pdb=" C PHE A 79 " 0.045 2.00e-02 2.50e+03 pdb=" O PHE A 79 " -0.017 2.00e-02 2.50e+03 pdb=" N GLY A 80 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY D 130 " -0.012 2.00e-02 2.50e+03 2.47e-02 6.11e+00 pdb=" C GLY D 130 " 0.043 2.00e-02 2.50e+03 pdb=" O GLY D 130 " -0.016 2.00e-02 2.50e+03 pdb=" N LEU D 131 " -0.015 2.00e-02 2.50e+03 ... (remaining 3301 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.35: 19 2.35 - 2.99: 9711 2.99 - 3.63: 26606 3.63 - 4.26: 41374 4.26 - 4.90: 72803 Nonbonded interactions: 150513 Sorted by model distance: nonbonded pdb=" OE2 GLU E 209 " pdb="FE FE E 602 " model vdw 1.716 3.000 nonbonded pdb=" OE2 GLU A 209 " pdb="FE FE A 602 " model vdw 1.729 3.000 nonbonded pdb=" ND1 HIS E 246 " pdb="FE FE E 602 " model vdw 1.784 3.080 nonbonded pdb=" OE2 GLU E 243 " pdb="FE FE E 602 " model vdw 1.860 3.000 nonbonded pdb=" OE1 GLU A 144 " pdb="FE FE A 601 " model vdw 1.887 3.000 ... (remaining 150508 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 9 through 395) selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } 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: 3.880 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: 0.020 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 16.100 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 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:6.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 18806 Z= 0.379 Angle : 0.770 9.763 25537 Z= 0.557 Chirality : 0.054 0.253 2657 Planarity : 0.004 0.049 3304 Dihedral : 14.513 89.418 6738 Min Nonbonded Distance : 1.716 Molprobity Statistics. All-atom Clashscore : 0.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.86 % Allowed : 3.00 % Favored : 96.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.18), residues: 2252 helix: 0.80 (0.15), residues: 1344 sheet: 2.31 (0.76), residues: 59 loop : -0.82 (0.20), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 419 TYR 0.011 0.001 TYR G 40 PHE 0.009 0.001 PHE A 39 TRP 0.027 0.001 TRP F 108 HIS 0.007 0.001 HIS A 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00531 / 0.38 (18806) covalent geometry : angle 0.76961 / 0.56 (25537) hydrogen bonds : bond 0.17833 / 12.04 ( 992) hydrogen bonds : angle 6.35217 / 4.63 ( 2895) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 196 time to evaluate : 0.749 Fit side-chains revert: symmetry clash REVERT: A 55 GLN cc_start: 0.8528 (mt0) cc_final: 0.8315 (pp30) REVERT: A 368 ASP cc_start: 0.8419 (m-30) cc_final: 0.8108 (m-30) REVERT: C 41 SER cc_start: 0.8419 (t) cc_final: 0.7993 (t) REVERT: C 47 SER cc_start: 0.8928 (t) cc_final: 0.8699 (t) REVERT: E 184 MET cc_start: 0.7957 (tpp) cc_final: 0.7755 (tpt) REVERT: E 240 GLU cc_start: 0.7918 (tm-30) cc_final: 0.7497 (tm-30) REVERT: F 159 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7668 (tp30) REVERT: F 236 GLU cc_start: 0.8174 (tp30) cc_final: 0.7614 (tp30) outliers start: 16 outliers final: 2 residues processed: 208 average time/residue: 0.6180 time to fit residues: 143.8923 Evaluate side-chains 149 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 147 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 17 ASN Chi-restraints excluded: chain E residue 188 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 216 optimal weight: 5.9990 chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 200 optimal weight: 4.9990 chunk 212 optimal weight: 0.8980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 467 HIS C 28 GLN D 9 ASN D 14 GLN E 133 GLN E 246 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.088415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.070911 restraints weight = 32530.645| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 2.88 r_work: 0.2732 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.1128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18806 Z= 0.132 Angle : 0.495 10.806 25537 Z= 0.270 Chirality : 0.039 0.158 2657 Planarity : 0.004 0.045 3304 Dihedral : 3.915 48.178 2504 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 1.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.23 % Allowed : 7.49 % Favored : 91.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.18), residues: 2252 helix: 1.52 (0.14), residues: 1374 sheet: 1.76 (0.64), residues: 70 loop : -0.70 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 265 TYR 0.011 0.001 TYR B 327 PHE 0.011 0.001 PHE A 39 TRP 0.021 0.001 TRP F 108 HIS 0.004 0.001 HIS A 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (18806) covalent geometry : angle 0.49453 / 0.27 (25537) hydrogen bonds : bond 0.06144 / 4.11 ( 992) hydrogen bonds : angle 4.51092 / 3.30 ( 2895) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 164 time to evaluate : 0.735 Fit side-chains revert: symmetry clash REVERT: A 368 ASP cc_start: 0.8699 (m-30) cc_final: 0.8360 (m-30) REVERT: B 394 LYS cc_start: 0.8916 (OUTLIER) cc_final: 0.8270 (pttm) REVERT: C 47 SER cc_start: 0.9168 (t) cc_final: 0.8961 (t) REVERT: C 87 ASP cc_start: 0.8053 (t0) cc_final: 0.7827 (t0) REVERT: D 85 GLU cc_start: 0.8260 (tt0) cc_final: 0.7721 (tm-30) REVERT: E 184 MET cc_start: 0.8536 (tpp) cc_final: 0.8137 (tpp) REVERT: E 240 GLU cc_start: 0.8116 (tm-30) cc_final: 0.7762 (tm-30) REVERT: F 159 GLU cc_start: 0.8377 (mm-30) cc_final: 0.8102 (tp30) outliers start: 23 outliers final: 8 residues processed: 177 average time/residue: 0.5685 time to fit residues: 113.9906 Evaluate side-chains 153 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 144 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain B residue 176 ASP Chi-restraints excluded: chain B residue 394 LYS Chi-restraints excluded: chain C residue 55 GLN Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 188 PHE Chi-restraints excluded: chain G residue 66 SER Chi-restraints excluded: chain G residue 141 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 208 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 211 optimal weight: 2.9990 chunk 85 optimal weight: 0.2980 chunk 184 optimal weight: 3.9990 chunk 219 optimal weight: 0.9990 chunk 108 optimal weight: 0.0970 chunk 95 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 110 optimal weight: 7.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 467 HIS C 28 GLN D 9 ASN D 14 GLN F 80 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.088841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.071397 restraints weight = 32564.944| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 2.89 r_work: 0.2732 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.1383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 18806 Z= 0.116 Angle : 0.456 9.432 25537 Z= 0.248 Chirality : 0.039 0.137 2657 Planarity : 0.003 0.043 3304 Dihedral : 3.873 52.133 2502 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 1.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.50 % Allowed : 7.97 % Favored : 90.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.18), residues: 2252 helix: 1.81 (0.14), residues: 1370 sheet: 1.86 (0.62), residues: 70 loop : -0.64 (0.21), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 265 TYR 0.011 0.001 TYR B 327 PHE 0.013 0.001 PHE A 188 TRP 0.019 0.001 TRP F 108 HIS 0.005 0.001 HIS A 467 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.12 (18806) covalent geometry : angle 0.45632 / 0.25 (25537) hydrogen bonds : bond 0.05502 / 3.67 ( 992) hydrogen bonds : angle 4.32777 / 3.17 ( 2895) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 154 time to evaluate : 0.746 Fit side-chains revert: symmetry clash REVERT: A 240 GLU cc_start: 0.8454 (tp30) cc_final: 0.8238 (tp30) REVERT: A 368 ASP cc_start: 0.8716 (m-30) cc_final: 0.8334 (m-30) REVERT: B 47 LYS cc_start: 0.9203 (mmmt) cc_final: 0.8990 (tppp) REVERT: B 394 LYS cc_start: 0.8924 (OUTLIER) cc_final: 0.8259 (pttm) REVERT: C 47 SER cc_start: 0.9168 (t) cc_final: 0.8542 (t) REVERT: D 85 GLU cc_start: 0.8257 (tt0) cc_final: 0.7569 (tm-30) REVERT: E 184 MET cc_start: 0.8486 (tpp) cc_final: 0.8059 (tpp) REVERT: E 186 ARG cc_start: 0.8619 (OUTLIER) cc_final: 0.7926 (ttt90) REVERT: E 209 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.8377 (tt0) REVERT: E 240 GLU cc_start: 0.8040 (tm-30) cc_final: 0.7620 (tm-30) REVERT: F 159 GLU cc_start: 0.8308 (mm-30) cc_final: 0.8008 (tp30) outliers start: 28 outliers final: 13 residues processed: 173 average time/residue: 0.5846 time to fit residues: 114.9054 Evaluate side-chains 160 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 144 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain B residue 176 ASP Chi-restraints excluded: chain B residue 394 LYS Chi-restraints excluded: chain C residue 55 GLN Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain E residue 78 GLN Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 186 ARG Chi-restraints excluded: chain E residue 188 PHE Chi-restraints excluded: chain E residue 209 GLU Chi-restraints excluded: chain E residue 244 LEU Chi-restraints excluded: chain F residue 173 CYS Chi-restraints excluded: chain G residue 66 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 121 optimal weight: 4.9990 chunk 155 optimal weight: 1.9990 chunk 125 optimal weight: 0.9980 chunk 213 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 219 optimal weight: 2.9990 chunk 149 optimal weight: 8.9990 chunk 191 optimal weight: 0.0870 chunk 99 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 overall best weight: 0.9560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 214 ASN B 43 GLN C 28 GLN D 9 ASN D 14 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.087894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.070490 restraints weight = 32673.377| |-----------------------------------------------------------------------------| r_work (start): 0.2873 rms_B_bonded: 2.87 r_work: 0.2718 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 18806 Z= 0.120 Angle : 0.458 8.506 25537 Z= 0.248 Chirality : 0.039 0.151 2657 Planarity : 0.003 0.042 3304 Dihedral : 3.867 51.853 2502 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 1.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.50 % Allowed : 9.31 % Favored : 89.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.18), residues: 2252 helix: 1.92 (0.14), residues: 1362 sheet: 1.89 (0.62), residues: 70 loop : -0.56 (0.21), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 265 TYR 0.011 0.001 TYR B 327 PHE 0.015 0.001 PHE A 188 TRP 0.017 0.001 TRP F 108 HIS 0.005 0.001 HIS A 467 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (18806) covalent geometry : angle 0.45807 / 0.25 (25537) hydrogen bonds : bond 0.05506 / 3.67 ( 992) hydrogen bonds : angle 4.27655 / 3.13 ( 2895) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 148 time to evaluate : 0.732 Fit side-chains revert: symmetry clash REVERT: B 47 LYS cc_start: 0.9194 (mmmt) cc_final: 0.8982 (tppp) REVERT: B 383 ASP cc_start: 0.8256 (p0) cc_final: 0.7999 (m-30) REVERT: B 394 LYS cc_start: 0.8945 (OUTLIER) cc_final: 0.8282 (pttm) REVERT: D 85 GLU cc_start: 0.8265 (tt0) cc_final: 0.7616 (tm-30) REVERT: E 184 MET cc_start: 0.8496 (tpp) cc_final: 0.8052 (tpp) REVERT: E 368 ASP cc_start: 0.8749 (m-30) cc_final: 0.8327 (m-30) REVERT: F 159 GLU cc_start: 0.8345 (mm-30) cc_final: 0.8006 (tp30) outliers start: 28 outliers final: 17 residues processed: 168 average time/residue: 0.5737 time to fit residues: 109.9734 Evaluate side-chains 158 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 140 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 HIS Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain B residue 176 ASP Chi-restraints excluded: chain B residue 394 LYS Chi-restraints excluded: chain C residue 55 GLN Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain E residue 78 GLN Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 188 PHE Chi-restraints excluded: chain E residue 467 HIS Chi-restraints excluded: chain F residue 173 CYS Chi-restraints excluded: chain G residue 10 ASN Chi-restraints excluded: chain G residue 66 SER Chi-restraints excluded: chain G residue 141 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 55 optimal weight: 0.4980 chunk 143 optimal weight: 5.9990 chunk 93 optimal weight: 4.9990 chunk 186 optimal weight: 5.9990 chunk 125 optimal weight: 1.9990 chunk 187 optimal weight: 0.7980 chunk 166 optimal weight: 3.9990 chunk 213 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 127 optimal weight: 3.9990 chunk 151 optimal weight: 8.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 467 HIS A 521 ASN B 77 GLN B 80 HIS C 28 GLN D 9 ASN D 14 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.083484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.065888 restraints weight = 33091.008| |-----------------------------------------------------------------------------| r_work (start): 0.2780 rms_B_bonded: 2.89 r_work: 0.2621 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 18806 Z= 0.200 Angle : 0.520 8.811 25537 Z= 0.285 Chirality : 0.042 0.164 2657 Planarity : 0.004 0.042 3304 Dihedral : 4.086 51.182 2502 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.55 % Allowed : 10.43 % Favored : 88.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.18), residues: 2252 helix: 1.79 (0.14), residues: 1363 sheet: 1.76 (0.61), residues: 70 loop : -0.71 (0.20), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 265 TYR 0.016 0.001 TYR G 40 PHE 0.017 0.001 PHE A 39 TRP 0.013 0.001 TRP F 108 HIS 0.007 0.001 HIS A 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.20 (18806) covalent geometry : angle 0.52021 / 0.29 (25537) hydrogen bonds : bond 0.07210 / 4.79 ( 992) hydrogen bonds : angle 4.45806 / 3.27 ( 2895) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 147 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 47 LYS cc_start: 0.9220 (mmmt) cc_final: 0.9010 (tppp) REVERT: B 394 LYS cc_start: 0.8987 (OUTLIER) cc_final: 0.8328 (pttm) REVERT: D 85 GLU cc_start: 0.8208 (tt0) cc_final: 0.7648 (tm-30) REVERT: E 184 MET cc_start: 0.8493 (tpp) cc_final: 0.8034 (tpp) REVERT: F 381 ASP cc_start: 0.8391 (p0) cc_final: 0.7949 (p0) REVERT: F 383 ASP cc_start: 0.7904 (p0) cc_final: 0.7674 (p0) REVERT: G 9 GLU cc_start: 0.8270 (mm-30) cc_final: 0.7812 (mp0) outliers start: 29 outliers final: 14 residues processed: 166 average time/residue: 0.6022 time to fit residues: 113.5750 Evaluate side-chains 151 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 136 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain B residue 176 ASP Chi-restraints excluded: chain B residue 394 LYS Chi-restraints excluded: chain C residue 28 GLN Chi-restraints excluded: chain C residue 55 GLN Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain E residue 78 GLN Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 188 PHE Chi-restraints excluded: chain E residue 318 ILE Chi-restraints excluded: chain F residue 173 CYS Chi-restraints excluded: chain G residue 66 SER Chi-restraints excluded: chain G residue 141 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 38 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 206 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 134 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 163 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 43 GLN C 168 GLN D 14 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.083682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.066140 restraints weight = 32788.838| |-----------------------------------------------------------------------------| r_work (start): 0.2787 rms_B_bonded: 2.89 r_work: 0.2628 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 18806 Z= 0.177 Angle : 0.508 8.800 25537 Z= 0.279 Chirality : 0.041 0.156 2657 Planarity : 0.004 0.041 3304 Dihedral : 4.117 51.582 2502 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.50 % Allowed : 11.13 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.18), residues: 2252 helix: 1.75 (0.14), residues: 1363 sheet: 1.73 (0.62), residues: 70 loop : -0.79 (0.20), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 265 TYR 0.015 0.001 TYR G 40 PHE 0.012 0.001 PHE A 39 TRP 0.013 0.001 TRP F 108 HIS 0.006 0.001 HIS A 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.18 (18806) covalent geometry : angle 0.50755 / 0.28 (25537) hydrogen bonds : bond 0.06869 / 4.57 ( 992) hydrogen bonds : angle 4.44060 / 3.26 ( 2895) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 143 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLU cc_start: 0.8246 (mp0) cc_final: 0.7893 (mp0) REVERT: B 47 LYS cc_start: 0.9199 (mmmt) cc_final: 0.8989 (tppp) REVERT: B 383 ASP cc_start: 0.8261 (p0) cc_final: 0.7978 (m-30) REVERT: B 394 LYS cc_start: 0.8991 (OUTLIER) cc_final: 0.8322 (pttm) REVERT: D 85 GLU cc_start: 0.8223 (tt0) cc_final: 0.7665 (tm-30) REVERT: E 66 GLU cc_start: 0.7792 (mt-10) cc_final: 0.7454 (mt-10) REVERT: E 184 MET cc_start: 0.8506 (tpp) cc_final: 0.8061 (tpp) REVERT: E 247 MET cc_start: 0.7916 (OUTLIER) cc_final: 0.7194 (mmm) REVERT: F 381 ASP cc_start: 0.8389 (p0) cc_final: 0.7961 (p0) REVERT: F 383 ASP cc_start: 0.7905 (p0) cc_final: 0.7673 (p0) REVERT: G 9 GLU cc_start: 0.8134 (mm-30) cc_final: 0.7836 (mp0) outliers start: 28 outliers final: 13 residues processed: 161 average time/residue: 0.6016 time to fit residues: 109.9864 Evaluate side-chains 155 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 140 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain B residue 176 ASP Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 394 LYS Chi-restraints excluded: chain C residue 55 GLN Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain E residue 78 GLN Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 188 PHE Chi-restraints excluded: chain E residue 247 MET Chi-restraints excluded: chain E residue 318 ILE Chi-restraints excluded: chain F residue 173 CYS Chi-restraints excluded: chain G residue 66 SER Chi-restraints excluded: chain G residue 141 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 214 optimal weight: 2.9990 chunk 199 optimal weight: 1.9990 chunk 218 optimal weight: 7.9990 chunk 188 optimal weight: 3.9990 chunk 173 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 42 optimal weight: 5.9990 chunk 166 optimal weight: 2.9990 chunk 204 optimal weight: 5.9990 chunk 108 optimal weight: 8.9990 chunk 162 optimal weight: 5.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 467 HIS C 28 GLN D 9 ASN D 14 GLN E 133 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.082009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.064449 restraints weight = 33338.868| |-----------------------------------------------------------------------------| r_work (start): 0.2753 rms_B_bonded: 2.89 r_work: 0.2592 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 18806 Z= 0.223 Angle : 0.545 8.395 25537 Z= 0.300 Chirality : 0.043 0.164 2657 Planarity : 0.004 0.041 3304 Dihedral : 4.236 51.696 2502 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.23 % Allowed : 11.93 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.18), residues: 2252 helix: 1.59 (0.14), residues: 1371 sheet: 1.85 (0.60), residues: 77 loop : -0.89 (0.20), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 265 TYR 0.017 0.001 TYR G 40 PHE 0.017 0.002 PHE A 188 TRP 0.013 0.001 TRP B 143 HIS 0.007 0.001 HIS A 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00525 / 0.22 (18806) covalent geometry : angle 0.54538 / 0.30 (25537) hydrogen bonds : bond 0.07651 / 5.08 ( 992) hydrogen bonds : angle 4.54241 / 3.34 ( 2895) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 143 time to evaluate : 0.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 47 LYS cc_start: 0.9218 (mmmt) cc_final: 0.9015 (tppp) REVERT: B 383 ASP cc_start: 0.8223 (p0) cc_final: 0.7922 (m-30) REVERT: B 394 LYS cc_start: 0.9023 (OUTLIER) cc_final: 0.8344 (pttm) REVERT: D 85 GLU cc_start: 0.8231 (tt0) cc_final: 0.7776 (tm-30) REVERT: E 184 MET cc_start: 0.8523 (tpp) cc_final: 0.8054 (tpp) REVERT: E 247 MET cc_start: 0.7967 (OUTLIER) cc_final: 0.7279 (mmm) REVERT: E 260 ASP cc_start: 0.7785 (t0) cc_final: 0.7355 (t0) REVERT: F 381 ASP cc_start: 0.8414 (p0) cc_final: 0.7997 (p0) REVERT: F 383 ASP cc_start: 0.7893 (p0) cc_final: 0.7542 (p0) REVERT: G 9 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7856 (mp0) REVERT: G 41 SER cc_start: 0.8813 (t) cc_final: 0.8441 (t) outliers start: 23 outliers final: 13 residues processed: 159 average time/residue: 0.6177 time to fit residues: 111.2290 Evaluate side-chains 153 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 138 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain B residue 176 ASP Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 394 LYS Chi-restraints excluded: chain C residue 55 GLN Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain E residue 78 GLN Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 188 PHE Chi-restraints excluded: chain E residue 247 MET Chi-restraints excluded: chain E residue 318 ILE Chi-restraints excluded: chain F residue 173 CYS Chi-restraints excluded: chain G residue 66 SER Chi-restraints excluded: chain G residue 141 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 111 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 chunk 127 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 198 optimal weight: 3.9990 chunk 171 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 28 GLN C 168 GLN D 14 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.084478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.066947 restraints weight = 32612.845| |-----------------------------------------------------------------------------| r_work (start): 0.2802 rms_B_bonded: 2.88 r_work: 0.2644 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18806 Z= 0.145 Angle : 0.500 8.079 25537 Z= 0.273 Chirality : 0.040 0.162 2657 Planarity : 0.004 0.041 3304 Dihedral : 4.125 51.635 2502 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.96 % Allowed : 12.68 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.18), residues: 2252 helix: 1.74 (0.14), residues: 1360 sheet: 1.98 (0.62), residues: 75 loop : -0.85 (0.20), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 265 TYR 0.013 0.001 TYR D 102 PHE 0.019 0.001 PHE A 188 TRP 0.016 0.001 TRP E 354 HIS 0.005 0.001 HIS A 467 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (18806) covalent geometry : angle 0.50016 / 0.27 (25537) hydrogen bonds : bond 0.06308 / 4.20 ( 992) hydrogen bonds : angle 4.41373 / 3.24 ( 2895) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 146 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLU cc_start: 0.8219 (mp0) cc_final: 0.7958 (mp0) REVERT: A 368 ASP cc_start: 0.8690 (m-30) cc_final: 0.8274 (m-30) REVERT: B 383 ASP cc_start: 0.8198 (p0) cc_final: 0.7896 (m-30) REVERT: B 394 LYS cc_start: 0.8998 (OUTLIER) cc_final: 0.8316 (pttm) REVERT: D 85 GLU cc_start: 0.8254 (tt0) cc_final: 0.7728 (tm-30) REVERT: E 184 MET cc_start: 0.8524 (tpp) cc_final: 0.8094 (tpp) REVERT: E 260 ASP cc_start: 0.7755 (t0) cc_final: 0.7342 (t0) REVERT: F 381 ASP cc_start: 0.8389 (p0) cc_final: 0.7984 (p0) REVERT: F 383 ASP cc_start: 0.7794 (p0) cc_final: 0.7527 (p0) REVERT: G 9 GLU cc_start: 0.8122 (mm-30) cc_final: 0.7839 (mp0) REVERT: G 27 ASP cc_start: 0.7997 (p0) cc_final: 0.7746 (OUTLIER) REVERT: G 41 SER cc_start: 0.8728 (t) cc_final: 0.8332 (t) outliers start: 18 outliers final: 13 residues processed: 159 average time/residue: 0.5858 time to fit residues: 106.0524 Evaluate side-chains 153 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 140 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain B residue 176 ASP Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 394 LYS Chi-restraints excluded: chain C residue 55 GLN Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain E residue 78 GLN Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 188 PHE Chi-restraints excluded: chain F residue 173 CYS Chi-restraints excluded: chain G residue 66 SER Chi-restraints excluded: chain G residue 141 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 31 optimal weight: 0.6980 chunk 71 optimal weight: 0.9990 chunk 147 optimal weight: 0.2980 chunk 98 optimal weight: 7.9990 chunk 166 optimal weight: 3.9990 chunk 211 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 186 optimal weight: 6.9990 chunk 130 optimal weight: 0.0870 chunk 207 optimal weight: 5.9990 chunk 197 optimal weight: 0.9980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 GLN D 14 GLN E 227 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.088299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.070886 restraints weight = 32106.640| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 2.86 r_work: 0.2725 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 18806 Z= 0.109 Angle : 0.475 8.832 25537 Z= 0.255 Chirality : 0.038 0.153 2657 Planarity : 0.003 0.040 3304 Dihedral : 3.936 51.208 2502 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.91 % Allowed : 13.00 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.18), residues: 2252 helix: 1.90 (0.14), residues: 1354 sheet: 2.02 (0.62), residues: 75 loop : -0.71 (0.21), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 69 TYR 0.012 0.001 TYR A 324 PHE 0.011 0.001 PHE E 39 TRP 0.020 0.001 TRP E 308 HIS 0.006 0.001 HIS A 467 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 (18806) covalent geometry : angle 0.47492 / 0.26 (25537) hydrogen bonds : bond 0.04907 / 3.28 ( 992) hydrogen bonds : angle 4.27429 / 3.14 ( 2895) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 151 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLU cc_start: 0.8137 (mp0) cc_final: 0.7910 (mp0) REVERT: A 240 GLU cc_start: 0.8473 (tp30) cc_final: 0.7769 (tp30) REVERT: B 383 ASP cc_start: 0.8164 (p0) cc_final: 0.7852 (m-30) REVERT: B 394 LYS cc_start: 0.8975 (OUTLIER) cc_final: 0.8279 (pttm) REVERT: D 30 GLN cc_start: 0.8060 (mm-40) cc_final: 0.7848 (mm110) REVERT: D 85 GLU cc_start: 0.8185 (tt0) cc_final: 0.7726 (tm-30) REVERT: E 184 MET cc_start: 0.8377 (tpp) cc_final: 0.7943 (tpp) REVERT: E 260 ASP cc_start: 0.7646 (t0) cc_final: 0.7252 (t0) REVERT: E 368 ASP cc_start: 0.8693 (m-30) cc_final: 0.8248 (m-30) REVERT: F 381 ASP cc_start: 0.8330 (p0) cc_final: 0.7933 (p0) REVERT: F 383 ASP cc_start: 0.7768 (p0) cc_final: 0.7533 (p0) REVERT: G 27 ASP cc_start: 0.7875 (p0) cc_final: 0.7658 (OUTLIER) outliers start: 17 outliers final: 10 residues processed: 165 average time/residue: 0.5347 time to fit residues: 101.0661 Evaluate side-chains 145 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 135 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain B residue 176 ASP Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 394 LYS Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 188 PHE Chi-restraints excluded: chain F residue 173 CYS Chi-restraints excluded: chain G residue 10 ASN Chi-restraints excluded: chain G residue 66 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 19 optimal weight: 0.1980 chunk 30 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 221 optimal weight: 6.9990 chunk 50 optimal weight: 0.5980 chunk 117 optimal weight: 6.9990 chunk 91 optimal weight: 0.9980 chunk 112 optimal weight: 6.9990 chunk 45 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 28 GLN D 14 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.086966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.069485 restraints weight = 32419.565| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 2.88 r_work: 0.2705 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18806 Z= 0.123 Angle : 0.486 8.647 25537 Z= 0.262 Chirality : 0.039 0.159 2657 Planarity : 0.004 0.041 3304 Dihedral : 3.911 51.116 2502 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.75 % Allowed : 13.59 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.18), residues: 2252 helix: 1.93 (0.14), residues: 1356 sheet: 1.81 (0.62), residues: 70 loop : -0.71 (0.21), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 265 TYR 0.011 0.001 TYR B 327 PHE 0.009 0.001 PHE A 188 TRP 0.016 0.001 TRP E 308 HIS 0.006 0.001 HIS A 467 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (18806) covalent geometry : angle 0.48570 / 0.26 (25537) hydrogen bonds : bond 0.05311 / 3.54 ( 992) hydrogen bonds : angle 4.28370 / 3.15 ( 2895) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 136 time to evaluate : 0.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLU cc_start: 0.8154 (mp0) cc_final: 0.7924 (mp0) REVERT: A 240 GLU cc_start: 0.8486 (tp30) cc_final: 0.7792 (tp30) REVERT: B 383 ASP cc_start: 0.8166 (p0) cc_final: 0.7863 (m-30) REVERT: B 394 LYS cc_start: 0.8981 (OUTLIER) cc_final: 0.8278 (pttm) REVERT: D 85 GLU cc_start: 0.8211 (tt0) cc_final: 0.7745 (tm-30) REVERT: E 184 MET cc_start: 0.8412 (tpp) cc_final: 0.7957 (tpp) REVERT: E 260 ASP cc_start: 0.7691 (t0) cc_final: 0.7295 (t0) REVERT: F 381 ASP cc_start: 0.8337 (p0) cc_final: 0.7939 (p0) REVERT: F 383 ASP cc_start: 0.7763 (p0) cc_final: 0.7520 (p0) REVERT: G 27 ASP cc_start: 0.7905 (p0) cc_final: 0.7680 (OUTLIER) outliers start: 14 outliers final: 11 residues processed: 148 average time/residue: 0.5359 time to fit residues: 91.0140 Evaluate side-chains 147 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 136 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain B residue 176 ASP Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 394 LYS Chi-restraints excluded: chain C residue 55 GLN Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 188 PHE Chi-restraints excluded: chain F residue 173 CYS Chi-restraints excluded: chain G residue 66 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 34 optimal weight: 0.8980 chunk 170 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 176 optimal weight: 7.9990 chunk 140 optimal weight: 0.9980 chunk 200 optimal weight: 0.6980 chunk 16 optimal weight: 0.3980 chunk 108 optimal weight: 7.9990 chunk 143 optimal weight: 5.9990 chunk 179 optimal weight: 0.1980 chunk 214 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 28 GLN D 14 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.088399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.070999 restraints weight = 32196.139| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 2.87 r_work: 0.2736 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 18806 Z= 0.110 Angle : 0.478 8.533 25537 Z= 0.257 Chirality : 0.038 0.159 2657 Planarity : 0.003 0.041 3304 Dihedral : 3.850 50.740 2502 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.64 % Allowed : 13.75 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.18), residues: 2252 helix: 1.97 (0.14), residues: 1355 sheet: 1.86 (0.62), residues: 70 loop : -0.67 (0.21), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 265 TYR 0.010 0.001 TYR A 324 PHE 0.010 0.001 PHE E 39 TRP 0.016 0.001 TRP F 108 HIS 0.006 0.001 HIS A 467 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (18806) covalent geometry : angle 0.47801 / 0.26 (25537) hydrogen bonds : bond 0.04868 / 3.25 ( 992) hydrogen bonds : angle 4.23778 / 3.12 ( 2895) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4275.89 seconds wall clock time: 74 minutes 9.95 seconds (4449.95 seconds total)