Starting phenix.real_space_refine on Thu Sep 18 16:41:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xiw_38391/09_2025/8xiw_38391.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xiw_38391/09_2025/8xiw_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_38391/09_2025/8xiw_38391.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xiw_38391/09_2025/8xiw_38391.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xiw_38391/09_2025/8xiw_38391.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xiw_38391/09_2025/8xiw_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/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, 2 Unusual residues: {' FE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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: 4.36, per 1000 atoms: 0.24 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: 1.81 Conformation dependent library (CDL) restraints added in 761.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.65 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: 2.86 Time building geometry restraints manager: 2.29 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 2.260 nonbonded pdb=" OE2 GLU A 209 " pdb="FE FE A 602 " model vdw 1.729 2.260 nonbonded pdb=" ND1 HIS E 246 " pdb="FE FE E 602 " model vdw 1.784 2.340 nonbonded pdb=" OE2 GLU E 243 " pdb="FE FE E 602 " model vdw 1.860 2.260 nonbonded pdb=" OE1 GLU A 144 " pdb="FE FE A 601 " model vdw 1.887 2.260 ... (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: 3.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 17.300 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: 0.010 Load rotamer database and sin/cos tables:6.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 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 aren 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 covalent geometry : bond 0.00531 (18806) covalent geometry : angle 0.76961 (25537) hydrogen bonds : bond 0.17833 ( 992) hydrogen bonds : angle 6.35217 ( 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 : 0.734 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: 0.6902 time to fit residues: 159.7611 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 : 0.626 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3188 r_free = 0.3188 target = 0.088511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.070808 restraints weight = 32347.825| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 2.92 r_work: 0.2748 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.1094 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= 0.131 Angle : 0.494 10.769 25537 Z= 0.269 Chirality : 0.039 0.159 2657 Planarity : 0.004 0.045 3304 Dihedral : 3.913 48.041 2504 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 1.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.12 % Allowed : 7.54 % Favored : 91.33 % 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 aren 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 0.006 0.000 ARG B 265 TYR 0.011 0.001 TYR G 40 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 covalent geometry : bond 0.00276 (18806) covalent geometry : angle 0.49403 (25537) hydrogen bonds : bond 0.06207 ( 992) hydrogen bonds : angle 4.51658 ( 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 182 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 161 time to evaluate : 0.751 Fit side-chains revert: symmetry clash REVERT: A 368 ASP cc_start: 0.8689 (m-30) cc_final: 0.8350 (m-30) REVERT: B 394 LYS cc_start: 0.8917 (OUTLIER) cc_final: 0.8275 (pttm) REVERT: C 47 SER cc_start: 0.9166 (t) cc_final: 0.8954 (t) REVERT: C 87 ASP cc_start: 0.8067 (t0) cc_final: 0.7854 (t0) REVERT: D 85 GLU cc_start: 0.8244 (tt0) cc_final: 0.7700 (tm-30) REVERT: E 184 MET cc_start: 0.8527 (tpp) cc_final: 0.8119 (tpp) REVERT: E 240 GLU cc_start: 0.8150 (tm-30) cc_final: 0.7797 (tm-30) REVERT: F 159 GLU cc_start: 0.8364 (mm-30) cc_final: 0.8089 (tp30) outliers start: 21 outliers final: 8 residues processed: 174 average time/residue: 0.6065 time to fit residues: 119.3004 Evaluate side-chains 154 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 145 time to evaluate : 0.725 ------------------------------------------------------------------------------- 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: 6.9990 chunk 89 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 211 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 chunk 184 optimal weight: 3.9990 chunk 219 optimal weight: 0.7980 chunk 108 optimal weight: 5.9990 chunk 95 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 110 optimal weight: 7.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 467 HIS A 521 ASN B 77 GLN B 80 HIS C 28 GLN D 9 ASN D 14 GLN F 80 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.084504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.066932 restraints weight = 32814.135| |-----------------------------------------------------------------------------| r_work (start): 0.2814 rms_B_bonded: 2.87 r_work: 0.2656 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 18806 Z= 0.177 Angle : 0.509 10.251 25537 Z= 0.279 Chirality : 0.041 0.159 2657 Planarity : 0.004 0.043 3304 Dihedral : 4.053 52.071 2502 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 1.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.39 % Allowed : 8.19 % Favored : 90.42 % 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 aren not related in a simple way. whole: 1.29 (0.18), residues: 2252 helix: 1.71 (0.14), residues: 1364 sheet: 1.74 (0.61), residues: 70 loop : -0.68 (0.21), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 265 TYR 0.015 0.001 TYR G 40 PHE 0.015 0.001 PHE A 188 TRP 0.019 0.001 TRP F 108 HIS 0.007 0.001 HIS A 343 Details of bonding type rmsd covalent geometry : bond 0.00406 (18806) covalent geometry : angle 0.50885 (25537) hydrogen bonds : bond 0.06951 ( 992) hydrogen bonds : angle 4.47248 ( 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 177 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 151 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 368 ASP cc_start: 0.8725 (m-30) cc_final: 0.8325 (m-30) REVERT: B 47 LYS cc_start: 0.9224 (mmmt) cc_final: 0.9016 (tppp) REVERT: B 299 GLU cc_start: 0.8170 (tm-30) cc_final: 0.7966 (tm-30) REVERT: B 394 LYS cc_start: 0.8960 (OUTLIER) cc_final: 0.8314 (pttm) REVERT: C 47 SER cc_start: 0.9216 (t) cc_final: 0.8994 (t) REVERT: D 85 GLU cc_start: 0.8265 (tt0) cc_final: 0.7726 (tm-30) REVERT: E 184 MET cc_start: 0.8503 (tpp) cc_final: 0.8078 (tpp) REVERT: E 186 ARG cc_start: 0.8634 (OUTLIER) cc_final: 0.7881 (ttt90) REVERT: E 240 GLU cc_start: 0.8164 (tm-30) cc_final: 0.7759 (tm-30) REVERT: F 381 ASP cc_start: 0.8374 (p0) cc_final: 0.7960 (p0) REVERT: F 383 ASP cc_start: 0.7829 (p0) cc_final: 0.7529 (p0) outliers start: 26 outliers final: 13 residues processed: 166 average time/residue: 0.5323 time to fit residues: 100.1939 Evaluate side-chains 152 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 137 time to evaluate : 0.627 ------------------------------------------------------------------------------- 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 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 186 ARG 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 Chi-restraints excluded: chain G residue 141 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 121 optimal weight: 0.9990 chunk 155 optimal weight: 0.9980 chunk 125 optimal weight: 0.9980 chunk 213 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 219 optimal weight: 0.7980 chunk 149 optimal weight: 8.9990 chunk 191 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 116 optimal weight: 6.9990 chunk 97 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 467 HIS 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 = 0.3139 r_free = 0.3139 target = 0.085339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.067741 restraints weight = 32664.743| |-----------------------------------------------------------------------------| r_work (start): 0.2825 rms_B_bonded: 2.87 r_work: 0.2667 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18806 Z= 0.146 Angle : 0.481 9.999 25537 Z= 0.263 Chirality : 0.040 0.153 2657 Planarity : 0.004 0.042 3304 Dihedral : 4.037 51.608 2502 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 1.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.44 % Allowed : 9.31 % Favored : 89.25 % 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 aren not related in a simple way. whole: 1.36 (0.18), residues: 2252 helix: 1.79 (0.14), residues: 1360 sheet: 1.76 (0.62), residues: 70 loop : -0.69 (0.20), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 265 TYR 0.013 0.001 TYR G 40 PHE 0.015 0.001 PHE A 188 TRP 0.017 0.001 TRP F 108 HIS 0.005 0.001 HIS A 343 Details of bonding type rmsd covalent geometry : bond 0.00327 (18806) covalent geometry : angle 0.48086 (25537) hydrogen bonds : bond 0.06326 ( 992) hydrogen bonds : angle 4.39990 ( 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 168 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 141 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 368 ASP cc_start: 0.8722 (m-30) cc_final: 0.8322 (m-30) REVERT: B 47 LYS cc_start: 0.9199 (mmmt) cc_final: 0.8997 (tppp) REVERT: B 299 GLU cc_start: 0.8117 (tm-30) cc_final: 0.7903 (tm-30) REVERT: B 383 ASP cc_start: 0.8263 (p0) cc_final: 0.8005 (m-30) REVERT: B 394 LYS cc_start: 0.8974 (OUTLIER) cc_final: 0.8317 (pttm) REVERT: C 47 SER cc_start: 0.9217 (t) cc_final: 0.8993 (t) REVERT: D 85 GLU cc_start: 0.8240 (tt0) cc_final: 0.7715 (tm-30) REVERT: E 184 MET cc_start: 0.8515 (tpp) cc_final: 0.8086 (tpp) REVERT: E 186 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.7818 (ttt90) REVERT: E 240 GLU cc_start: 0.8159 (tm-30) cc_final: 0.7730 (tm-30) outliers start: 27 outliers final: 13 residues processed: 159 average time/residue: 0.5847 time to fit residues: 105.2014 Evaluate side-chains 154 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 139 time to evaluate : 0.710 ------------------------------------------------------------------------------- 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 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 186 ARG 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 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: 2.9990 chunk 143 optimal weight: 0.2980 chunk 93 optimal weight: 4.9990 chunk 186 optimal weight: 5.9990 chunk 125 optimal weight: 0.9980 chunk 187 optimal weight: 0.9980 chunk 166 optimal weight: 0.7980 chunk 213 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 127 optimal weight: 3.9990 chunk 151 optimal weight: 8.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 ASN C 28 GLN D 9 ASN D 14 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.087542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.070032 restraints weight = 32390.709| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 2.86 r_work: 0.2706 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 18806 Z= 0.113 Angle : 0.446 8.274 25537 Z= 0.243 Chirality : 0.038 0.150 2657 Planarity : 0.003 0.041 3304 Dihedral : 3.935 51.272 2502 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.28 % Allowed : 10.17 % Favored : 88.55 % 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 aren not related in a simple way. whole: 1.49 (0.18), residues: 2252 helix: 1.88 (0.14), residues: 1362 sheet: 1.79 (0.62), residues: 70 loop : -0.61 (0.21), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 265 TYR 0.012 0.001 TYR A 324 PHE 0.013 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 covalent geometry : bond 0.00236 (18806) covalent geometry : angle 0.44588 (25537) hydrogen bonds : bond 0.05401 ( 992) hydrogen bonds : angle 4.30054 ( 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 174 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 150 time to evaluate : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 GLU cc_start: 0.8220 (mp0) cc_final: 0.7837 (mp0) REVERT: B 47 LYS cc_start: 0.9207 (mmmt) cc_final: 0.8991 (tppp) REVERT: B 394 LYS cc_start: 0.8974 (OUTLIER) cc_final: 0.8296 (pttm) REVERT: C 47 SER cc_start: 0.9187 (t) cc_final: 0.8961 (t) REVERT: D 85 GLU cc_start: 0.8191 (tt0) cc_final: 0.7552 (tm-30) REVERT: E 184 MET cc_start: 0.8424 (tpp) cc_final: 0.7990 (tpp) REVERT: E 240 GLU cc_start: 0.8025 (tm-30) cc_final: 0.7586 (tm-30) REVERT: F 381 ASP cc_start: 0.8335 (p0) cc_final: 0.7895 (p0) REVERT: G 9 GLU cc_start: 0.8120 (mm-30) cc_final: 0.7657 (mp0) outliers start: 24 outliers final: 11 residues processed: 167 average time/residue: 0.6349 time to fit residues: 119.5609 Evaluate side-chains 153 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 141 time to evaluate : 0.787 ------------------------------------------------------------------------------- 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 38 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 206 optimal weight: 3.9990 chunk 85 optimal weight: 0.5980 chunk 74 optimal weight: 4.9990 chunk 134 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 163 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 43 GLN E 78 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.085306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.067710 restraints weight = 32358.385| |-----------------------------------------------------------------------------| r_work (start): 0.2825 rms_B_bonded: 2.87 r_work: 0.2663 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 18806 Z= 0.154 Angle : 0.481 8.128 25537 Z= 0.263 Chirality : 0.040 0.157 2657 Planarity : 0.004 0.041 3304 Dihedral : 3.978 50.543 2502 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.18 % Allowed : 11.24 % Favored : 87.59 % 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 aren not related in a simple way. whole: 1.43 (0.18), residues: 2252 helix: 1.86 (0.14), residues: 1363 sheet: 1.80 (0.62), residues: 70 loop : -0.69 (0.20), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 265 TYR 0.014 0.001 TYR G 40 PHE 0.016 0.001 PHE A 188 TRP 0.013 0.001 TRP F 108 HIS 0.006 0.001 HIS A 343 Details of bonding type rmsd covalent geometry : bond 0.00352 (18806) covalent geometry : angle 0.48104 (25537) hydrogen bonds : bond 0.06211 ( 992) hydrogen bonds : angle 4.34944 ( 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 173 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 151 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 GLU cc_start: 0.8287 (mp0) cc_final: 0.7879 (mp0) REVERT: B 47 LYS cc_start: 0.9189 (mmmt) cc_final: 0.8988 (tppp) REVERT: B 383 ASP cc_start: 0.8251 (p0) cc_final: 0.7988 (m-30) REVERT: B 394 LYS cc_start: 0.8979 (OUTLIER) cc_final: 0.8301 (pttm) REVERT: C 47 SER cc_start: 0.9241 (t) cc_final: 0.9012 (t) REVERT: D 85 GLU cc_start: 0.8230 (tt0) cc_final: 0.7693 (tm-30) REVERT: E 184 MET cc_start: 0.8509 (tpp) cc_final: 0.8050 (tpp) REVERT: E 240 GLU cc_start: 0.8182 (tm-30) cc_final: 0.7720 (tm-30) REVERT: E 247 MET cc_start: 0.7960 (OUTLIER) cc_final: 0.7221 (mmm) REVERT: E 368 ASP cc_start: 0.8784 (m-30) cc_final: 0.8379 (m-30) REVERT: F 381 ASP cc_start: 0.8393 (p0) cc_final: 0.7967 (p0) REVERT: F 383 ASP cc_start: 0.7931 (p0) cc_final: 0.7702 (p0) REVERT: G 9 GLU cc_start: 0.8136 (mm-30) cc_final: 0.7743 (mp0) outliers start: 22 outliers final: 12 residues processed: 165 average time/residue: 0.6002 time to fit residues: 112.4049 Evaluate side-chains 153 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 139 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 HIS 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 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 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: 0.9990 chunk 173 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 42 optimal weight: 5.9990 chunk 166 optimal weight: 2.9990 chunk 204 optimal weight: 0.0040 chunk 108 optimal weight: 7.9990 chunk 162 optimal weight: 5.9990 overall best weight: 1.1398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 43 GLN C 28 GLN D 9 ASN D 14 GLN E 78 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.085982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.068458 restraints weight = 32604.546| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 2.88 r_work: 0.2677 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18806 Z= 0.131 Angle : 0.467 7.433 25537 Z= 0.255 Chirality : 0.039 0.155 2657 Planarity : 0.003 0.041 3304 Dihedral : 3.962 50.646 2502 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.18 % Allowed : 11.72 % Favored : 87.11 % 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 aren not related in a simple way. whole: 1.45 (0.18), residues: 2252 helix: 1.88 (0.14), residues: 1363 sheet: 1.85 (0.62), residues: 70 loop : -0.69 (0.21), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 265 TYR 0.014 0.001 TYR A 324 PHE 0.016 0.001 PHE A 188 TRP 0.014 0.001 TRP F 108 HIS 0.005 0.001 HIS A 467 Details of bonding type rmsd covalent geometry : bond 0.00290 (18806) covalent geometry : angle 0.46681 (25537) hydrogen bonds : bond 0.05809 ( 992) hydrogen bonds : angle 4.31206 ( 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 171 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 149 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLU cc_start: 0.8271 (mp0) cc_final: 0.7872 (mp0) REVERT: B 383 ASP cc_start: 0.8244 (p0) cc_final: 0.7946 (m-30) REVERT: B 394 LYS cc_start: 0.8970 (OUTLIER) cc_final: 0.8282 (pttm) REVERT: C 47 SER cc_start: 0.9227 (t) cc_final: 0.9001 (t) REVERT: D 85 GLU cc_start: 0.8210 (tt0) cc_final: 0.7675 (tm-30) REVERT: E 184 MET cc_start: 0.8503 (tpp) cc_final: 0.8047 (tpp) REVERT: E 240 GLU cc_start: 0.8165 (tm-30) cc_final: 0.7702 (tm-30) REVERT: E 368 ASP cc_start: 0.8781 (m-30) cc_final: 0.8362 (m-30) REVERT: F 381 ASP cc_start: 0.8382 (p0) cc_final: 0.7970 (p0) REVERT: F 383 ASP cc_start: 0.7917 (p0) cc_final: 0.7690 (p0) REVERT: G 9 GLU cc_start: 0.8114 (mm-30) cc_final: 0.7880 (mp0) REVERT: G 27 ASP cc_start: 0.8129 (p0) cc_final: 0.7902 (OUTLIER) outliers start: 22 outliers final: 17 residues processed: 164 average time/residue: 0.6458 time to fit residues: 119.4505 Evaluate side-chains 160 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 143 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 HIS Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain B residue 176 ASP Chi-restraints excluded: chain B residue 337 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 D residue 124 ILE 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 450 ASP Chi-restraints excluded: chain E residue 467 HIS 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: 3.9990 chunk 13 optimal weight: 3.9990 chunk 23 optimal weight: 7.9990 chunk 93 optimal weight: 4.9990 chunk 127 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 198 optimal weight: 3.9990 chunk 171 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 467 HIS B 43 GLN B 158 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 = 0.3090 r_free = 0.3090 target = 0.082145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.064629 restraints weight = 32824.038| |-----------------------------------------------------------------------------| r_work (start): 0.2758 rms_B_bonded: 2.86 r_work: 0.2598 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 18806 Z= 0.223 Angle : 0.550 7.671 25537 Z= 0.302 Chirality : 0.043 0.166 2657 Planarity : 0.004 0.041 3304 Dihedral : 4.190 50.620 2502 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.02 % Allowed : 12.47 % Favored : 86.52 % 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 aren not related in a simple way. whole: 1.20 (0.18), residues: 2252 helix: 1.67 (0.14), residues: 1369 sheet: 1.77 (0.62), residues: 70 loop : -0.80 (0.20), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 265 TYR 0.019 0.001 TYR G 40 PHE 0.014 0.002 PHE E 39 TRP 0.013 0.001 TRP B 143 HIS 0.008 0.001 HIS A 343 Details of bonding type rmsd covalent geometry : bond 0.00526 (18806) covalent geometry : angle 0.55006 (25537) hydrogen bonds : bond 0.07677 ( 992) hydrogen bonds : angle 4.52724 ( 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: 19 poor density : 145 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLU cc_start: 0.8252 (mp0) cc_final: 0.7812 (mp0) REVERT: B 383 ASP cc_start: 0.8187 (p0) cc_final: 0.7923 (m-30) REVERT: B 394 LYS cc_start: 0.9017 (OUTLIER) cc_final: 0.8342 (pttm) REVERT: C 47 SER cc_start: 0.9188 (t) cc_final: 0.8933 (t) REVERT: D 85 GLU cc_start: 0.8223 (tt0) cc_final: 0.7767 (tm-30) REVERT: E 184 MET cc_start: 0.8494 (tpp) cc_final: 0.8028 (tpp) REVERT: E 240 GLU cc_start: 0.8173 (tm-30) cc_final: 0.7711 (tm-30) REVERT: E 260 ASP cc_start: 0.7818 (t0) cc_final: 0.7390 (t0) REVERT: F 381 ASP cc_start: 0.8399 (p0) cc_final: 0.7981 (p0) REVERT: F 383 ASP cc_start: 0.7905 (p0) cc_final: 0.7661 (p0) REVERT: G 9 GLU cc_start: 0.8159 (mm-30) cc_final: 0.7863 (mp0) REVERT: G 41 SER cc_start: 0.8846 (t) cc_final: 0.8480 (t) outliers start: 19 outliers final: 12 residues processed: 159 average time/residue: 0.6293 time to fit residues: 112.8567 Evaluate side-chains 151 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 138 time to evaluate : 0.759 ------------------------------------------------------------------------------- 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 95 VAL Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 188 PHE Chi-restraints excluded: chain E residue 450 ASP 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: 2.9990 chunk 71 optimal weight: 0.5980 chunk 147 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 chunk 166 optimal weight: 0.9990 chunk 211 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 186 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 207 optimal weight: 4.9990 chunk 197 optimal weight: 0.4980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 43 GLN C 28 GLN D 14 GLN E 78 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.085504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.067856 restraints weight = 32352.391| |-----------------------------------------------------------------------------| r_work (start): 0.2819 rms_B_bonded: 2.88 r_work: 0.2662 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.1810 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= 0.128 Angle : 0.486 7.320 25537 Z= 0.266 Chirality : 0.039 0.159 2657 Planarity : 0.004 0.040 3304 Dihedral : 4.073 50.994 2502 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.07 % Allowed : 12.47 % Favored : 86.46 % 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 aren not related in a simple way. whole: 1.33 (0.18), residues: 2252 helix: 1.80 (0.14), residues: 1359 sheet: 2.00 (0.61), residues: 75 loop : -0.80 (0.20), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 265 TYR 0.014 0.001 TYR D 102 PHE 0.008 0.001 PHE E 39 TRP 0.017 0.001 TRP E 308 HIS 0.006 0.001 HIS A 467 Details of bonding type rmsd covalent geometry : bond 0.00279 (18806) covalent geometry : angle 0.48584 (25537) hydrogen bonds : bond 0.05963 ( 992) hydrogen bonds : angle 4.38282 ( 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 163 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 143 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLU cc_start: 0.8218 (mp0) cc_final: 0.7818 (mp0) REVERT: A 240 GLU cc_start: 0.8466 (tp30) cc_final: 0.7680 (tp30) REVERT: A 368 ASP cc_start: 0.8724 (m-30) cc_final: 0.8299 (m-30) REVERT: B 383 ASP cc_start: 0.8197 (p0) cc_final: 0.7908 (m-30) REVERT: B 394 LYS cc_start: 0.8998 (OUTLIER) cc_final: 0.8317 (pttm) REVERT: C 47 SER cc_start: 0.9199 (t) cc_final: 0.8953 (t) REVERT: D 85 GLU cc_start: 0.8219 (tt0) cc_final: 0.7697 (tm-30) REVERT: E 184 MET cc_start: 0.8488 (tpp) cc_final: 0.8062 (tpp) REVERT: E 240 GLU cc_start: 0.8159 (tm-30) cc_final: 0.7746 (tm-30) REVERT: E 260 ASP cc_start: 0.7777 (t0) cc_final: 0.7358 (t0) REVERT: F 381 ASP cc_start: 0.8379 (p0) cc_final: 0.7967 (p0) REVERT: F 383 ASP cc_start: 0.7875 (p0) cc_final: 0.7532 (p0) REVERT: G 9 GLU cc_start: 0.8105 (mm-30) cc_final: 0.7848 (mp0) REVERT: G 27 ASP cc_start: 0.7931 (p0) cc_final: 0.7697 (OUTLIER) outliers start: 20 outliers final: 14 residues processed: 159 average time/residue: 0.5713 time to fit residues: 103.0414 Evaluate side-chains 151 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 137 time to evaluate : 0.587 ------------------------------------------------------------------------------- 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 337 ASP Chi-restraints excluded: chain B residue 339 VAL 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 19 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 221 optimal weight: 5.9990 chunk 50 optimal weight: 0.0970 chunk 117 optimal weight: 6.9990 chunk 91 optimal weight: 0.7980 chunk 112 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 43 GLN C 28 GLN C 168 GLN E 78 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.085926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.068410 restraints weight = 32516.736| |-----------------------------------------------------------------------------| r_work (start): 0.2831 rms_B_bonded: 2.88 r_work: 0.2675 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18806 Z= 0.127 Angle : 0.491 9.158 25537 Z= 0.267 Chirality : 0.039 0.160 2657 Planarity : 0.004 0.040 3304 Dihedral : 4.000 50.643 2502 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.86 % Allowed : 12.89 % Favored : 86.25 % 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 aren not related in a simple way. whole: 1.39 (0.18), residues: 2252 helix: 1.84 (0.14), residues: 1361 sheet: 2.01 (0.62), residues: 75 loop : -0.78 (0.20), residues: 816 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 0.009 0.001 PHE E 39 TRP 0.024 0.001 TRP E 308 HIS 0.006 0.001 HIS A 467 Details of bonding type rmsd covalent geometry : bond 0.00279 (18806) covalent geometry : angle 0.49057 (25537) hydrogen bonds : bond 0.05729 ( 992) hydrogen bonds : angle 4.34476 ( 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 159 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 143 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLU cc_start: 0.8189 (mp0) cc_final: 0.7805 (mp0) REVERT: A 240 GLU cc_start: 0.8471 (tp30) cc_final: 0.7704 (tp30) REVERT: B 383 ASP cc_start: 0.8196 (p0) cc_final: 0.7909 (m-30) REVERT: B 394 LYS cc_start: 0.8992 (OUTLIER) cc_final: 0.8315 (pttm) REVERT: C 47 SER cc_start: 0.9192 (t) cc_final: 0.8953 (t) REVERT: D 85 GLU cc_start: 0.8203 (tt0) cc_final: 0.7755 (tm-30) REVERT: E 184 MET cc_start: 0.8464 (tpp) cc_final: 0.8011 (tpp) REVERT: E 240 GLU cc_start: 0.8209 (tm-30) cc_final: 0.7888 (tm-30) REVERT: E 260 ASP cc_start: 0.7760 (t0) cc_final: 0.7360 (t0) REVERT: E 368 ASP cc_start: 0.8745 (m-30) cc_final: 0.8324 (m-30) REVERT: F 381 ASP cc_start: 0.8361 (p0) cc_final: 0.7955 (p0) REVERT: F 383 ASP cc_start: 0.7792 (p0) cc_final: 0.7527 (p0) REVERT: G 9 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7847 (mp0) REVERT: G 27 ASP cc_start: 0.7941 (p0) cc_final: 0.7715 (OUTLIER) outliers start: 16 outliers final: 13 residues processed: 156 average time/residue: 0.6145 time to fit residues: 108.6958 Evaluate side-chains 151 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 138 time to evaluate : 0.628 ------------------------------------------------------------------------------- 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 95 VAL Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 188 PHE Chi-restraints excluded: chain E residue 450 ASP 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 34 optimal weight: 0.0570 chunk 170 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 176 optimal weight: 6.9990 chunk 140 optimal weight: 0.9990 chunk 200 optimal weight: 5.9990 chunk 16 optimal weight: 0.7980 chunk 108 optimal weight: 6.9990 chunk 143 optimal weight: 9.9990 chunk 179 optimal weight: 2.9990 chunk 214 optimal weight: 0.9990 overall best weight: 1.1704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 43 GLN C 28 GLN E 78 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.085617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.068074 restraints weight = 32540.306| |-----------------------------------------------------------------------------| r_work (start): 0.2824 rms_B_bonded: 2.89 r_work: 0.2668 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18806 Z= 0.136 Angle : 0.489 7.581 25537 Z= 0.267 Chirality : 0.039 0.160 2657 Planarity : 0.004 0.041 3304 Dihedral : 3.984 50.472 2502 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.96 % Allowed : 12.89 % Favored : 86.14 % 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 aren not related in a simple way. whole: 1.37 (0.18), residues: 2252 helix: 1.84 (0.14), residues: 1361 sheet: 1.76 (0.62), residues: 70 loop : -0.78 (0.20), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 265 TYR 0.013 0.001 TYR G 40 PHE 0.010 0.001 PHE A 39 TRP 0.021 0.001 TRP E 308 HIS 0.006 0.001 HIS A 467 Details of bonding type rmsd covalent geometry : bond 0.00307 (18806) covalent geometry : angle 0.48864 (25537) hydrogen bonds : bond 0.05852 ( 992) hydrogen bonds : angle 4.36227 ( 2895) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4203.85 seconds wall clock time: 72 minutes 50.51 seconds (4370.51 seconds total)